PEER-FEEDBACK AND ONLINE INTERACTION: A CASE STUDY

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Martha Isabel Espitia

2013-08-01

Full Text Available The implementation of information and communication technologies (ICTs in the English as a Foreign Language (EFL classroom has led to different practices and types of interaction. Online interaction allows teachers and students to use the target language beyond the classroom and provides students with more time to be exposed to and use the language. This case study aimed at understanding how a group of twelve students at Universidad de la Sabana, who participated in online forums as part of the requirements of a blended EFL course, interacted online to provide peer-feedback on written compositions. It also analyzed how online interaction was undertaken when using online forums. Findings suggest that participants raised awareness about the relevance of editing to avoid possible language problems by reviewing their peers' products and that the implementation of online peer feedback as an assessment strategy reveals students' beliefs towards language assessment.

Structure and mechanism of calmodulin binding to a signaling sphingolipid reveal new aspects of lipid-protein interactions

Science.gov (United States)

Kovacs, Erika; Harmat, Veronika; Tóth, Judit; Vértessy, Beáta G.; Módos, Károly; Kardos, József; Liliom, Károly

2010-01-01

Lipid-protein interactions are rarely characterized at a structural molecular level due to technical difficulties; however, the biological significance of understanding the mechanism of these interactions is outstanding. In this report, we provide mechanistic insight into the inhibitory complex formation of the lipid mediator sphingosylphosphorylcholine with calmodulin, the most central and ubiquitous regulator protein in calcium signaling. We applied crystallographic, thermodynamic, kinetic, and spectroscopic approaches using purified bovine calmodulin and bovine cerebral microsomal fraction to arrive at our conclusions. Here we present 1) a 1.6-Å resolution crystal structure of their complex, in which the sphingolipid occupies the conventional hydrophobic binding site on calmodulin; 2) a peculiar stoichiometry-dependent binding process: at low or high protein-to-lipid ratio calmodulin binds lipid micelles or a few lipid molecules in a compact globular conformation, respectively, and 3) evidence that the sphingolipid displaces calmodulin from its targets on cerebral microsomes. We have ascertained the specificity of the interaction using structurally related lipids as controls. Our observations reveal the structural basis of selective calmodulin inhibition by the sphingolipid. On the basis of the crystallographic and biophysical characterization of the calmodulin–sphingosylphosphorylcholine interaction, we propose a novel lipid-protein binding model, which might be applicable to other interactions as well.—Kovacs, E., Harmat, V., Tóth, J., Vértessy, B. G., Módos, K., Kardos, J., Liliom, K. Structure and mechanism of calmodulin binding to a signaling sphingolipid reveal new aspects of lipid-protein interactions. PMID:20522785

Lateral and medial ventral occipitotemporal regions interact during the recognition of images revealed from noise

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Barbara eNordhjem

2016-01-01

Full Text Available Several studies suggest different functional roles for the medial and the lateral ventral sections in object recognition. Texture and surface information is processed in medial regions, while shape information is processed in lateral sections. This begs the question whether and how these functionally specialized sections interact with each other and with early visual cortex to facilitate object recognition. In the current research, we set out to answer this question. In an fMRI study, thirteen subjects viewed and recognized images of objects and animals that were gradually revealed from noise while their brains were being scanned. We applied dynamic causal modeling (DCM – a method to characterize network interactions – to determine the modulatory effect of object recognition on a network comprising the primary visual cortex (V1, the lingual gyrus (LG in medial ventral cortex and the lateral occipital cortex (LO. We found that object recognition modulated the bilateral connectivity between LG and LO. Moreover, the feed-forward connectivity from V1 to LG and LO was modulated, while there was no evidence for feedback from these regions to V1 during object recognition. In particular, the interaction between medial and lateral areas supports a framework in which visual recognition of objects is achieved by networked regions that integrate information on image statistics, scene content and shape – rather than by a single categorically specialized region – within the ventral visual cortex.

A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study

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Francesco Gentile

2018-02-01

Full Text Available The Toll-Like Receptor 7 (TLR7 is an endosomal membrane receptor involved in the innate immune system response. Its best-known small molecule activators are imidazoquinoline derivatives such as imiquimod (R-837 and resiquimod (R-848. Recently, an interaction between R-837 and the colchicine binding site of tubulin was reported. To investigate the possibility of an interaction between structural analogues of colchicine and the TLR7, a recent computational model for the dimeric form of the TLR7 receptor was used to determine a possible interaction with a colchicine derivative called CR42-24, active as a tubulin polymerization inhibitor. The estimated values of the binding energy of this molecule with respect to the TLR7 receptor were comparable to the energies of known binders as reported in a previous study. The binding to the TLR7 was further assessed by introducing genetic transformations in the TLR7 gene in cancer cell lines and exposing them to the compound. A negative shift of the IC50 value in terms of cell growth was observed in cell lines carrying the mutated TLR7 gene. The reported study suggests a possible interaction between TLR7 and a colchicine derivative, which can be explored for rational design of new drugs acting on this receptor by using a colchicine scaffold for additional modifications.

A spectroscopic study of interaction of cationic dyes with heparin

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R. Nandini

2010-01-01

Full Text Available The interaction of two cationic dyes namely, acridine orange and pinacyanol chloride with an anionic polyelectrolyte, heparin, has been investigated by spectrophotometric method.The polymer induced metachromasy in the dyes resulting in the shift of the absorption maxima of the dyes towards shorter wavelengths. The stability of the complexes formed between acridine orange and heparin was found to be lesser than that formed between pinacyanol chloride and heparin. This fact was further confirmed by reversal studies using alcohols, urea and surfactants. The interaction of acridine orange with heparin has also been investigated fluorimetrically.The interaction parameters revealed that binding between acridine orange and heparin arises due to electrostatic interaction while that between pinacyanol chloride and heparin is found to involve both electrostatic and hydrophobic forces. The effect of the structure of the dye in inducing metachromasy has also been discussed.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

OpenAIRE

Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

Process-Based Species Pools Reveal the Hidden Signature of Biotic Interactions Amid the Influence of Temperature Filtering.

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Lessard, Jean-Philippe; Weinstein, Ben G; Borregaard, Michael K; Marske, Katharine A; Martin, Danny R; McGuire, Jimmy A; Parra, Juan L; Rahbek, Carsten; Graham, Catherine H

2016-01-01

A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations, and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature-but not precipitation or dispersal limitation-acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.

Revisiting interaction specificity reveals neuronal and adipocyte Munc18 membrane fusion regulatory proteins differ in their binding interactions with partner SNARE Syntaxins.

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Michelle P Christie

Full Text Available The efficient delivery of cellular cargo relies on the fusion of cargo-carrying vesicles with the correct membrane at the correct time. These spatiotemporal fusion events occur when SNARE proteins on the vesicle interact with cognate SNARE proteins on the target membrane. Regulatory Munc18 proteins are thought to contribute to SNARE interaction specificity through interaction with the SNARE protein Syntaxin. Neuronal Munc18a interacts with Syntaxin1 but not Syntaxin4, and adipocyte Munc18c interacts with Syntaxin4 but not Syntaxin1. Here we show that this accepted view of specificity needs revision. We find that Munc18c interacts with both Syntaxin4 and Syntaxin1, and appears to bind "non-cognate" Syntaxin1 a little more tightly than Syntaxin4. Munc18a binds Syntaxin1 and Syntaxin4, though it interacts with its cognate Syntaxin1 much more tightly. We also observed that when bound to non-cognate Munc18c, Syntaxin1 captures its neuronal SNARE partners SNAP25 and VAMP2, and Munc18c can bind to pre-formed neuronal SNARE ternary complex. These findings reveal that Munc18a and Munc18c bind Syntaxins differently. Munc18c relies principally on the Syntaxin N-peptide interaction for binding Syntaxin4 or Syntaxin1, whereas Munc18a can bind Syntaxin1 tightly whether or not the Syntaxin1 N-peptide is present. We conclude that Munc18a and Munc18c differ in their binding interactions with Syntaxins: Munc18a has two tight binding modes/sites for Syntaxins as defined previously but Munc18c has just one that requires the N-peptide. These results indicate that the interactions between Munc18 and Syntaxin proteins, and the consequences for in vivo function, are more complex than can be accounted for by binding specificity alone.

Andreev spectrum with high spin-orbit interactions: Revealing spin splitting and topologically protected crossings

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Murani, A.; Chepelianskii, A.; Guéron, S.; Bouchiat, H.

2017-10-01

In order to point out experimentally accessible signatures of spin-orbit interaction, we investigate numerically the Andreev spectrum of a multichannel mesoscopic quantum wire (N) with high spin-orbit interaction coupled to superconducting electrodes (S), contrasting topological and nontopological behaviors. In the nontopological case (square lattice with Rashba interactions), we find that the Kramers degeneracy of Andreev levels is lifted by a phase difference between the S reservoirs except at multiples of π , when the normal quantum wires can host several conduction channels. The level crossings at these points invariant by time-reversal symmetry are not lifted by disorder. Whereas the dc Josephson current is insensitive to these level crossings, the high-frequency admittance (susceptibility) at finite temperature reveals these level crossings and the lifting of their degeneracy at π by a small Zeeman field. We have also investigated the hexagonal lattice with intrinsic spin-orbit interaction in the range of parameters where it is a two-dimensional topological insulator with one-dimensional helical edges protected against disorder. Nontopological superconducting contacts can induce topological superconductivity in this system characterized by zero-energy level crossing of Andreev levels. Both Josephson current and finite-frequency admittance carry then very specific signatures at low temperature of this disorder-protected Andreev level crossing at π and zero energy.

Two crystal structures of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveal protein–ligand interactions including a structural basis for observed antifolate resistance

Energy Technology Data Exchange (ETDEWEB)

Anderson, Amy C., E-mail: aca@dartmouth.edu [Dartmouth College, Department of Chemistry, Burke Laboratories, Hanover, NH 03755 (United States)

2005-03-01

An analysis of the protein–ligand interactions in two crystal structures of DHFR-TS from C. hominis reveals a possible structural basis for observed antifolate resistance in C. hominis DHFR. A comparison with the structure of human DHFR reveals residue substitutions that may be exploited for the design of species-selective inhibitors. Cryptosporidium hominis is a protozoan parasite that causes acute gastrointestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein–ligand interactions in two crystal structures of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from C. hominis, determined at 2.8 and 2.87 Å resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of species-selective inhibitors.

Spatial interactions reveal inhibitory cortical networks in human amblyopia.

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Wong, Erwin H; Levi, Dennis M; McGraw, Paul V

2005-10-01

Humans with amblyopia have a well-documented loss of sensitivity for first-order, or luminance defined, visual information. Recent studies show that they also display a specific loss of sensitivity for second-order, or contrast defined, visual information; a type of image structure encoded by neurons found predominantly in visual area A18/V2. In the present study, we investigate whether amblyopia disrupts the normal architecture of spatial interactions in V2 by determining the contrast detection threshold of a second-order target in the presence of second-order flanking stimuli. Adjacent flanks facilitated second-order detectability in normal observers. However, in marked contrast, they suppressed detection in each eye of the majority of amblyopic observers. Furthermore, strabismic observers with no loss of visual acuity show a similar pattern of detection suppression. We speculate that amblyopia results in predominantly inhibitory cortical interactions between second-order neurons.

Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin–dockerin interactions

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Yuval Hamberg

2014-10-01

Full Text Available Cellulosic waste represents a significant and underutilized carbon source for the biofuel industry. Owing to the recalcitrance of crystalline cellulose to enzymatic degradation, it is necessary to design economical methods of liberating the fermentable sugars required for bioethanol production. One route towards unlocking the potential of cellulosic waste lies in a highly complex class of molecular machines, the cellulosomes. Secreted mainly by anaerobic bacteria, cellulosomes are structurally diverse, cell surface-bound protein assemblies that can contain dozens of catalytic components. The key feature of the cellulosome is its modularity, facilitated by the ultra-high affinity cohesin–dockerin interaction. Due to the enormous number of cohesin and dockerin modules found in a typical cellulolytic organism, a major bottleneck in understanding the biology of cellulosomics is the purification of each cohesin- and dockerin-containing component, prior to analyses of their interaction. As opposed to previous approaches, the present study utilized proteins contained in unpurified whole-cell extracts. This strategy was made possible due to an experimental design that allowed for the relevant proteins to be “purified” via targeted affinity interactions as a function of the binding assay. The approach thus represents a new strategy, appropriate for future medium- to high-throughput screening of whole genomes, to determine the interactions between cohesins and dockerins. We have selected the cellulosome of Acetivibrio cellulolyticus for this work due to its exceptionally complex cellulosome systems and intriguing diversity of its cellulosomal modular components. Containing 41 cohesins and 143 dockerins, A. cellulolyticus has one of the largest number of potential cohesin–dockerin interactions of any organism, and contains unusual and novel cellulosomal features. We have surveyed a representative library of cohesin and dockerin modules spanning the

Revealing the large extra dimension effective interaction at an e+e- collider with polarized beams

International Nuclear Information System (INIS)

Pankov, A. A.; Tsytrinov, A. V.; Paver, N.

2007-01-01

Several types of new physics scenarios are represented by contactlike effective interactions. An example is the exchange of nonstandard quanta of very large mass scales, beyond the kinematical limit for direct production set by the available collider energy. This kind of interactions can be revealed only through deviations of observables from the standard model predictions. If such deviations were observed, the relevant source should be identified among the possible models that could explain them. Here, we assess the expected 'identification reach' on the ADD model of gravity in large compactified extra dimensions, against the compositeness-inspired four-fermion contact interaction. As basic observables we take the differential cross sections for fermion-pair production at a 0.5-1 TeV electron-positron linear collider with both beams longitudinally polarized. For the four-fermion contact interaction, we assume a general linear combination of the individual models with definite chiralities, with arbitrary coupling constants. In this sense, the estimated identification reach on the ADD model can be considered as 'model independent'. In the analysis, we give estimates also for the expected ''discovery reaches'' on the various scenarios. We emphasize the substantial role of beams polarization in enhancing the sensitivity to the contactlike interactions under consideration

Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

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Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

2018-02-12

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

Science.gov (United States)

Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

2014-12-01

2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. Copyright © 2014 Elsevier B.V. All rights reserved.

Raft-based sphingomyelin interactions revealed by new fluorescent sphingomyelin analogs

Science.gov (United States)

Kinoshita, Masanao; Suzuki, Kenichi G.N.; Takada, Misa; Ano, Hikaru; Abe, Mitsuhiro; Makino, Asami; Kobayashi, Toshihide; Hirosawa, Koichiro M.; Fujiwara, Takahiro K.; Murata, Michio

2017-01-01

Sphingomyelin (SM) has been proposed to form cholesterol-dependent raft domains and sphingolipid domains in the plasma membrane (PM). How SM contributes to the formation and function of these domains remains unknown, primarily because of the scarcity of suitable fluorescent SM analogs. We developed new fluorescent SM analogs by conjugating a hydrophilic fluorophore to the SM choline headgroup without eliminating its positive charge, via a hydrophilic nonaethylene glycol linker. The new analogs behaved similarly to the native SM in terms of their partitioning behaviors in artificial liquid order-disorder phase-separated membranes and detergent-resistant PM preparations. Single fluorescent molecule tracking in the live-cell PM revealed that they indirectly interact with each other in cholesterol- and sphingosine backbone–dependent manners, and that, for ∼10–50 ms, they undergo transient colocalization-codiffusion with a glycosylphosphatidylinositol (GPI)-anchored protein, CD59 (in monomers, transient-dimer rafts, and clusters), in CD59-oligomer size–, cholesterol-, and GPI anchoring–dependent manners. These results suggest that SM continually and rapidly exchanges between CD59-associated raft domains and the bulk PM. PMID:28330937

Theoretical study on the interaction of pregabalin and olanzapine with DNA

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ZibaHooshiarSodagar

2016-12-01

Full Text Available This paper aims is to study the interaction of two drugs including pregabalin and olanzapine with DNA. For this purpose, density functional theory calculations and docking were used. The structure of pregabalin and olanzapine using B3Lyp theory level and the basis set 6-311 G(d,p was optimized. Highest occupied molecular orbital (HOMO and lowest unoccupied molecular orbital (LUMO calculated for each drugs. The obtained results showed that olanzapine is more reactive than pregabalin. Docking of drugs with DNA was performed and the results showed that binding affinity of olanzapine is higher than pregabalin. Also, the graphical results revealed that olanzapine interact with DNA via 5-terminal major groove of DNA, whereas pregabalin interact with DNA via 3- termind major groove.

Dislocation Interactions in Olivine Revealed by HR-EBSD

NARCIS (Netherlands)

Wallis, D.; Hansen, Lars N.; Britton, T. Ben; Wilkinson, Angus J.

2017-01-01

Interactions between dislocations potentially provide a control on strain rates produced bydislocation motion during creep of rocks at high temperatures. However, it has been difficult to establishthe dominant types of interactions and their influence on the rheological properties of creeping rocks

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

Science.gov (United States)

Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

2011-01-01

As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

Directory of Open Access Journals (Sweden)

Mohan Babu

2011-11-01

Full Text Available As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium and prototrophic (minimal medium culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens and an important target.

Studies of interaction between two alkaloids and double helix DNA

International Nuclear Information System (INIS)

Sun, Yantao; Peng, Tingting; Zhao, Lei; Jiang, Dayu; Cui, Yuncheng

2014-01-01

This article presents the study on the interaction of two alkaloids (matrine and evodiamine) and hs-DNA by absorption, fluorescence, circular dichroism (CD), DNA melting and viscosity experiments. The spectroscopic studies suggested that two alkaloids can bind to DNA through an intercalative mode. The viscosity measurement and thermal denaturation also indicated that two alkaloids can intercalate to DNA. The binding constants (K A ) and the number of binding sites (n) were determined. At the same time, some significant thermodynamic parameters of the binding of the alkaloids to DNA were obtained. Competitive binding studies revealed that alkaloids had an effect on ethidium bromide (EB) bound DNA. In addition, it was also proved that the fluorescence quenching was influenced by ionic strength. - Highlights: • Interaction between two alkaloids and DNA is studied by spectral methods. • The binding constant and the binding sites between two alkaloids and DNA are obtained. • There are a classical intercalative mode between alkaloids and DNA. • The binding of matrine with DNA is weaker than that of evodiamine. • It is important for us to understand the alkaloids–DNA interactions at a molecular level

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

Science.gov (United States)

Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

2018-01-01

Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

Age differences in adults' daily social interactions: An ecological momentary assessment study.

Science.gov (United States)

Zhaoyang, Ruixue; Sliwinski, Martin J; Martire, Lynn M; Smyth, Joshua M

2018-04-30

Prevailing research has suggested that social relationships get better with age, but this evidence has been largely based on studies with lengthy reporting intervals. Using an ecological momentary assessment approach, the present study examined age differences in several characteristics of social interactions as reported in near-real time: the frequency, quality, and partner type. Participants (N = 173) ages 20-79 years reported their social interactions at 5 random times throughout the day for 1 week. Results revealed that age was associated with higher frequency of interacting with family and lower frequency of interacting with peripheral partners. These age effects, however, became nonsignificant after accounting for contextual factors such as race, gender, education, employment status, family structure, and living arrangement. In contrast, a curvilinear relationship best characterized age differences in both positive and negative ratings of daily social interaction quality, with middle-aged adults reporting the lowest positive ratings and older adults reporting the lowest negative ratings among all ages. Contextual factors did not account for these patterns of age differences in interaction quality. Furthermore, the intraindividual variability of interaction frequency with peripheral partners, partner diversity, and interaction quality (positivity and negativity) was lower among older adults than among younger adults. Findings from the present study portray a nuanced picture of social interactions in daily life and advance the understanding of social interactions across the life span. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

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Rajani Rai

2015-11-01

Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

Interactions between Metal-binding Domains Modulate Intracellular Targeting of Cu(I)-ATPase ATP7B, as Revealed by Nanobody Binding*

Science.gov (United States)

Huang, Yiping; Nokhrin, Sergiy; Hassanzadeh-Ghassabeh, Gholamreza; Yu, Corey H.; Yang, Haojun; Barry, Amanda N.; Tonelli, Marco; Markley, John L.; Muyldermans, Serge; Dmitriev, Oleg Y.; Lutsenko, Svetlana

2014-01-01

The biologically and clinically important membrane transporters are challenging proteins to study because of their low level of expression, multidomain structure, and complex molecular dynamics that underlies their activity. ATP7B is a copper transporter that traffics between the intracellular compartments in response to copper elevation. The N-terminal domain of ATP7B (N-ATP7B) is involved in binding copper, but the role of this domain in trafficking is controversial. To clarify the role of N-ATP7B, we generated nanobodies that interact with ATP7B in vitro and in cells. In solution NMR studies, nanobodies revealed the spatial organization of N-ATP7B by detecting transient functionally relevant interactions between metal-binding domains 1–3. Modulation of these interactions by nanobodies in cells enhanced relocalization of the endogenous ATP7B toward the plasma membrane linking molecular and cellular dynamics of the transporter. Stimulation of ATP7B trafficking by nanobodies in the absence of elevated copper provides direct evidence for the important role of N-ATP7B structural dynamics in regulation of ATP7B localization in a cell. PMID:25253690

Information theory and robotics meet to study predator-prey interactions

Science.gov (United States)

Neri, Daniele; Ruberto, Tommaso; Cord-Cruz, Gabrielle; Porfiri, Maurizio

2017-07-01

Transfer entropy holds promise to advance our understanding of animal behavior, by affording the identification of causal relationships that underlie animal interactions. A critical step toward the reliable implementation of this powerful information-theoretic concept entails the design of experiments in which causal relationships could be systematically controlled. Here, we put forward a robotics-based experimental approach to test the validity of transfer entropy in the study of predator-prey interactions. We investigate the behavioral response of zebrafish to a fear-evoking robotic stimulus, designed after the morpho-physiology of the red tiger oscar and actuated along preprogrammed trajectories. From the time series of the positions of the zebrafish and the robotic stimulus, we demonstrate that transfer entropy correctly identifies the influence of the stimulus on the focal subject. Building on this evidence, we apply transfer entropy to study the interactions between zebrafish and a live red tiger oscar. The analysis of transfer entropy reveals a change in the direction of the information flow, suggesting a mutual influence between the predator and the prey, where the predator adapts its strategy as a function of the movement of the prey, which, in turn, adjusts its escape as a function of the predator motion. Through the integration of information theory and robotics, this study posits a new approach to study predator-prey interactions in freshwater fish.

Interaction of quinones with three pyrimidine bases: A laser flash photolysis study

Energy Technology Data Exchange (ETDEWEB)

Bose, Adity [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Basu, Samita, E-mail: samita.basu@saha.ac.i [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India)

2009-11-15

The interaction between three different pyrimidine bases, uracil (U), cytosine (C) and thymine (T) and two quinones, 2-methyl-1,4-naphthoquinone or menadione (MQ) and 9,10-anthraquinone (AQ) have been studied using laser flash photolysis technique in organic homogeneous medium. The three pyrimidines have revealed a difference in their extent of reactivity towards the quinones, which has been attributed to their structural difference. Our works have revealed that the difference in structural dimension of the quinones is also responsible for affecting the reactivity of these pyrimidines in homogeneous medium.

Interaction of quinones with three pyrimidine bases: A laser flash photolysis study

International Nuclear Information System (INIS)

Bose, Adity; Basu, Samita

2009-01-01

The interaction between three different pyrimidine bases, uracil (U), cytosine (C) and thymine (T) and two quinones, 2-methyl-1,4-naphthoquinone or menadione (MQ) and 9,10-anthraquinone (AQ) have been studied using laser flash photolysis technique in organic homogeneous medium. The three pyrimidines have revealed a difference in their extent of reactivity towards the quinones, which has been attributed to their structural difference. Our works have revealed that the difference in structural dimension of the quinones is also responsible for affecting the reactivity of these pyrimidines in homogeneous medium.

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

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Art F Y Poon

2007-11-01

Full Text Available The third variable loop (V3 of the human immunodeficiency virus type 1 (HIV-1 envelope is a principal determinant of antibody neutralization and progression to AIDS. Although it is undoubtedly an important target for vaccine research, extensive genetic variation in V3 remains an obstacle to the development of an effective vaccine. Comparative methods that exploit the abundance of sequence data can detect interactions between residues of rapidly evolving proteins such as the HIV-1 envelope, revealing biological constraints on their variability. However, previous studies have relied implicitly on two biologically unrealistic assumptions: (1 that founder effects in the evolutionary history of the sequences can be ignored, and; (2 that statistical associations between residues occur exclusively in pairs. We show that comparative methods that neglect the evolutionary history of extant sequences are susceptible to a high rate of false positives (20%-40%. Therefore, we propose a new method to detect interactions that relaxes both of these assumptions. First, we reconstruct the evolutionary history of extant sequences by maximum likelihood, shifting focus from extant sequence variation to the underlying substitution events. Second, we analyze the joint distribution of substitution events among positions in the sequence as a Bayesian graphical model, in which each branch in the phylogeny is a unit of observation. We perform extensive validation of our models using both simulations and a control case of known interactions in HIV-1 protease, and apply this method to detect interactions within V3 from a sample of 1,154 HIV-1 envelope sequences. Our method greatly reduces the number of false positives due to founder effects, while capturing several higher-order interactions among V3 residues. By mapping these interactions to a structural model of the V3 loop, we find that the loop is stratified into distinct evolutionary clusters. We extend our model to

A comparative study on the flow experience in web-based and text-based interaction environments.

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Huang, Li-Ting; Chiu, Chen-An; Sung, Kai; Farn, Cheng-Kiang

2011-01-01

The purpose of this study was to explore a substantial phenomenon related to flow experiences (immersion) in text-based interaction systems. Most previous research emphasizes the effects of challenge/skill, focused attention, telepresence, web characteristics, and systems' interface design on users' flow experiences in online environments. However, text-based interaction systems without telepresence features and web characteristics still seem to create opportunities for flow experience. To explore this phenomenon, this study incorporates subject involvement and interpersonal interaction as critical antecedents into the model of flow experience, as well as considers the existence of telepresence. Results reveal that subject involvement, interpersonal interaction, and interactivity speed are critical to focused attention, which enhances users' immersion. With regard to the effect of telepresence, the perceived attractiveness of the interface is a significant facilitator determining users' immersion in web-based, rather than in text-based, interaction environments. Interactivity speed is unrelated to immersion in both web-based and text-based interaction environments. The influence of interpersonal involvement is diminished in web-based interaction environments. The implications and limitations of this study are discussed.

Content-Related Interactions in Self-initiated Study Groups

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Christian, Karen; Talanquer, Vicente

2012-09-01

The central goal of the present exploratory study was to investigate the nature of the content-related interactions in study groups independently organized by college organic chemistry students. We were particularly interested in the identification of the different factors that affected the emergence of opportunities for students to co-construct understanding and engage in higher levels of cognitive processing. Our results are based on the analysis of in situ observations of 34 self-initiated study sessions involving over a 100 students in three academic semesters. The investigation revealed three major types of social regulation processes, teaching, tutoring, and co-construction in the observed study sessions. However, the extent to which students engaged in each of them varied widely from one session to another. This variability was mostly determined by the specific composition of the study groups and the nature of the study tasks in which they were engaged. Decisions about how to organize the study session, the relative content knowledge and conceptual understanding expressed by the participants, as well as the cognitive level of the problems that guided group work had a strong impact on the nature of student interactions. Nevertheless, group talk in the observed study groups was mostly focused on low-level cognitive processes. The results of our work provide insights on how to better support students' productive engagement in study groups.

Study of pionic specific heat in 32S-emulsion interactions at 200 AGeV

International Nuclear Information System (INIS)

Ghosh, Dipak; Deb, Argha; Mallick, Asok Kumar; Chatterjee, Rini; Lahiri, Madhumita; Bhattacharyya, Swarnapratim; Sahoo, Swarup Ranjan; Patra, Kanchan Kumar; Mondal, Mitali; Haldar, Prabir Kumar

2002-01-01

Multifractality reveals self-similarity in particle production process. Studies on multifractality of pions from 32 S-emulsion interactions at 200 AGeV by Takagi method which is assumed to be free from the shortcomings encountered by G-moment method is presented

Functional Complementation Studies Reveal Different Interaction Partners of Escherichia coli IscS and Human NFS1.

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Bühning, Martin; Friemel, Martin; Leimkühler, Silke

2017-08-29

The trafficking and delivery of sulfur to cofactors and nucleosides is a highly regulated and conserved process among all organisms. All sulfur transfer pathways generally have an l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of sulfur-containing biomolecules like iron-sulfur (Fe-S) clusters, thiamine, biotin, lipoic acid, the molybdenum cofactor (Moco), and thiolated nucleosides in tRNA. The human l-cysteine desulfurase NFS1 and the Escherichia coli homologue IscS share a level of amino acid sequence identity of ∼60%. While E. coli IscS has a versatile role in the cell and was shown to have numerous interaction partners, NFS1 is mainly localized in mitochondria with a crucial role in the biosynthesis of Fe-S clusters. Additionally, NFS1 is also located in smaller amounts in the cytosol with a role in Moco biosynthesis and mcm 5 s 2 U34 thio modifications of nucleosides in tRNA. NFS1 and IscS were conclusively shown to have different interaction partners in their respective organisms. Here, we used functional complementation studies of an E. coli iscS deletion strain with human NFS1 to dissect their conserved roles in the transfer of sulfur to a specific target protein. Our results show that human NFS1 and E. coli IscS share conserved binding sites for proteins involved in Fe-S cluster assembly like IscU, but not with proteins for tRNA thio modifications or Moco biosynthesis. In addition, we show that human NFS1 was almost fully able to complement the role of IscS in Moco biosynthesis when its specific interaction partner protein MOCS3 from humans was also present.

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility.

Science.gov (United States)

Bush, W S; McCauley, J L; DeJager, P L; Dudek, S M; Hafler, D A; Gibson, R A; Matthews, P M; Kappos, L; Naegelin, Y; Polman, C H; Hauser, S L; Oksenberg, J; Haines, J L; Ritchie, M D

2011-07-01

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also increases power to detect weak main effects. We conducted a knowledge-driven interaction analysis of a GWAS of 931 multiple sclerosis (MS) trios to discover gene-gene interactions within established biological contexts. We identify heterogeneous signals, including a gene-gene interaction between CHRM3 (muscarinic cholinergic receptor 3) and MYLK (myosin light-chain kinase) (joint P=0.0002), an interaction between two phospholipase C-β isoforms, PLCβ1 and PLCβ4 (joint P=0.0098), and a modest interaction between ACTN1 (actinin alpha 1) and MYH9 (myosin heavy chain 9) (joint P=0.0326), all localized to calcium-signaled cytoskeletal regulation. Furthermore, we discover a main effect (joint P=5.2E-5) previously unidentified by single-locus analysis within another related gene, SCIN (scinderin), a calcium-binding cytoskeleton regulatory protein. This work illustrates that knowledge-driven interaction analysis of GWAS data is a feasible approach to identify new genetic effects. The results of this study are among the first gene-gene interactions and non-immune susceptibility loci for MS. Further, the implicated genes cluster within inter-related biological mechanisms that suggest a neurodegenerative component to MS.

The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria

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Meghan Zuck

2017-11-01

Full Text Available Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016. A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

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Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy.

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Vladislav V Melekhov

Full Text Available Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

Single-virus tracking approach to reveal the interaction of Dengue virus with autophagy during the early stage of infection

Science.gov (United States)

Chu, Li-Wei; Huang, Yi-Lung; Lee, Jin-Hui; Huang, Long-Ying; Chen, Wei-Jun; Lin, Ya-Hsuan; Chen, Jyun-Yu; Xiang, Rui; Lee, Chau-Hwang; Ping, Yueh-Hsin

2014-01-01

Dengue virus (DENV) is one of the major infectious pathogens worldwide. DENV infection is a highly dynamic process. Currently, no antiviral drug is available for treating DENV-induced diseases since little is known regarding how the virus interacts with host cells during infection. Advanced molecular imaging technologies are powerful tools to understand the dynamics of intracellular interactions and molecular trafficking. This study exploited a single-virus particle tracking technology to address whether DENV interacts with autophagy machinery during the early stage of infection. Using confocal microscopy and three-dimensional image analysis, we showed that DENV triggered the formation of green fluorescence protein-fused microtubule-associated protein 1A/1B-light chain 3 (GFP-LC3) puncta, and DENV-induced autophagosomes engulfed DENV particles within 15-min postinfection. Moreover, single-virus particle tracking revealed that both DENV particles and autophagosomes traveled together during the viral infection. Finally, in the presence of autophagy suppressor 3-methyladenine, the replication of DENV was inhibited and the location of DENV particles spread in cytoplasma. In contrast, the numbers of newly synthesized DENV were elevated and the co-localization of DENV particles and autophagosomes was detected while the cells were treated with autophagy inducer rapamycin. Taken together, we propose that DENV particles interact with autophagosomes at the early stage of viral infection, which promotes the replication of DENV.

Hyperspectral remote sensing and long term monitoring reveal watershed-estuary ecosystem interactions

Science.gov (United States)

Hestir, E. L.; Schoellhamer, D. H.; Santos, M. J.; Greenberg, J. A.; Morgan-King, T.; Khanna, S.; Ustin, S.

2016-02-01

Estuarine ecosystems and their biogeochemical processes are extremely vulnerable to climate and environmental changes, and are threatened by sea level rise and upstream activities such as land use/land cover and hydrological changes. Despite the recognized threat to estuaries, most aspects of how change will affect estuaries are not well understood due to the poorly resolved understanding of the complex physical, chemical and biological processes and their interactions in estuarine systems. Remote sensing technologies such as high spectral resolution optical systems enable measurements of key environmental parameters needed to establish baseline conditions and improve modeling efforts. The San Francisco Bay-Delta is a highly modified estuary system in a state of ecological crisis due to the numerous threats to its sustainability. In this study, we used a combination of hyperspectral remote sensing and long-term in situ monitoring records to investigate how water clarity has been responding to extreme climatic events, anthropogenic watershed disturbances, and submerged aquatic vegetation (SAV) invasions. From the long-term turbidity monitoring record, we found that water clarity underwent significant increasing step changes associated with sediment depletion and El Nino-extreme run-off events. Hyperspectral remote sensing data revealed that invasive submerged aquatic pant species have facultative C3 and C4-like photosynthetic pathways that give them a competitive advantage under the changing water clarity conditions of the Bay-Delta system. We postulate that this adaptation facilitated the rapid expansion of SAV following the significant step changes in increasing water clarity caused by watershed disturbances and the 1982-1983 El Nino events. Using SAV maps from hyperspectral remote sensing, we estimate that SAV-water clarity feedbacks were responsible for 20-70% of the increasing water clarity trend in the Bay-Delta. Ongoing and future developments in airborne and

Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid

Science.gov (United States)

Asai, Shuta; Caillaud, Marie-Cécile; Furzer, Oliver J.; Ishaque, Naveed; Wirthmueller, Lennart; Fabro, Georgina; Shirasu, Ken; Jones, Jonathan D. G.

2014-01-01

Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome. PMID:25329884

Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid.

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Shuta Asai

2014-10-01

Full Text Available Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome.

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility

NARCIS (Netherlands)

Bush, W.S.; McCauley, J.L.; DeJager, P.L.; Dudek, S.M.; Hafler, D.A.; Gibson, R.A.; Matthews, P.M.; Kappos, L.; Naegelin, Y.; Polman, C.H.; Hauser, S.L.; Oksenberg, J.; Haines, J.L.; Ritchie, M.D.

2011-01-01

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also

Interactions between Skeletal Muscle Myoblasts and their Extracellular Matrix Revealed by a Serum Free Culture System.

Science.gov (United States)

Chaturvedi, Vishal; Dye, Danielle E; Kinnear, Beverley F; van Kuppevelt, Toin H; Grounds, Miranda D; Coombe, Deirdre R

2015-01-01

Decellularisation of skeletal muscle provides a system to study the interactions of myoblasts with muscle extracellular matrix (ECM). This study describes the efficient decellularisation of quadriceps muscle with the retention of matrix components and the use of this matrix for myoblast proliferation and differentiation under serum free culture conditions. Three decellularisation approaches were examined; the most effective was phospholipase A2 treatment, which removed cellular material while maximizing the retention of ECM components. Decellularised muscle matrices were then solubilized and used as substrates for C2C12 mouse myoblast serum free cultures. The muscle matrix supported myoblast proliferation and differentiation equally as well as collagen and fibronectin. Immunofluorescence analyses revealed that myoblasts seeded on muscle matrix and fibronectin differentiated to form long, well-aligned myotubes, while myoblasts seeded on collagen were less organized. qPCR analyses showed a time dependent increase in genes involved in skeletal muscle differentiation and suggested that muscle-derived matrix may stimulate an increased rate of differentiation compared to collagen and fibronectin. Decellularized whole muscle three-dimensional scaffolds also supported cell adhesion and spreading, with myoblasts aligning along specific tracts of matrix proteins within the scaffolds. Thus, under serum free conditions, intact acellular muscle matrices provided cues to direct myoblast adhesion and migration. In addition, myoblasts were shown to rapidly secrete and organise their own matrix glycoproteins to create a localized ECM microenvironment. This serum free culture system has revealed that the correct muscle ECM facilitates more rapid cell organisation and differentiation than single matrix glycoprotein substrates.

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

Science.gov (United States)

Freilich, Mara A; Wieters, Evie; Broitman, Bernardo R; Marquet, Pablo A; Navarrete, Sergio A

2018-03-01

Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction

Mutual influence between triel bond and cation-π interactions: an ab initio study

Science.gov (United States)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2017-12-01

Using ab initio calculations, the cooperative and solvent effects on cation-π and B...N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation-π and B...N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation-π interaction increases covalency of B...N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation-π and B...N interactions in these systems. Solvent effects on the cooperativity of cation-π and B...N interactions are also investigated.

Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies.

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Zahra Aghili

Full Text Available Herein, the interaction of hen egg white lysozyme (HEWL with iron nanoparticle (Fe NP was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV to HEWL (8.57±0.54 mV can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV. In addition, dynamic light scattering (DLS study revealed that addition of Fe NP (92.95±6.11 nm to HEWL (2.68±0.37 nm increases suspension potential of protein/nanoparticle system (51.17±3.19 nm. Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein-ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL.

Reveal genes functionally associated with ACADS by a network study.

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Chen, Yulong; Su, Zhiguang

2015-09-15

Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. Copyright © 2015 Elsevier B.V. All rights reserved.

An immersion calorimetric study of the interactions between some organic molecules and functionalized carbon nanotube surfaces

International Nuclear Information System (INIS)

Castillejos-López, E.; Bachiller-Baeza, B.; Guerrero-Ruiz, A.; Rodriguez-Ramos, I.

2013-01-01

Highlights: ► The interaction of organic chemicals with the surface of modified CNTs was studied. ► Specific π–π interactions between graphitic CNTs and toluene have been considered. ► Confinement effects in CNTs increase the adsorption strength of aromatic compounds. ► Methanol molecules form H-bonds with the oxygen functional groups on CNT surfaces. - Abstract: The interaction of organic chemicals with the surface of carbon nanotubes has been studied by immersion calorimetry revealing significant differences in the properties when these materials are modified thermally or chemically. Therefore, multiwall carbon nanotubes have been synthesized using a chemical vapour deposition procedure and subsequently aliquots were treated with HNO 3 at reflux, maintaining the reaction during different times, in order to incorporate oxygen surface groups, or were treated at 2873 K under inert atmosphere. The aim of this thermal treatment is to eliminate structural defects of the carbon nanostructures and to graphitize the amorphous carbon phases. These features were confirmed by high-resolution transmission electron microscopy. The immersion in organic compounds, including toluene, methanol and methylcyclohexane, of all these carbon nanotubes samples reveals that the surface properties are remarkably modified. Thus, the formation of different types of interaction, depending on the surface, gives place to changes in the immersion enthalpies

The Dynamic Reactance Interaction - How Vested Interests Affect People's Experience, Behavior, and Cognition in Social Interactions.

Science.gov (United States)

Steindl, Christina; Jonas, Eva

2015-01-01

In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner's freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor-client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor) or a patient (client). In both studies we incorporated a vested interest. In Study 1 (N = 82) we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N = 207) further demonstrated that doctors expressed their reactance in a subtle way: they revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically.

Possible interaction between baryons and dark-matter particles revealed by the first stars

Science.gov (United States)

Barkana, Rennan

2018-03-01

The cosmic radio-frequency spectrum is expected to show a strong absorption signal corresponding to the 21-centimetre-wavelength transition of atomic hydrogen around redshift 20, which arises from Lyman-α radiation from some of the earliest stars. By observing this 21-centimetre signal—either its sky-averaged spectrum or maps of its fluctuations, obtained using radio interferometers—we can obtain information about cosmic dawn, the era when the first astrophysical sources of light were formed. The recent detection of the global 21-centimetre spectrum reveals a stronger absorption than the maximum predicted by existing models, at a confidence level of 3.8 standard deviations. Here we report that this absorption can be explained by the combination of radiation from the first stars and excess cooling of the cosmic gas induced by its interaction with dark matter. Our analysis indicates that the spatial fluctuations of the 21-centimetre signal at cosmic dawn could be an order of magnitude larger than previously expected and that the dark-matter particle is no heavier than several proton masses, well below the commonly predicted mass of weakly interacting massive particles. Our analysis also confirms that dark matter is highly non-relativistic and at least moderately cold, and primordial velocities predicted by models of warm dark matter are potentially detectable. These results indicate that 21-centimetre cosmology can be used as a dark-matter probe.

Possible interaction between baryons and dark-matter particles revealed by the first stars.

Science.gov (United States)

Barkana, Rennan

2018-02-28

The cosmic radio-frequency spectrum is expected to show a strong absorption signal corresponding to the 21-centimetre-wavelength transition of atomic hydrogen around redshift 20, which arises from Lyman-α radiation from some of the earliest stars. By observing this 21-centimetre signal-either its sky-averaged spectrum or maps of its fluctuations, obtained using radio interferometers-we can obtain information about cosmic dawn, the era when the first astrophysical sources of light were formed. The recent detection of the global 21-centimetre spectrum reveals a stronger absorption than the maximum predicted by existing models, at a confidence level of 3.8 standard deviations. Here we report that this absorption can be explained by the combination of radiation from the first stars and excess cooling of the cosmic gas induced by its interaction with dark matter. Our analysis indicates that the spatial fluctuations of the 21-centimetre signal at cosmic dawn could be an order of magnitude larger than previously expected and that the dark-matter particle is no heavier than several proton masses, well below the commonly predicted mass of weakly interacting massive particles. Our analysis also confirms that dark matter is highly non-relativistic and at least moderately cold, and primordial velocities predicted by models of warm dark matter are potentially detectable. These results indicate that 21-centimetre cosmology can be used as a dark-matter probe.

Study of the chemical interactions of actinide cations in solution at macroscopic concentrations

International Nuclear Information System (INIS)

Maurice, C.

1983-01-01

The aim of this work was to study the interactions of pentavalent neptunium in dodecane-diluted tributyl phosphate with other metallic cations, especially uranium VI and ruthenium present in reprocessing solutions. Pentavalent neptunium on its own was shown to exist in several forms complexed by water and TBP and also to dimerise. In the complex it forms with uranium VI the interaction via the neptunyl oxygen is considerably enhanced in organic solution. Dibutyl phosphoric acid strengthens the interaction between neptunium and uranium. The Np V-ruthenium interaction reveals the existence of a new cation-cation complex; the process takes place in two successive stage and leads to the formation, reinforced and accelerated by HDBP, of a highly to the formation, reinforced and accelerated by HDBP, of a highly stable complex. These results contribute towards a better knowledge of the behaviour of neptunium in the reprocessing operation [fr

Social phenotype extended to communities: expanded multilevel social selection analysis reveals fitness consequences of interspecific interactions.

Science.gov (United States)

Campobello, Daniela; Hare, James F; Sarà, Maurizio

2015-04-01

In social species, fitness consequences are associated with both individual and social phenotypes. Social selection analysis has quantified the contribution of conspecific social traits to individual fitness. There has been no attempt, however, to apply a social selection approach to quantify the fitness implications of heterospecific social phenotypes. Here, we propose a novel social selection based approach integrating the role of all social interactions at the community level. We extended multilevel selection analysis by including a term accounting for the group phenotype of heterospecifics. We analyzed nest activity as a model social trait common to two species, the lesser kestrel (Falco naumanni) and jackdaw (Corvus monedula), nesting in either single- or mixed-species colonies. By recording reproductive outcome as a measure of relative fitness, our results reveal an asymmetric system wherein only jackdaw breeding performance was affected by the activity phenotypes of both conspecific and heterospecific neighbors. Our model incorporating heterospecific social phenotypes is applicable to animal communities where interacting species share a common social trait, thus allowing an assessment of the selection pressure imposed by interspecific interactions in nature. Finally, we discuss the potential role of ecological limitations accounting for random or preferential assortments among interspecific social phenotypes, and the implications of such processes to community evolution. © 2015 The Author(s).

Yeast-yeast interactions revealed by aromatic profile analysis of Sauvignon Blanc wine fermented by single or co-culture of non-Saccharomyces and Saccharomyces yeasts.

Science.gov (United States)

Sadoudi, Mohand; Tourdot-Maréchal, Raphaëlle; Rousseaux, Sandrine; Steyer, Damien; Gallardo-Chacón, Joan-Josep; Ballester, Jordi; Vichi, Stefania; Guérin-Schneider, Rémi; Caixach, Josep; Alexandre, Hervé

2012-12-01

There has been increasing interest in the use of selected non-Saccharomyces yeasts in co-culture with Saccharomyces cerevisiae. The main reason is that the multistarter fermentation process is thought to simulate indigenous fermentation, thus increasing wine aroma complexity while avoiding the risks linked to natural fermentation. However, multistarter fermentation is characterised by complex and largely unknown interactions between yeasts. Consequently the resulting wine quality is rather unpredictable. In order to better understand the interactions that take place between non-Saccharomyces and Saccharomyces yeasts during alcoholic fermentation, we analysed the volatile profiles of several mono-culture and co-cultures. Candida zemplinina, Torulaspora delbrueckii and Metschnikowia pulcherrima were used to conduct fermentations either in mono-culture or in co-culture with S. cerevisiae. Up to 48 volatile compounds belonging to different chemical families were quantified. For the first time, we show that C. zemplinina is a strong producer of terpenes and lactones. We demonstrate by means of multivariate analysis that different interactions exist between the co-cultures studied. We observed a synergistic effect on aromatic compound production when M. pulcherrima was in co-culture with S. cerevisiae. However a negative interaction was observed between C. zemplinina and S. cerevisiae, which resulted in a decrease in terpene and lactone content. These interactions are independent of biomass production. The aromatic profiles of T. delbrueckii and S. cerevisiae in mono-culture and in co-culture are very close, and are biomass-dependent, reflecting a neutral interaction. This study reveals that a whole family of compounds could be altered by such interactions. These results suggest that the entire metabolic pathway is affected by these interactions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Microscopy based studies on the interaction of bio-based silver nanoparticles with Bombyx mori Nuclear Polyhedrosis virus.

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Tamilselvan, Selvaraj; Ashokkumar, Thirunavukkarasu; Govindaraju, Kasivelu

2017-04-01

In the present investigation, silver nanoparticles (AgNPs) interactions with Bombyx mori Nuclear Polyhedrosis virus (BmNPV) were characterized using High-Resolution Scanning Electron Microscopy (HR-SEM), Energy Dispersive X-ray Analysis (EDAX), Transmission Electron Microscopy (TEM), Atomic Force Microcopy (AFM) and Confocal Microscope (CM). HR-SEM study reveals that the biosynthesized AgNPs have interacted with BmNPV and were found on the surface. TEM micrographs of normal and viral polyhedra treated with AgNPs showed that the nanoparticles were accumulated in the membrane and it was noted that some of the AgNPs successfully penetrated the membrane by reaching the capsid of BmNPV. AFM and confocal microscopy studies reveal that the disruption in the shell membrane tends to lose its stability due to exposure of AgNPs to BmNPV. Copyright © 2017 Elsevier B.V. All rights reserved.

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

Science.gov (United States)

Hu, Xiaotang; Li, Hongbin

2014-10-01

Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Coalescence and movement of nanobubbles studied with tapping mode AFM and tip-bubble interaction analysis

International Nuclear Information System (INIS)

Bhushan, Bharat; Wang Yuliang; Maali, Abdelhamid

2008-01-01

Imaging of a polystyrene (PS) coated silicon wafer immersed in deionized (DI) water was conducted using atomic force microscopy (AFM) in the tapping mode (TMAFM). As reported earlier, spherical cap-like domains, referred to as nanobubbles, were observed to be distributed on the PS surface. Experiments reveal that, in addition to the well-known parameter of scan load, scan speed is also an important parameter which affects nanobubble coalescence. The process of nanobubble coalescence was studied. It was found that during coalescence, small nanobubbles were easily moved and merged into bigger ones. Based on the interaction between the AFM cantilever tip and a bubble in the so-called force modulation mode of TMAFM, bubble height and adhesive force information for a given bubble was extracted. A viscoelastic model is used to obtain the interaction stiffness and damping coefficient, which provides a method to obtain the mechanical properties of nanobubbles. The model was further used to study the effect of surface tension force on attractive interaction force and contact angle hysteresis on the changes of the interaction damping coefficient during tip-bubble interaction.

The dynamic reactance interaction – How vested interests affect people’s experience, behavior, and cognition in social interactions

Directory of Open Access Journals (Sweden)

Christina eSteindl

2015-11-01

Full Text Available In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner’s freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor-client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor or a patient (client. In both studies we incorporated a vested interest. In Study 1 (N=82 we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N=207 further demonstrated that doctors expressed their reactance in a subtle way: They revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically.

The Dynamic Reactance Interaction – How Vested Interests Affect People’s Experience, Behavior, and Cognition in Social Interactions

Science.gov (United States)

Steindl, Christina; Jonas, Eva

2015-01-01

In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner’s freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor–client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor) or a patient (client). In both studies we incorporated a vested interest. In Study 1 (N = 82) we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N = 207) further demonstrated that doctors expressed their reactance in a subtle way: they revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically. PMID:26640444

Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes.

Science.gov (United States)

Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

2015-11-14

Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.

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

International Nuclear Information System (INIS)

Dusinska, Maria; Staruchova, Marta; Horska, Alexandra; Smolkova, Bozena; Collins, Andrew; Bonassi, Stefano; Volkovova, Katarina

2012-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-08-01

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

Interactions between calves of Amazonian manatees in Peru: a study case

Directory of Open Access Journals (Sweden)

Alexander Roldán Arévalo-Sandi

2016-05-01

Full Text Available Trichechus inunguis is an endemic species of the Amazon, which inhabits mainly in lakes and calm rivers. The objective of this study case was to describe the social behaviour of two female-orphaned calves, of T. inunguis in captivity. They were kept in the same pool at the facilities of the Amazon Rescue Center (ARC, Iquitos, Peruvian Amazon. Between February and October 2011, the individuals were observed during day and night times, completing 352 hours of observation. Through ad libitum observation of the individuals, we developed a catalogue of social behaviors that includes descriptions of 93 behaviours, classified in eight behavioural categories. The frequency of behaviours was assessed by instantaneous sampling (for states and continuous recording (for events. Manatees displayed mainly social behaviours, and the most frequent interaction was the simultaneous starting of the same behaviour by both individuals. Most of social behaviours occurred during the day, but 'group resting' was recorded mostly at night. 'Synchronized breathing' and 'group feeding' did not have temporary variation between days or between daytimes. Regarding the use of the space, the majority of interactions occurred in shaded places. This study revealed strong interactions between confined calves, suggesting that social activity may play an important role in their learning process.

Laboratory simulation reveals significant impacts of ocean acidification on microbial community composition and host-pathogen interactions between the blood clam and Vibrio harveyi.

Science.gov (United States)

Zha, Shanjie; Liu, Saixi; Su, Wenhao; Shi, Wei; Xiao, Guoqiang; Yan, Maocang; Liu, Guangxu

2017-12-01

It has been suggested that climate change may promote the outbreaks of diseases in the sea through altering the host susceptibility, the pathogen virulence, and the host-pathogen interaction. However, the impacts of ocean acidification (OA) on the pathogen components of bacterial community and the host-pathogen interaction of marine bivalves are still poorly understood. Therefore, 16S rRNA high-throughput sequencing and host-pathogen interaction analysis between blood clam (Tegillarca granosa) and Vibrio harveyi were conducted in the present study to gain a better understanding of the ecological impacts of ocean acidification. The results obtained revealed a significant impact of ocean acidification on the composition of microbial community at laboratory scale. Notably, the abundance of Vibrio, a major group of pathogens to many marine organisms, was significantly increased under ocean acidification condition. In addition, the survival rate and haemolytic activity of V. harveyi were significantly higher in the presence of haemolymph of OA treated T. granosa, indicating a compromised immunity of the clam and enhanced virulence of V. harveyi under future ocean acidification scenarios. Conclusively, the results obtained in this study suggest that future ocean acidification may increase the risk of Vibrio pathogen infection for marine bivalve species, such as blood clams. Copyright © 2017 Elsevier Ltd. All rights reserved.

Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions.

Science.gov (United States)

Katti, Sachin; Nyenhuis, Sarah B; Her, Bin; Srivastava, Atul K; Taylor, Alexander B; Hart, P John; Cafiso, David S; Igumenova, Tatyana I

2017-06-27

C2 domains are independently folded modules that often target their host proteins to anionic membranes in a Ca 2+ -dependent manner. In these cases, membrane association is triggered by Ca 2+ binding to the negatively charged loop region of the C2 domain. Here, we used a non-native metal ion, Cd 2+ , in lieu of Ca 2+ to gain insight into the contributions made by long-range Coulombic interactions and direct metal ion-lipid bridging to membrane binding. Using X-ray crystallography, NMR, Förster resonance energy transfer, and vesicle cosedimentation assays, we demonstrate that, although Cd 2+ binds to the loop region of C2A/B domains of synaptotagmin 1 with high affinity, long-range Coulombic interactions are too weak to support membrane binding of individual domains. We attribute this behavior to two factors: the stoichiometry of Cd 2+ binding to the loop regions of the C2A and C2B domains and the impaired ability of Cd 2+ to directly coordinate the lipids. In contrast, electron paramagnetic resonance experiments revealed that Cd 2+ does support membrane binding of the C2 domains in full-length synaptotagmin 1, where the high local lipid concentrations that result from membrane tethering can partially compensate for lack of a full complement of divalent metal ions and specific lipid coordination in Cd 2+ -complexed C2A/B domains. Our data suggest that long-range Coulombic interactions alone can drive the initial association of C2A/B with anionic membranes and that Ca 2+ further augments membrane binding by the formation of metal ion-lipid coordination bonds and additional Ca 2+ ion binding to the C2 domain loop regions.

Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

Energy Technology Data Exchange (ETDEWEB)

Han, Chao; Fang, Senbiao; Cao, Huiming; Lu, Yan; Ma, Yaqiong [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Wei, Dongfeng [Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700 (China); Xie, Xiaoyun [College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000 (China); Liu, Xiaohua [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Li, Xin [College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471003 (China); Fei, Dongqing [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Zhao, Chunyan, E-mail: zhaochy07@lzu.edu.cn [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China)

2013-03-15

Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum.

The Role of Cognitive and Affective Empathy in Spouses' Support Interactions: An Observational Study

Science.gov (United States)

Verhofstadt, Lesley; Devoldre, Inge; Buysse, Ann; Stevens, Michael; Hinnekens, Céline; Ickes, William; Davis, Mark

2016-01-01

The present study examined how support providers’ empathic dispositions (dispositional perspective taking, empathic concern, and personal distress) as well as their situational empathic reactions (interaction-based perspective taking, empathic concern, and personal distress) relate to the provision of spousal support during observed support interactions. Forty-five committed couples provided questionnaire data and participated in two ten-minute social support interactions designed to assess behaviors when partners are offering and soliciting social support. A video-review task was used to assess situational forms of perspective taking (e.g., empathic accuracy), empathic concern and personal distress. Data were analyzed by means of the multi-level Actor-Partner Interdependence Model. Results revealed that providers scoring higher on affective empathy (i.e., dispositional empathic concern), provided lower levels of negative support. In addition, for male partners, scoring higher on cognitive empathy (i.e., situational perspective taking) was related to lower levels of negative support provision. For both partners, higher scores on cognitive empathy (i.e., situational perspective taking) correlated with more instrumental support provision. Male providers scoring higher on affective empathy (i.e., situational personal distress) provided higher levels of instrumental support. Dispositional perspective taking was related to higher scores on emotional support provision for male providers. The current study furthers our insight into the empathy-support link, by revealing differential effects (a) for men and women, (b) of both cognitive and affective empathy, and (c) of dispositional as well as situational empathy, on different types of support provision. PMID:26910769

Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction.

Science.gov (United States)

Huang, Richard Y-C; Krystek, Stanley R; Felix, Nathan; Graziano, Robert F; Srinivasan, Mohan; Pashine, Achal; Chen, Guodong

2018-01-01

TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1's binding epitope on TL1A. HDX coupled with electron-transfer dissociation MS provided residue-level epitope information. The HDX dataset, in combination with solvent accessible surface area (SASA) analysis and computational modeling, revealed a discontinuous epitope within the predicted interaction interface of TL1A and DR3. The epitope regions span a distance within the approximate size of the variable domains of mAb1's heavy and light chains, indicating it uses a unique mechanism of action to block the TL1A/DR3 interaction.

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

Directory of Open Access Journals (Sweden)

Matthias Stein

Full Text Available Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

Interactions With Robots: The Truths We Reveal About Ourselves.

Science.gov (United States)

Broadbent, Elizabeth

2017-01-03

In movies, robots are often extremely humanlike. Although these robots are not yet reality, robots are currently being used in healthcare, education, and business. Robots provide benefits such as relieving loneliness and enabling communication. Engineers are trying to build robots that look and behave like humans and thus need comprehensive knowledge not only of technology but also of human cognition, emotion, and behavior. This need is driving engineers to study human behavior toward other humans and toward robots, leading to greater understanding of how humans think, feel, and behave in these contexts, including our tendencies for mindless social behaviors, anthropomorphism, uncanny feelings toward robots, and the formation of emotional attachments. However, in considering the increased use of robots, many people have concerns about deception, privacy, job loss, safety, and the loss of human relationships. Human-robot interaction is a fascinating field and one in which psychologists have much to contribute, both to the development of robots and to the study of human behavior.

Simple analytical model reveals the functional role of embodied sensorimotor interaction in hexapod gaits

Science.gov (United States)

Aoi, Shinya; Nachstedt, Timo; Manoonpong, Poramate; Wörgötter, Florentin; Matsuno, Fumitoshi

2018-01-01

Insects have various gaits with specific characteristics and can change their gaits smoothly in accordance with their speed. These gaits emerge from the embodied sensorimotor interactions that occur between the insect’s neural control and body dynamic systems through sensory feedback. Sensory feedback plays a critical role in coordinated movements such as locomotion, particularly in stick insects. While many previously developed insect models can generate different insect gaits, the functional role of embodied sensorimotor interactions in the interlimb coordination of insects remains unclear because of their complexity. In this study, we propose a simple physical model that is amenable to mathematical analysis to explain the functional role of these interactions clearly. We focus on a foot contact sensory feedback called phase resetting, which regulates leg retraction timing based on touchdown information. First, we used a hexapod robot to determine whether the distributed decoupled oscillators used for legs with the sensory feedback generate insect-like gaits through embodied sensorimotor interactions. The robot generated two different gaits and one had similar characteristics to insect gaits. Next, we proposed the simple model as a minimal model that allowed us to analyze and explain the gait mechanism through the embodied sensorimotor interactions. The simple model consists of a rigid body with massless springs acting as legs, where the legs are controlled using oscillator phases with phase resetting, and the governed equations are reduced such that they can be explained using only the oscillator phases with some approximations. This simplicity leads to analytical solutions for the hexapod gaits via perturbation analysis, despite the complexity of the embodied sensorimotor interactions. This is the first study to provide an analytical model for insect gaits under these interaction conditions. Our results clarified how this specific foot contact sensory

A rice gid1 suppressor mutant reveals that gibberellin is not always required for interaction between its receptor, GID1, and DELLA proteins.

Science.gov (United States)

Yamamoto, Yuko; Hirai, Takaaki; Yamamoto, Eiji; Kawamura, Mayuko; Sato, Tomomi; Kitano, Hidemi; Matsuoka, Makoto; Ueguchi-Tanaka, Miyako

2010-11-01

To investigate gibberellin (GA) signaling using the rice (Oryza sativa) GA receptor GIBBERELLIN-INSENSITIVE DWARF1 (GID1) mutant gid1-8, we isolated a suppressor mutant, Suppressor of gid1-1 (Sgd-1). Sgd-1 is an intragenic mutant containing the original gid1-8 mutation (L45F) and an additional amino acid substitution (P99S) in the loop region. GID1(P99S) interacts with the rice DELLA protein SLENDER RICE1 (SLR1), even in the absence of GA. Substitution of the 99th Pro with other amino acids revealed that substitution with Ala (P99A) caused the highest level of GA-independent interaction. Physicochemical analysis using surface plasmon resonance revealed that GID1(P99A) has smaller K(a) (association) and K(d) (dissociation) values for GA(4) than does wild-type GID1. This suggests that the GID1(P99A) lid is at least partially closed, resulting in both GA-independent and GA-hypersensitive interactions with SLR1. One of the three Arabidopsis thaliana GID1s, At GID1b, can also interact with DELLA proteins in the absence of GA, so we investigated whether GA-independent interaction of At GID1b depends on a mechanism similar to that of rice GID1(P99A). Substitution of the loop region or a few amino acids of At GID1b with those of At GID1a diminished its GA-independent interaction with GAI while maintaining the GA-dependent interaction. Soybean (Glycine max) and Brassica napus also have GID1s similar to At GID1b, indicating that these unique GID1s occur in various dicots and may have important functions in these plants.

Social patterns revealed through random matrix theory

Science.gov (United States)

Sarkar, Camellia; Jalan, Sarika

2014-11-01

Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

Protein-Flavonoid Interaction Studies by a Taylor Dispersion Surface Plasmon Resonance (SPR Technique: A Novel Method to Assess Biomolecular Interactions

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Preejith P. Vachali

2016-02-01

Full Text Available Flavonoids are common polyphenolic compounds widely distributed in fruits and vegetables. These pigments have important pharmacological relevance because emerging research suggests possible anti-cancer and anti-inflammatory properties as well other beneficial health effects. These compounds are relatively hydrophobic molecules, suggesting the role of blood transport proteins in their delivery to tissues. In this study, we assess the binding interactions of four flavonoids (kaempferol, luteolin, quercetin, and resveratrol with human serum albumin (HSA, the most abundant protein in the blood, and with glutathione S-transferase pi isoform-1 (GSTP1, an enzyme with well-characterized hydrophobic binding sites that plays an important role in detoxification of xenobiotics with reduced glutathione, using a novel Taylor dispersion surface plasmon resonance (SPR technique. For the first time, HSA sites revealed a high-affinity binding site for flavonoid interactions. Out of the four flavonoids that we examined, quercetin and kaempferol showed the strongest equilibrium binding affinities (KD of 63 ± 0.03 nM and 37 ± 0.07 nM, respectively. GSTP1 displayed lower affinities in the micromolar range towards all of the flavonoids tested. The interactions of flavonoids with HSA and GSTP1 were studied successfully using this novel SPR assay method. The new method is compatible with both kinetic and equilibrium analyses.

Spectroscopic and thermodynamic studies on ferulic acid - Alpha-2-macroglobulin interaction

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Rehman, Ahmed Abdur; Sarwar, Tarique; Arif, Hussain; Ali, Syed Saqib; Ahsan, Haseeb; Tabish, Mohammad; Khan, Fahim Halim

2017-09-01

Ferulic acid is a major phenolic acid found in numerous plant species in conjugated form. It binds to enzymes and oligomeric proteins and modifies their structure and function. This study was designed to examine the interaction of ferulic acid, an active ingredient of some important medicines, with α2M, a key serum proteinase, under physiological conditions. The mechanism of interaction was studied by spectroscopic techniques such as, UV-visible absorption, fluorescence spectroscopy, circular dichroism along with isothermal titration calorimetry. Fluorescence quenching of α2M by ferulic acid demonstrated the formation of α2M-ferulic acid complex by static quenching mechanism. Binding parameters calculated by Stern-Volmer method showed that ferulic acid binds to α2M with moderate affinity of the order of ∼104 M-1. The thermodynamic signatures reveal that binding was enthalpy driven and hydrogen bonding played a major role in ferulic acid-α2M binding. CD spectra analysis suggests very little conformational changes in α2M on ferulic acid binding.

Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

KAUST Repository

Simone, Giuseppina

2013-02-11

Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental study on thermal interaction between a high-temperature molten jet and plates

International Nuclear Information System (INIS)

Sato, K.; Saito, M.; Furutani, A.; Isozaki, M.; Imahori, S.; Konishi, K.

1994-01-01

This paper summarizes the recent simulant experiments to study molten corium-structure interactions under postulated core disruptive accident (CDA) conditions in liquid-metal fast breeder reactors (LMFMRs). These experiments were conducted in the MELT-II facility generating high-temperature molten simulants by an induction heating technique. From a series of molten jet-structure interaction experiments, the effects of the solidified crust layer and molten layer on the erosion behavior were identified, and analytical models were developed to assess the structure erosion rate with and without crust formation. Especially, we revealed the inherent mitigation mechanism that when the molten oxide jet with high melting point falls down onto the structure plate, solidified crust of the oxide can significantly reduce the erosion rate. (author)

COMT and MTHFR polymorphisms interaction on cognition in schizophrenia: an exploratory study.

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Kontis, Dimitrios; Theochari, Eirini; Fryssira, Helen; Kleisas, Spyridon; Sofocleous, Christalena; Andreopoulou, Angeliki; Kalogerakou, Stamatina; Gazi, Anthia; Boniatsi, Lucia; Chaidemenos, Alexandros; Tsaltas, Eleftheria

2013-03-14

The investigation of the catechol-O-methyltransferase (COMT-[rs4680]) and methylenetetrahydrofolate reductase (MTHFR-[rs1801133]) polymorphisms' interaction might shed light into the pathogenetic mechanisms of the cognitive dysfunction in schizophrenia. In an exploratory study, we hypothesized that the MTHFR 677T allele which has been related to a hypoactive MTHFR enzyme would augment the unfavorable effects of COMT Val158 homozygosity which has been associated with COMT enzyme hyperfunction. 90 schizophrenia patients and 55 healthy volunteers were assessed on psychomotor speed, pattern and spatial recognition memory (SRM), spatial working memory (SWM), attentional flexibility and planning (Stockings of Cambridge-SOC). IQ scores in a random subgroup of patients were also measured. A significant COMT×MTHFR interaction on SWM (p=0.048) and planning (p=0.026) was revealed in both groups. Among COMT-Val/Val participants, MTHFR-C/C made more SWM errors (p=0.033) and solved fewer SOC problems (p=0.025) than MTHFR-T carriers. In patients, there was a significant COMT×MTHFR interaction on full scale IQ (p=0.035): among COMT-Met carriers, MTHFR-T carriers performed significantly worse than MTHFR-C/C (p=0.021), which was driven by a COMT×MTHFR interaction involving performance IQ (p=0.047). In conclusion, COMT and MTHFR polymorphisms interacted on cognition, suggesting that the MTHFR enzyme activity might moderate the effects of the COMT enzyme. In contrast to our initial hypothesis, the MTHFR T-allele attenuated the cognitive effects of COMT Val homozygosity. In this preliminary study, we propose that dopaminergic and intracellular methylation mechanisms could interact on cognitive deficits in schizophrenia. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A protein interaction map of the kalimantacin biosynthesis assembly line

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Birgit Uytterhoeven

2016-11-01

Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

Concurrent TMS-fMRI Reveals Interactions between Dorsal and Ventral Attentional Systems

DEFF Research Database (Denmark)

Leitao, Joana; Thielscher, Axel; Tuennerhoff, Johannes

2015-01-01

interactively in this process. This fMRI study used concurrent transcranial magnetic stimulation (TMS) as a causal perturbation approach to investigate the interactions between dorsal and ventral attentional systems and sensory processing areas. In a sustained spatial attention paradigm, human participants......Adaptive behavior relies on combining bottom-up sensory inputs with top-down control signals to guide responses in line with current goals and task demands. Over the past decade, accumulating evidence has suggested that the dorsal and ventral frontoparietal attentional systems are recruited......-TMS relative to Sham-TMS increased activation in the parietal cortex regardless of sensory stimulation, confirming the neural effectiveness of TMS stimulation. Visual targets increased activations in the anterior insula, a component of the ventral attentional system responsible for salience detection...

A simulation study on estimating biomarker-treatment interaction effects in randomized trials with prognostic variables.

Science.gov (United States)

Haller, Bernhard; Ulm, Kurt

2018-02-20

To individualize treatment decisions based on patient characteristics, identification of an interaction between a biomarker and treatment is necessary. Often such potential interactions are analysed using data from randomized clinical trials intended for comparison of two treatments. Tests of interactions are often lacking statistical power and we investigated if and how a consideration of further prognostic variables can improve power and decrease the bias of estimated biomarker-treatment interactions in randomized clinical trials with time-to-event outcomes. A simulation study was performed to assess how prognostic factors affect the estimate of the biomarker-treatment interaction for a time-to-event outcome, when different approaches, like ignoring other prognostic factors, including all available covariates or using variable selection strategies, are applied. Different scenarios regarding the proportion of censored observations, the correlation structure between the covariate of interest and further potential prognostic variables, and the strength of the interaction were considered. The simulation study revealed that in a regression model for estimating a biomarker-treatment interaction, the probability of detecting a biomarker-treatment interaction can be increased by including prognostic variables that are associated with the outcome, and that the interaction estimate is biased when relevant prognostic variables are not considered. However, the probability of a false-positive finding increases if too many potential predictors are included or if variable selection is performed inadequately. We recommend undertaking an adequate literature search before data analysis to derive information about potential prognostic variables and to gain power for detecting true interaction effects and pre-specifying analyses to avoid selective reporting and increased false-positive rates.

[Study on the interaction of doxycycline with human serum albumin].

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Hu, Tao-Ying; Chen, Lin; Liu, Ying

2014-05-01

The present study was designed to investigate the interaction of doxycycline (DC) with human serum albumin (HSA) by the inner filter effects, displacement experiments and molecular docking methods, based on classic multi-spectroscopy. With fluorescence quenching method at 298 and 310 K, the binding constants Ka, were determined to be 2. 73 X 10(5) and 0. 74X 10(5) L mol-1, respectively, and there was one binding site between DC and HSA, indicating that the binding of DC to HSA was strong, and the quenching mechanism was a static quenching. The thermodynamic parameters (enthalpy change, AH and enthropy change, delta S) were calculated to be -83. 55 kJ mol-1 and -176. 31 J mol-1 K-1 via the Vant' Hoff equation, which indicated that the interaction of DC with HSA was driven mainly by hydrogen bonding and van der Waals forces. Based on the Föster's theory of non-radiation energy transfer, the specific binding distance between Trp-214 (acceptor) and DC (donor) was 4. 98 nm, which was similar to the result confirmed by molecular docking. Through displacement experiments, sub-domain IIA of HSA was assigned to possess the high-affinity binding site of DC. Three-dimensional fluorescence spectra indicated that the binding of DC to HSA induced the conformation change of HSA and increased the disclosure of some part of hydrophobic regions that had been buried before. The results of FTIR spectroscopy showed that DC bound to HSA led to the slight unfolding of the polypeptide chain of HSA. Furthermore, the binding details between DC and HSA were further confirmed by molecular docking methods, which revealed that DC was bound at sub-domain IIA through multiple interactions, such as hydrophobic effect, polar forces and pi-pi interactions. The experimental results provide theoretical basis and reliable data for the study of the interaction between small drug molecule and human serum albumin

Interaction of chloroquine and its analogues with heme: An isothermal titration calorimetric study.

Science.gov (United States)

Bachhawat, K; Thomas, C J; Surolia, N; Surolia, A

2000-10-05

Quinoline-containing drugs such as chloroquine and quinine have had a long and successful history in antimalarial chemotherapy. Identification of ferriprotoporphyrin IX ([Fe(III)PPIX], haematin) as the drug receptors for these antimalarials called for investigations of the binding affinity, mode of interaction, and the conditions affecting the interaction. The parameters obtained are significant in recent times with the emergence of chloroquine resistant strains of the malaria parasites. This has underlined the need to unravel the molecular mechanism of their action so as to meet the requirement of an alternative to the existing antimalarial drugs. The isothermal titration calorimetric studies on the interaction of chloroquine with haematin lead us to propose an altered mode of binding. The initial recognition is ionic in nature mediated by the propionyl group of haematin with the quaternary nitrogen on CQ. This ionic interaction induces a conformational change, such as to favour binding of subsequent CQ molecules. On the contrary, conditions emulating the cytosolic environment (pH 7.4 and 150 mM salt) reveal the hydrophobic force to be the sole contributor driving the interaction. Interaction of a carefully selected panel of quinoline antimalarial drugs with monomeric ferriprotoporphyrin IX has also been investigated at pH 5.6 mimicking the acidic environment prevalent in the food vacuoles of parasite, the center of drug activity, which are consistent with their antimalarial activity. Copyright 2000 Academic Press.

Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies.

Science.gov (United States)

Chen, Huilun; Rao, Honghao; Yang, Jian; Qiao, Yongxiang; Wang, Fei; Yao, Jun

2016-01-01

This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10(4) L mol(-1) at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II).

Understanding the Symbolic Capital of Intercultural Interactions: A Case Study of International Students in Australia

Science.gov (United States)

Pham, Lien; Tran, Ly

2015-01-01

Intercultural interaction plays an important role in contributing to international students' learning and wellbeing in the host country. While research on international students' intercultural interactions reveals multifaceted aspects of personal and social factors, there is a tendency to consider language barrier and cultural differences as…

Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

KAUST Repository

Simone, Giuseppina; Malara, Natalia Maria; Trunzo, Valentina; Perozziello, Gerardo; Neužil, Pavel; Francardi, Marco; Roveda, Laura; Renne, Maria; Prati, Ubaldo; Mollace, Vincenzo; Manz, Andreas; Di Fabrizio, Enzo M.

2013-01-01

Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction's strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dual-EEG of joint finger tapping: what can two interacting brains teach us about social interaction?

DEFF Research Database (Denmark)

Konvalinka, Ivana

-frequency analysis revealed a left-motor and right-frontal suppression at 10 Hz during task execution, when carrying the task out interactively in contrast with the uncoupled computer-driven task. We used machine-learning approaches to identify the brain signals driving the interaction. The raw-power at 10 Hz during...... tapping emanating from electrodes of member one and member two were used as features. We combined data from both participants in each pair, and applied logistic regression using feature selection in order to classify the two conditions. The first seven (frontal) electrodes consistently emerged as good...... classifiers, with 85-99% accuracy. There was a tendency for one member’s frontal electrodes to drive the classifier over the other’s, which predicted the leader of the interaction in 8/9 pairs. This study reveals new neural mechanisms underlying two-person interactions. It also shows how analyzing two...

In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop.

Science.gov (United States)

Shivhare, Devendra; Mueller-Cajar, Oliver

2017-07-01

To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice ( Oryza sativa ) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca Further mutational analysis suggested that Glu-217 restricts the flexibility of the α4-β4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function. © 2017 American Society of Plant Biologists. All Rights Reserved.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.

Science.gov (United States)

A Santos, Jose C; Nassif, Houssam; Page, David; Muggleton, Stephen H; E Sternberg, Michael J

2012-07-11

There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. In addition to confirming literature results, ProGolem's model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

Hypernetworks Reveal Compound Variables That Capture Cooperative and Competitive Interactions in a Soccer Match.

Science.gov (United States)

Ramos, João; Lopes, Rui J; Marques, Pedro; Araújo, Duarte

2017-01-01

The combination of sports sciences theorization and social networks analysis (SNA) has offered useful new insights for addressing team behavior. However, SNA typically represents the dynamics of team behavior during a match in dyadic interactions and in a single cumulative snapshot. This study aims to overcome these limitations by using hypernetworks to describe illustrative cases of team behavior dynamics at various other levels of analyses. Hypernetworks simultaneously access cooperative and competitive interactions between teammates and opponents across space and time during a match. Moreover, hypernetworks are not limited to dyadic relations, which are typically represented by edges in other types of networks. In a hypernetwork, n-ary relations (with n > 2) and their properties are represented with hyperedges connecting more than two players simultaneously (the so-called simplex -plural, simplices ). Simplices can capture the interactions of sets of players that may include an arbitrary number of teammates and opponents. In this qualitative study, we first used the mathematical formalisms of hypernetworks to represent a multilevel team behavior dynamics, including micro (interactions between players), meso (dynamics of a given critical event, e.g., an attack interaction), and macro (interactions between sets of players) levels. Second, we investigated different features that could potentially explain the occurrence of critical events, such as, aggregation or disaggregation of simplices relative to goal proximity. Finally, we applied hypernetworks analysis to soccer games from the English premier league (season 2010-2011) by using two-dimensional player displacement coordinates obtained with a multiple-camera match analysis system provided by STATS (formerly Prozone). Our results show that (i) at micro level the most frequently occurring simplices configuration is 1vs.1 (one attacker vs. one defender); (ii) at meso level, the dynamics of simplices

Hypernetworks Reveal Compound Variables That Capture Cooperative and Competitive Interactions in a Soccer Match

Directory of Open Access Journals (Sweden)

João Ramos

2017-08-01

Full Text Available The combination of sports sciences theorization and social networks analysis (SNA has offered useful new insights for addressing team behavior. However, SNA typically represents the dynamics of team behavior during a match in dyadic interactions and in a single cumulative snapshot. This study aims to overcome these limitations by using hypernetworks to describe illustrative cases of team behavior dynamics at various other levels of analyses. Hypernetworks simultaneously access cooperative and competitive interactions between teammates and opponents across space and time during a match. Moreover, hypernetworks are not limited to dyadic relations, which are typically represented by edges in other types of networks. In a hypernetwork, n-ary relations (with n > 2 and their properties are represented with hyperedges connecting more than two players simultaneously (the so-called simplex—plural, simplices. Simplices can capture the interactions of sets of players that may include an arbitrary number of teammates and opponents. In this qualitative study, we first used the mathematical formalisms of hypernetworks to represent a multilevel team behavior dynamics, including micro (interactions between players, meso (dynamics of a given critical event, e.g., an attack interaction, and macro (interactions between sets of players levels. Second, we investigated different features that could potentially explain the occurrence of critical events, such as, aggregation or disaggregation of simplices relative to goal proximity. Finally, we applied hypernetworks analysis to soccer games from the English premier league (season 2010–2011 by using two-dimensional player displacement coordinates obtained with a multiple-camera match analysis system provided by STATS (formerly Prozone. Our results show that (i at micro level the most frequently occurring simplices configuration is 1vs.1 (one attacker vs. one defender; (ii at meso level, the dynamics of simplices

Interaction between vitamin D 2 and magnesium in liposomes: Differential scanning calorimetry and FTIR spectroscopy studies

Science.gov (United States)

Toyran, Neslihan; Severcan, Feride

2007-08-01

Magnesium (Mg 2+) ion is of great importance in physiology by its intervention in 300 enzymatic systems, its role in membrane structure, its function in neuromuscular excitability and vitamin D metabolism and/or action. In the present study, the interaction of Mg 2+, at low (1 mole %) and high (7 mole %) concentrations with dipalmitoyl phosphatidylcholine (DPPC) liposomes has been studied in the presence and absence of vitamin D 2 (1 mole %) by using two noninvasive techniques, namely differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) spectroscopy. DSC studies reveal that the presence of vitamin D 2 in the pure or Mg 2+ (at both low and high concentrations) containing liposomes diminishes the pretransition. The calorimetric results also reveal that, inclusion of Mg 2+ (more significantly at high concentration) into pure or vitamin D 2 containing DPPC liposomes increases the main phase transition temperature. The investigation of the CH 2 symmetric, the CH 3 asymmetric, the C dbnd O stretching, and the PO2- antisymmetric double bond stretching bands in FTIR spectra with respect to changes occurring in the wavenumber and/or the bandwidth values as a function of temperature reveal that, inclusion of vitamin D 2 or Mg 2+ into pure DPPC liposomes orders and decreases the dynamics of the acyl chains in both gel and liquid-crystalline phases and does not induce hydrogen bond formation in the interfacial region. Furthermore, the dynamics of the head groups of the liposomes decreases in both phases. Our findings reveal that, simultaneous presence of vitamin D 2 and Mg 2+ alters the effect of each other, which is reflected as a decrease in the interactions between these two additives within the model membrane.

Outrun or Outmaneuver: Predator-Prey Interactions as a Model System for Integrating Biomechanical Studies in a Broader Ecological and Evolutionary Context.

Science.gov (United States)

Moore, Talia Y; Biewener, Andrew A

2015-12-01

Behavioral studies performed in natural habitats provide a context for the development of hypotheses and the design of experiments relevant both to biomechanics and to evolution. In particular, predator-prey interactions are a model system for integrative study because success or failure of predation has a direct effect on fitness and drives the evolution of specialized performance in both predator and prey. Although all predators share the goal of capturing prey, and all prey share the goal of survival, the behavior of predators and prey are diverse in nature. This article presents studies of some predator-prey interactions sharing common predation strategies that reveal general principles governing the behaviors of predator and prey, even in distantly related taxa. Studies of predator-prey interactions also reveal that maximal performance observed in a laboratory setting is not necessarily the performance that determines fitness. Thus, considering locomotion in the context of predation ecology can aid in evolutionarily relevant experimental design. Classification by strategy reveals that displaying unpredictable trajectories is a relevant anti-predator behavior in response to multiple predation strategies. A predator's perception and pursuit of prey can be affected indirectly by divergent locomotion of similar animals that share an ecosystem. Variation in speed and direction of locomotion that directly increases the unpredictability of a prey's trajectory can be increased through genetic mutation that affects locomotor patterns, musculoskeletal changes that affect maneuverability, and physical interactions between an animal and the environment. By considering the interconnectedness of ecology, physical constraints, and the evolutionary history of behavior, studies in biomechanics can be designed to inform each of these fields. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights

Experimentally reduced root–microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

Science.gov (United States)

Lee, Mei-Ho; Comas, Louise H.; Callahan, Hilary S.

2014-01-01

Background and Aims Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous. Methods To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations. Key Results Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10–20 %) and increased specific root length (approx. 10–30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples. Conclusions The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root

Experimentally reduced root-microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus.

Science.gov (United States)

Lee, Mei-Ho; Comas, Louise H; Callahan, Hilary S

2014-02-01

Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous. To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations. Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10-20 %) and increased specific root length (approx. 10-30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples. The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root trait variation, interactions with symbionts and recent

Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration

Science.gov (United States)

Tsvetkova, Milena; García-Gavilanes, Ruth; Yasseri, Taha

2016-11-01

Disagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.

Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

Science.gov (United States)

Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

2017-10-01

Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

Head-head interactions of resting myosin crossbridges in intact frog skeletal muscles, revealed by synchrotron x-ray fiber diffraction.

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Kanji Oshima

Full Text Available The intensities of the myosin-based layer lines in the x-ray diffraction patterns from live resting frog skeletal muscles with full thick-thin filament overlap from which partial lattice sampling effects had been removed were analyzed to elucidate the configurations of myosin crossbridges around the thick filament backbone to nanometer resolution. The repeat of myosin binding protein C (C-protein molecules on the thick filaments was determined to be 45.33 nm, slightly longer than that of myosin crossbridges. With the inclusion of structural information for C-proteins and a pre-powerstroke head shape, modeling in terms of a mixed population of regular and perturbed regions of myosin crown repeats along the filament revealed that the myosin filament had azimuthal perturbations of crossbridges in addition to axial perturbations in the perturbed region, producing pseudo-six-fold rotational symmetry in the structure projected down the filament axis. Myosin crossbridges had a different organization about the filament axis in each of the regular and perturbed regions. In the regular region that lacks C-proteins, there were inter-molecular interactions between the myosin heads in axially adjacent crown levels. In the perturbed region that contains C-proteins, in addition to inter-molecular interactions between the myosin heads in the closest adjacent crown levels, there were also intra-molecular interactions between the paired heads on the same crown level. Common features of the interactions in both regions were interactions between a portion of the 50-kDa-domain and part of the converter domain of the myosin heads, similar to those found in the phosphorylation-regulated invertebrate myosin. These interactions are primarily electrostatic and the converter domain is responsible for the head-head interactions. Thus multiple head-head interactions of myosin crossbridges also characterize the switched-off state and have an important role in the regulation

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

Science.gov (United States)

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction

Reasons for Low Levels of Interactivity

DEFF Research Database (Denmark)

Etter, Michael

2013-01-01

The interactivity levels of online CSR communication are typically low. This study explores the reasons for the low levels of interactivity in the popular social media tool Twitter. An analysis of 41,864 Twitter messages (tweets) from the thirty most central corporate accounts in a CSR Twitter...... network is conducted. Comparisons (t-test) between CSR tweets and general tweets and between specialized CSR Twitter accounts and general accounts reveal that the low levels of interactivity are due to a reactive interaction approach and a lack of specialization....

Peptide-Graphene Interactions Enhance the Mechanical Properties of Silk Fibroin.

Science.gov (United States)

Cheng, Yuan; Koh, Leng-Duei; Li, Dechang; Ji, Baohua; Zhang, Yingyan; Yeo, Jingjie; Guan, Guijian; Han, Ming-Yong; Zhang, Yong-Wei

2015-10-07

Studies reveal that biomolecules can form intriguing molecular structures with fascinating functionalities upon interaction with graphene. Then, interesting questions arise. How does silk fibroin interact with graphene? Does such interaction lead to an enhancement in its mechanical properties? In this study, using large-scale molecular dynamics simulations, we first examine the interaction of graphene with several typical peptide structures of silk fibroin extracted from different domains of silk fibroin, including pure amorphous (P1), pure crystalline (P2), a segment from N-terminal (P3), and a combined amorphous and crystalline segment (P4), aiming to reveal their structural modifications. Our study shows that graphene can have intriguing influences on the structures formed by the peptides with sequences representing different domains of silk fibroin. In general, for protein domains with stable structure and strong intramolecular interaction (e.g., β-sheets), graphene tends to compete with the intramolecular interactions and thus weaken the interchain interaction and reduce the contents of β-sheets. For the silk domains with random or less ordered secondary structures and weak intramolecular interactions, graphene tends to enhance the stability of peptide structures; in particular, it increases the contents of helical structures. Thereafter, tensile simulations were further performed on the representative peptides to investigate how such structure modifications affect their mechanical properties. It was found that the strength and resilience of the peptides are enhanced through their interaction with graphene. The present work reveals interesting insights into the interactions between silk peptides and graphene, and contributes in the efforts to enhance the mechanical properties of silk fibroin.

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

Science.gov (United States)

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

2016-07-14

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

Emission solvatochromic behavior of a pentacoordinated Zn(II) complex: A viable tool for studying the metallodrug–protein interaction

Energy Technology Data Exchange (ETDEWEB)

Ricciardi, Loredana, E-mail: loredana.ricciardi@unical.it [Department of Chemistry and Chemical Technology, University of Calabria, I-87036 Rende (CS) (Italy); Centre of Excellence “Functional Nanostructured Materials” CEMIF.CAL, LASCAMM and CR INSTM, INSTM Calabria Unit, and CNR-IPCF-UOS Cosenza - Licryl Laboratory, I-87036 Rende (CS) (Italy); Pucci, Daniela; Pirillo, Sante; La Deda, Massimo [Department of Chemistry and Chemical Technology, University of Calabria, I-87036 Rende (CS) (Italy); Centre of Excellence “Functional Nanostructured Materials” CEMIF.CAL, LASCAMM and CR INSTM, INSTM Calabria Unit, and CNR-IPCF-UOS Cosenza - Licryl Laboratory, I-87036 Rende (CS) (Italy)

2014-07-01

A metal complex with antitumoral activity, Zn(Curcumin)(bypiridine)Cl, was characterized from a photophysical point of view, showing a green emission and a positive solvatochromism. These characteristics can be conveniently used to study its interaction with Human Serum Albumin (HSA), a protein carrier of many non-aqueous biologically-active compounds in the blood stream. The intrinsic fluorescence of HSA was quenched by Fluorescence Resonance Energy Transfer toward the Zn(II) complex, and the Stern–Volmer equation was applied to determine the bimolecular quenching rate constant of the interaction. - Highlights: • Albumin binding information is a key characteristic of drug pharmacology. • Fluorescence spectroscopy offers a simple method for revealing drug–protein interaction. • The fluorescence of the Zn(II) complex and its solvatochromisms has allowed studying the binding from a dual perspective.

Experimental study of X-ray emission in laser-cluster interaction; Etude experimentale de l'emission X issue de l'interaction laser-agregats

Energy Technology Data Exchange (ETDEWEB)

Caillaud, T

2004-09-01

Rare gas cluster jets are an intermediate medium between solid and gas targets. Laser-cluster jets interaction may generate a great number of energetic particles as X-rays, UV, high harmonics, ions, electrons and neutrons. To understand all the mechanisms involved in such an interaction we need to make a complete study of individual cluster response to an ultra-short laser pulse. We studied the laser interaction with our argon cluster gas jet, which is well characterized in cluster size and density, to enlarge the knowledge of this interaction. We measured absorption, heating and X-ray emission spectra versus laser parameters and clusters size ({approx} 15-30 nm). We show that there is a strong refraction effect on laser propagation due to the residual gas density. This effect was confirmed by laser propagation simulation with a cylindrical 2-dimensional particle code WAKE. The role played by refraction was to limit maximum laser intensity on the focal spot and to increase interaction volume. By this way, X-ray emission was observed with laser intensity not so far from the ionization threshold (few 10{sup 14} W.cm{sup -2}). We also studied plasma expansion both at cluster scale and focal volume scale and deduced the deposited energy distribution as a function of time. Thanks to a simple hydrodynamic model, we used these results to study cluster expansion. X-ray emission is then simulated by TRANSPEC code in order to reproduce X-ray spectra and duration. Those results revealed an extremely brief X-ray emission consistent with a preliminary measure by streak camera (on ps scale). (author)

Whole body interaction with public displays

CERN Document Server

Walter, Robert

2017-01-01

This book develops valuable new approaches to digital out-of-home media and digital signage in urban environments. It offers solutions for communicating interactive features of digital signage to passers-by. Digital out-of-home media and digital signage screens are becoming increasingly interactive thanks to touch input technology and gesture recognition. To optimize their conversion rate, interactive public displays must 1) attract attention, 2) communicate to passers-by that they are interactive, 3) explain the interaction, and 4) provide a motivation for passers-by to interact. This book highlights solutions to problems 2 and 3 above. The focus is on whole-body interaction, where the positions and orientations of users and their individual body parts are captured by specialized sensors (e.g., depth cameras). The book presents revealing findings from a field study on communicating interactivity, a laboratory on analysing visual attention, a field study on mid-air gestures, and a field study on using mid-air...

A Rice gid1 Suppressor Mutant Reveals That Gibberellin Is Not Always Required for Interaction between Its Receptor, GID1, and DELLA Proteins[W][OA

Science.gov (United States)

Yamamoto, Yuko; Hirai, Takaaki; Yamamoto, Eiji; Kawamura, Mayuko; Sato, Tomomi; Kitano, Hidemi; Matsuoka, Makoto; Ueguchi-Tanaka, Miyako

2010-01-01

To investigate gibberellin (GA) signaling using the rice (Oryza sativa) GA receptor GIBBERELLIN-INSENSITIVE DWARF1 (GID1) mutant gid1-8, we isolated a suppressor mutant, Suppressor of gid1-1 (Sgd-1). Sgd-1 is an intragenic mutant containing the original gid1-8 mutation (L45F) and an additional amino acid substitution (P99S) in the loop region. GID1P99S interacts with the rice DELLA protein SLENDER RICE1 (SLR1), even in the absence of GA. Substitution of the 99th Pro with other amino acids revealed that substitution with Ala (P99A) caused the highest level of GA-independent interaction. Physicochemical analysis using surface plasmon resonance revealed that GID1P99A has smaller Ka (association) and Kd (dissociation) values for GA4 than does wild-type GID1. This suggests that the GID1P99A lid is at least partially closed, resulting in both GA-independent and GA-hypersensitive interactions with SLR1. One of the three Arabidopsis thaliana GID1s, At GID1b, can also interact with DELLA proteins in the absence of GA, so we investigated whether GA-independent interaction of At GID1b depends on a mechanism similar to that of rice GID1P99A. Substitution of the loop region or a few amino acids of At GID1b with those of At GID1a diminished its GA-independent interaction with GAI while maintaining the GA-dependent interaction. Soybean (Glycine max) and Brassica napus also have GID1s similar to At GID1b, indicating that these unique GID1s occur in various dicots and may have important functions in these plants. PMID:21098733

A double-mutant collection targeting MAP kinase related genes in Arabidopsis for studying genetic interactions.

Science.gov (United States)

Su, Shih-Heng; Krysan, Patrick J

2016-12-01

Mitogen-activated protein kinase cascades are conserved in all eukaryotes. In Arabidopsis thaliana there are approximately 80 genes encoding MAP kinase kinase kinases (MAP3K), 10 genes encoding MAP kinase kinases (MAP2K), and 20 genes encoding MAP kinases (MAPK). Reverse genetic analysis has failed to reveal abnormal phenotypes for a majority of these genes. One strategy for uncovering gene function when single-mutant lines do not produce an informative phenotype is to perform a systematic genetic interaction screen whereby double-mutants are created from a large library of single-mutant lines. Here we describe a new collection of 275 double-mutant lines derived from a library of single-mutants targeting genes related to MAP kinase signaling. To facilitate this study, we developed a high-throughput double-mutant generating pipeline using a system for growing Arabidopsis seedlings in 96-well plates. A quantitative root growth assay was used to screen for evidence of genetic interactions in this double-mutant collection. Our screen revealed four genetic interactions, all of which caused synthetic enhancement of the root growth defects observed in a MAP kinase 4 (MPK4) single-mutant line. Seeds for this double-mutant collection are publicly available through the Arabidopsis Biological Resource Center. Scientists interested in diverse biological processes can now screen this double-mutant collection under a wide range of growth conditions in order to search for additional genetic interactions that may provide new insights into MAP kinase signaling. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Anisotropic interaction rules in circular motions of pigeon flocks: An empirical study based on sparse Bayesian learning

Science.gov (United States)

Chen, Duxin; Xu, Bowen; Zhu, Tao; Zhou, Tao; Zhang, Hai-Tao

2017-08-01

Coordination shall be deemed to the result of interindividual interaction among natural gregarious animal groups. However, revealing the underlying interaction rules and decision-making strategies governing highly coordinated motion in bird flocks is still a long-standing challenge. Based on analysis of high spatial-temporal resolution GPS data of three pigeon flocks, we extract the hidden interaction principle by using a newly emerging machine learning method, namely the sparse Bayesian learning. It is observed that the interaction probability has an inflection point at pairwise distance of 3-4 m closer than the average maximum interindividual distance, after which it decays strictly with rising pairwise metric distances. Significantly, the density of spatial neighbor distribution is strongly anisotropic, with an evident lack of interactions along individual velocity. Thus, it is found that in small-sized bird flocks, individuals reciprocally cooperate with a variational number of neighbors in metric space and tend to interact with closer time-varying neighbors, rather than interacting with a fixed number of topological ones. Finally, extensive numerical investigation is conducted to verify both the revealed interaction and decision-making principle during circular flights of pigeon flocks.

Studying Wind Energy/Bird Interactions: A Guidance Document

Energy Technology Data Exchange (ETDEWEB)

Anderson, R. [California Energy Commission (US); Morrison, M. [California State Univ., Sacramento, CA (US); Sinclair, K. [Dept. of Energy/National Renewable Energy Lab. (US); Strickland, D. [WEST, Inc. (US)

1999-12-01

This guidance document is a product of the Avian Subcommittee of the National Wind Coordinating Committee (NWCC). The NWCC was formed to better understand and promote responsible, credible, and comparable avian/wind energy interaction studies. Bird mortality is a concern and wind power is a potential clean and green source of electricity, making study of wind energy/bird interactions essential. This document provides an overview for regulators and stakeholders concerned with wind energy/bird interactions, as well as a more technical discussion of the basic concepts and tools for studying such interactions.

Annonalide and derivatives: Semisynthesis, cytotoxic activities and studies on interaction of annonalide with DNA.

Science.gov (United States)

Marques, Ricardo A; Gomes, Akenaton O C V; de Brito, Maria V; Dos Santos, Ana L P; da Silva, Gladyane S; de Lima, Leandro B; Nunes, Fátima M; de Mattos, Marcos C; de Oliveira, Fátima C E; do Ó Pessoa, Cláudia; de Moraes, Manoel O; de Fátima, Ângelo; Franco, Lucas L; Silva, Marina de M; Dantas, Maria Dayanne de A; Santos, Josué C C; Figueiredo, Isis M; da Silva-Júnior, Edeíldo F; de Aquino, Thiago M; de Araújo-Júnior, João X; de Oliveira, Maria C F; Leslie Gunatilaka, A A

2018-02-01

The cytotoxic activity of the pimarane diterpene annonalide (1) and nine of its semisynthetic derivatives (2-10) was investigated against the human tumor cell lines HL-60 (leukemia), PC-3 (prostate adenocarcinoma), HepG2 (hepatocellular carcinoma), SF-295 (glioblastoma) and HCT-116 (colon cancer), and normal mouse fibroblast (L929) cells. The preparation of 2-10 involved derivatization of the side chain of 1 at C-13. Except for 2, all derivatives are being reported for the first time. Most of the tested compounds presented IC 50 s below 4.0 μM, being considered potential antitumor agents. The structures of all new compounds were elucidated by spectroscopic analyses including 2D NMR and HRMS. Additionally, the interaction of annonalide (1) with ctDNA was evaluated using spectroscopic techniques, and the formation of a supramolecular complex with the macromolecule was confirmed. Competition assays with fluorescent probes (Hoechst and ethidium bromide) and theoretical studies confirmed that 1 interacts preferentially via DNA intercalation with stoichiometric ratio of 1:1 (1:ctDNA). The ΔG value was calculated as -28.24 kJ mol -1 , and indicated that the interaction process occurs spontaneously. Docking studies revealed that van der Walls is the most important interaction in 1-DNA and EB-DNA complexes, and that both ligands (1 and EB) interact with the same DNA residues (DA6, DA17 and DT19). Copyright © 2018. Published by Elsevier B.V.

Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

Directory of Open Access Journals (Sweden)

Zheng Sun

2014-01-01

Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Trey K Sato

2016-10-01

Full Text Available The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3, a component of MAP Kinase (MAPK signaling (HOG1, a regulator of Protein Kinase A (PKA signaling (IRA2, and a scaffolding protein for mitochondrial iron-sulfur (Fe-S cluster biogenesis (ISU1. Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Science.gov (United States)

Sato, Trey K; Tremaine, Mary; Parreiras, Lucas S; Hebert, Alexander S; Myers, Kevin S; Higbee, Alan J; Sardi, Maria; McIlwain, Sean J; Ong, Irene M; Breuer, Rebecca J; Avanasi Narasimhan, Ragothaman; McGee, Mick A; Dickinson, Quinn; La Reau, Alex; Xie, Dan; Tian, Mingyuan; Reed, Jennifer L; Zhang, Yaoping; Coon, Joshua J; Hittinger, Chris Todd; Gasch, Audrey P; Landick, Robert

2016-10-01

The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3), a component of MAP Kinase (MAPK) signaling (HOG1), a regulator of Protein Kinase A (PKA) signaling (IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis (ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.

The challenges of genome-wide interaction studies: lessons to learn from the analysis of HDL blood levels.

Directory of Open Access Journals (Sweden)

Elisabeth M van Leeuwen

Full Text Available Genome-wide association studies (GWAS have revealed 74 single nucleotide polymorphisms (SNPs associated with high-density lipoprotein cholesterol (HDL blood levels. This study is, to our knowledge, the first genome-wide interaction study (GWIS to identify SNP×SNP interactions associated with HDL levels. We performed a GWIS in the Rotterdam Study (RS cohort I (RS-I using the GLIDE tool which leverages the massively parallel computing power of Graphics Processing Units (GPUs to perform linear regression on all genome-wide pairs of SNPs. By performing a meta-analysis together with Rotterdam Study cohorts II and III (RS-II and RS-III, we were able to filter 181 interaction terms with a p-value<1 · 10-8 that replicated in the two independent cohorts. We were not able to replicate any of these interaction term in the AGES, ARIC, CHS, ERF, FHS and NFBC-66 cohorts (Ntotal = 30,011 when adjusting for multiple testing. Our GWIS resulted in the consistent finding of a possible interaction between rs774801 in ARMC8 (ENSG00000114098 and rs12442098 in SPATA8 (ENSG00000185594 being associated with HDL levels. However, p-values do not reach the preset Bonferroni correction of the p-values. Our study suggest that even for highly genetically determined traits such as HDL the sample sizes needed to detect SNP×SNP interactions are large and the 2-step filtering approaches do not yield a solution. Here we present our analysis plan and our reservations concerning GWIS.

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Directory of Open Access Journals (Sweden)

A Santos Jose C

2012-07-01

Full Text Available Abstract Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP, which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

Interactions between Casein kinase Iepsilon (CKIepsilon and two substrates from disparate signaling pathways reveal mechanisms for substrate-kinase specificity.

Directory of Open Access Journals (Sweden)

Caroline Lund Dahlberg

Full Text Available Members of the Casein Kinase I (CKI family of serine/threonine kinases regulate diverse biological pathways. The seven mammalian CKI isoforms contain a highly conserved kinase domain and divergent amino- and carboxy-termini. Although they share a preferred target recognition sequence and have overlapping expression patterns, individual isoforms often have specific substrates. In an effort to determine how substrates recognize differences between CKI isoforms, we have examined the interaction between CKIepsilon and two substrates from different signaling pathways.CKIepsilon, but not CKIalpha, binds to and phosphorylates two proteins: Period, a transcriptional regulator of the circadian rhythms pathway, and Disheveled, an activator of the planar cell polarity pathway. We use GST-pull-down assays data to show that two key residues in CKIalpha's kinase domain prevent Disheveled and Period from binding. We also show that the unique C-terminus of CKIepsilon does not determine Dishevelled's and Period's preference for CKIepsilon nor is it essential for binding, but instead plays an auxillary role in stabilizing the interactions of CKIepsilon with its substrates. We demonstrate that autophosphorylation of CKIepsilon's C-terminal tail prevents substrate binding, and use mass spectrometry and chemical crosslinking to reveal how a phosphorylation-dependent interaction between the C-terminal tail and the kinase domain prevents substrate phosphorylation and binding.The biochemical interactions between CKIepsilon and Disheveled, Period, and its own C-terminus lead to models that explain CKIepsilon's specificity and regulation.

Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression

DEFF Research Database (Denmark)

Hermansen, Grith Miriam Maigaard; Sazinas, Pavelas; Kofod, Ditte

2018-01-01

Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction...... between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction...... also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense nc...

Different foraging preferences of hummingbirds on artificial and natural flowers reveal mechanisms structuring plant-pollinator interactions.

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Maglianesi, María A; Böhning-Gaese, Katrin; Schleuning, Matthias

2015-05-01

In plant-pollinator networks, the floral morphology of food plants is an important determinant of the interaction niche of pollinators. Studies on foraging preferences of pollinators combining experimental and observational approaches may help to understand the mechanisms behind patterns of interactions and niche partitioning within pollinator communities. In this study, we tested whether morphological floral traits were associated with foraging preferences of hummingbirds for artificial and natural flower types in Costa Rica. We performed field experiments with artificial feeders, differing in length and curvature of flower types, to quantify the hummingbirds' interaction niche under unlimited nectar resources. To quantify the interaction niche under real-world conditions of limited nectar resources, we measured foraging preferences of hummingbirds for a total of 34 plant species. Artificial feeders were visited by Eupherusa nigriventris and Phaethornis guy in the pre-montane forest, and Lampornis calolaemus in the lower montane forest. Under experimental conditions, all three hummingbird species overlapped their interaction niches and showed a preference for the short artificial flower type over the long-straight and the long-curved flower types. Under natural conditions, the two co-occurring hummingbird species preferred to feed on plant species with floral traits corresponding to their bill morphology. The short-billed hummingbird E. nigriventris preferred to feed on short and straight flowers, whereas the long- and curved-billed P. guy preferred long and curved natural flowers. The medium-size billed species L. calolaemus preferred to feed on flowers of medium length and did not show preferences for plant species with specific corolla curvature. Our results show that floral morphological traits constrain access by short-billed hummingbird species to nectar resources. Morphological constraints, therefore, represent one important mechanism structuring trophic

Clinically relevant potential drug-drug interactions among outpatients: A nationwide database study.

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Jazbar, Janja; Locatelli, Igor; Horvat, Nejc; Kos, Mitja

2018-06-01

Adverse drug events due to drug-drug interactions (DDIs) represent a considerable public health burden, also in Slovenia. A better understanding of the most frequently occurring potential DDIs may enable safer pharmacotherapy and minimize drug-related problems. The aim of this study was to evaluate the prevalence and predictors of potential DDIs among outpatients in Slovenia. An analysis of potential DDIs was performed using health claims data on prescription drugs from a nationwide database. The Lexi-Interact Module was used as the reference source of interactions. The influence of patient-specific predictors on the risk of potential clinically relevant DDIs was evaluated using logistic regression model. The study population included 1,179,803 outpatients who received 15,811,979 prescriptions. The total number of potential DDI cases identified was 3,974,994, of which 15.6% were potentially clinically relevant. Altogether, 9.3% (N = 191,213) of the total population in Slovenia is exposed to clinically relevant potential DDIs, and the proportion is higher among women and the elderly. After adjustment for cofactors, higher number of medications and older age are associated with higher odds of clinically relevant potential DDIs. The burden of DDIs is highest with drug combinations that increase risk of bleeding, enhance CNS depression or anticholinergic effects or cause cardiovascular complications. The current study revealed that 1 in 10 individuals in the total Slovenian population is exposed to clinically relevant potential DDIs yearly. Taking into account the literature based conservative estimate that approximately 1% of potential DDIs result in negative health outcomes, roughly 1800 individuals in Slovenia experience an adverse health outcome each year as a result of clinically relevant potential interactions alone. Copyright © 2017 Elsevier Inc. All rights reserved.

A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway.

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Salašová, Alena; Yokota, Chika; Potěšil, David; Zdráhal, Zbyněk; Bryja, Vítězslav; Arenas, Ernest

2017-07-11

Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson's disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson's disease patients. Co-immunoprecipitation and tandem mass spectrometry was performed in a mouse substantia nigra cell line (SN4741) and human HEK293T cell line in order to identify novel LRRK2 binding partners. Inhibition of the WNT/β-catenin reporter, TOPFlash, was used as a read-out of WNT/PCP pathway activation. The capacity of LRRK2 to regulate WNT/PCP signaling in vivo was tested in Xenopus laevis' early development. Our proteomic analysis identified that LRRK2 interacts with proteins involved in WNT/PCP signaling such as the PDZ domain-containing protein GIPC1 and Integrin-linked kinase (ILK) in dopaminergic cells in vitro and in the mouse ventral midbrain in vivo. Moreover, co-immunoprecipitation analysis revealed that LRRK2 binds to two core components of the WNT/PCP signaling pathway, PRICKLE1 and CELSR1, as well as to FLOTILLIN-2 and CULLIN-3, which regulate WNT secretion and inhibit WNT/β-catenin signaling, respectively. We also found that PRICKLE1 and LRRK2 localize in signalosomes and act as dual regulators of WNT/PCP and β-catenin signaling. Accordingly, analysis of the function of LRRK2 in vivo, in X. laevis revelaed that LRKK2 not only inhibits WNT/β-catenin pathway, but induces a classical WNT/PCP phenotype in vivo. Our study shows for the first time that LRRK2 activates the WNT

Study on the molecular interaction of graphene quantum dots with human serum albumin: Combined spectroscopic and electrochemical approaches

Energy Technology Data Exchange (ETDEWEB)

Huang, Shan; Qiu, Hangna; Lu, Shuangyan; Zhu, Fawei [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); Xiao, Qi, E-mail: qi.xiao@whu.edu.cn [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); State Key Laboratory of Virology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China)

2015-03-21

Highlights: • The interactions between GQDs and HSA were systematically investigated. • GQDs could quench the intrinsic fluorescence of HSA via static mode. • The binding site of GQDs was mainly located in site I of HSA. • The potential toxicity of GQDs resulted in the structural damage of HSA. - Abstract: Graphene quantum dots (GQDs) have attracted great attention in biological and biomedical applications due to their super properties, but their potential toxicity investigations are rarely involved. Since few studies have addressed whether GQDs could bind and alter the structure and function of human serum albumin (HSA), the molecular interaction between GQDs and HSA was systematically characterized by the combination of multispectroscopic and electrochemical approaches. GQDs could quench the intrinsic fluorescence of HSA via static mode. The competitive binding fluorescence assay revealed that the binding site of GQDs was site I of HSA. Some thermodynamic parameters suggested that GQDs interacted with HSA mainly through van der Waals interactions and hydrogen bonding interactions, and protonation might also participate in the process. As further revealed by FT-IR spectroscopy and circular dichroism technique, GQDs could cause the global and local conformational change of HSA, which illustrated the potential toxicity of GQDs that resulted in the structural damage of HSA. Electrochemical techniques demonstrated the complex formation between GQDs and HSA. Our results offered insights into the binding mechanism of GQDs with HSA and provided important information for possible toxicity risk of GQDs to human health.

Environmental confounding in gene-environment interaction studies.

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Vanderweele, Tyler J; Ko, Yi-An; Mukherjee, Bhramar

2013-07-01

We show that, in the presence of uncontrolled environmental confounding, joint tests for the presence of a main genetic effect and gene-environment interaction will be biased if the genetic and environmental factors are correlated, even if there is no effect of either the genetic factor or the environmental factor on the disease. When environmental confounding is ignored, such tests will in fact reject the joint null of no genetic effect with a probability that tends to 1 as the sample size increases. This problem with the joint test vanishes under gene-environment independence, but it still persists if estimating the gene-environment interaction parameter itself is of interest. Uncontrolled environmental confounding will bias estimates of gene-environment interaction parameters even under gene-environment independence, but it will not do so if the unmeasured confounding variable itself does not interact with the genetic factor. Under gene-environment independence, if the interaction parameter without controlling for the environmental confounder is nonzero, then there is gene-environment interaction either between the genetic factor and the environmental factor of interest or between the genetic factor and the unmeasured environmental confounder. We evaluate several recently proposed joint tests in a simulation study and discuss the implications of these results for the conduct of gene-environment interaction studies.

Exploration of molecular interactions in cholesterol superlattices: effect of multibody interactions.

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Huang, Juyang

2002-08-01

Experimental evidences have indicated that cholesterol may adapt highly regular lateral distributions (i.e., superlattices) in a phospholipid bilayer. We investigated the formations of superlattices at cholesterol mole fraction of 0.154, 0.25, 0.40, and 0.5 using Monte Carlo simulation. We found that in general, conventional pairwise-additive interactions cannot produce superlattices. Instead, a multibody (nonpairwise) interaction is required. Cholesterol superlattice formation reveals that although the overall interaction between cholesterol and phospholipids is favorable, it contains two large opposing components: an interaction favoring cholesterol-phospholipid mixing and an unfavorable acyl chain multibody interaction that increases nonlinearly with the number of cholesterol contacts. The magnitudes of interactions are in the order of kT. The physical origins of these interactions can be explained by our umbrella model. They most likely come from the requirement for polar phospholipid headgroups to cover the nonpolar cholesterol to avoid the exposure of cholesterol to water and from the sharp decreasing of acyl chain conformation entropy due to cholesterol contact. This study together with our previous work demonstrate that the driving force of cholesterol-phospholipid mixing is a hydrophobic interaction, and multibody interactions dominate others over a wide range of cholesterol concentration.

A fluvoxamine-caffeine interaction study

DEFF Research Database (Denmark)

Jeppesen, U; Loft, S; Poulsen, H E

1996-01-01

The selective serotonin reuptake inhibitor fluvoxamine is a very potent inhibitor of the liver enzyme CYP1A2, which is the major P450 catalysing the biotransformation of caffeine. Thus, a pharmacokinetic study was undertaken with the purpose of documenting a drug-drug interaction between fluvoxam......The selective serotonin reuptake inhibitor fluvoxamine is a very potent inhibitor of the liver enzyme CYP1A2, which is the major P450 catalysing the biotransformation of caffeine. Thus, a pharmacokinetic study was undertaken with the purpose of documenting a drug-drug interaction between...... fluvoxamine and caffeine. The study was carried out as a randomized, in vivo, cross-over study including eight healthy volunteers. In Period A of the study, each subject took 200 mg caffeine orally, and in Period B, the subjects took fluvoxamine 50 mg per day for 4 days and 100 mg per day for 8 days. On day 8...... fluvoxamine treatment may lead to caffeine intoxication. Finally, our study provides additional evidence that fluvoxamine can be used to probe CYP1A2 in drug metabolism....

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

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Gebala, Magdalena; Giambasu, George M.; Lipfert, Jan; Bisaria, Namita; Bonilla, Steve; Li, Guangchao; York, Darrin M.; Herschlag, Daniel

2016-01-01

The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that “count” the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation–anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation–anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4–P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new

Study of the interaction of lactoferricin B with phospholipid monolayers and bilayers.

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Arseneault, Marjolaine; Bédard, Sarah; Boulet-Audet, Maxime; Pézolet, Michel

2010-03-02

Bovine lactoferricin (LfcinB) is an antimicrobial peptide obtained from the pepsin cleavage of lactoferrin. The activity of LfcinB has been extensively studied on diverse pathogens, but its mechanism of action still has to be elucidated. Because of its nonspecificity, its mode of action is assumed to be related to interactions with membranes. In this study, the interaction of LfcinB with a negatively charged monolayer of dipalmitoylphosphatidylglycerol has been investigated as a function of the surface pressure of the lipid film using in situ Brewster angle and polarization modulation infrared reflection absorption spectroscopy and on transferred monolayers by atomic force microscopy and polarized attenuated total reflection infrared spectroscopy. The data show clearly that LfcinB forms stable films at the air-water interface. They also reveal that the interaction of LfcinB with the lipid monolayer is modulated by the surface pressure. At low surface pressure, LfcinB inserts within the lipid film with its long molecular axis oriented mainly parallel to the acyl chains, while at high surface pressure, LfcinB is adsorbed under the lipid film, the hairpin being preferentially aligned parallel to the plane of the interface. The threshold for which the behavior changes is 20 mN/m. At this critical surface pressure, LfcinB interacts with the monolayer to form discoidal lipid-peptide assemblies. This structure may actually represent the mechanism of action of this peptide. The results obtained on monolayers are correlated by fluorescent probe release measurements of dye-containing vesicles made of lipids in different phases and support the important role of the lipid fluidity and packing on the activity of LfcinB.

Study of the interactions between fluoroquinolones and human serum albumin by affinity capillary electrophoresis and fluorescence method

International Nuclear Information System (INIS)

Zhang Liwei; Wang Kun; Zhang Xinxiang

2007-01-01

The interactions between fluoroquinolones and human serum albumin (HSA) were investigated by affinity capillary electrophoresis (ACE) and fluorescence quenching technique. Based on the efficient separation of several fluoroquinolones using a simple phosphate buffer, the binding constants of fluoroquinolones with HSA were determined simultaneously during one set of electrophoresis by ACE method. The thermodynamic parameters were obtained from data at different temperatures, and the negative ΔH and ΔS values showed that both hydrogen bonds and van der Waals interaction played major roles in the binding of fluoroquinolones to HSA. The interactions were also studied by fluorescence quenching technique. The results of fluorescence titration revealed that fluoroquinolones had the strong ability to quenching the intrinsic fluorescence of HSA through the static quenching procedure. The binding site number n, apparent binding constant K b and the Stern-Volmer quenching constant K sv were determined. The thermodynamic parameters were also studied by fluorescence method, and the results were consonant with that of ACE

Social affiliation in same-class and cross-class interactions.

Science.gov (United States)

Côté, Stéphane; Kraus, Michael W; Carpenter, Nichelle C; Piff, Paul K; Beermann, Ursula; Keltner, Dacher

2017-02-01

Historically high levels of economic inequality likely have important consequences for relationships between people of the same and different social class backgrounds. Here, we test the prediction that social affiliation among same-class partners is stronger at the extremes of the class spectrum, given that these groups are highly distinctive and most separated from others by institutional and economic forces. An internal meta-analysis of 4 studies (N = 723) provided support for this hypothesis. Participant and partner social class were interactively, rather than additively, associated with social affiliation, indexed by affiliative behaviors and emotions during structured laboratory interactions and in daily life. Further, response surface analyses revealed that paired upper or lower class partners generally affiliated more than average-class pairs. Analyses with separate class indices suggested that these patterns are driven more by parental income and subjective social class than by parental education. The findings illuminate the dynamics of same- and cross-class interactions, revealing that not all same-class interactions feature the same degree of affiliation. They also reveal the importance of studying social class from an intergroup perspective. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Interactions among the early Escherichia coli divisome proteins revealed by bimolecular fluorescence complementation.

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Pazos, Manuel; Natale, Paolo; Margolin, William; Vicente, Miguel

2013-12-01

We used bimolecular fluorescence complementation (BiFC) assays to detect protein-protein interactions of all possible pairs of the essential Escherichia coli proto-ring components, FtsZ, FtsA and ZipA, as well as the non-essential FtsZ-associated proteins ZapA and ZapB. We found an unexpected interaction between ZipA and ZapB at potential cell division sites, and when co-overproduced, they induced long narrow constrictions at division sites that were dependent on FtsZ. These assays also uncovered an interaction between ZipA and ZapA that was mediated by FtsZ. BiFC with ZapA and ZapB showed that in addition to their expected interaction at midcell, they also interact at the cell poles. BiFC detected interaction between FtsZ and ZapB at midcell and close to the poles. Results from the remaining pairwise combinations confirmed known interactions between FtsZ and ZipA, and ZapB with itself. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative modeling and docking studies of p16ink4/Cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1

Directory of Open Access Journals (Sweden)

e Zahra Syeda Naqsh

2013-01-01

Full Text Available Abstract Background Lung cancer is the major cause of mortality worldwide. Major signalling pathways that could play significant role in lung cancer therapy include (1 Growth promoting pathways (Epidermal Growth Factor Receptor/Ras/ PhosphatidylInositol 3-Kinase (2 Growth inhibitory pathways (p53/Rb/P14ARF, STK11 (3 Apoptotic pathways (Bcl-2/Bax/Fas/FasL. Insilico strategy was implemented to solve the mystery behind selected lung cancer pathway by applying comparative modeling and molecular docking studies. Results YASARA [v 12.4.1] was utilized to predict structural models of P16-INK4 and RB1 genes using template 4ELJ-A and 1MX6-B respectively. WHAT CHECK evaluation tool demonstrated overall quality of predicted P16-INK4 and RB1 with Z-score of −0.132 and −0.007 respectively which showed a strong indication of reliable structure prediction. Protein-protein interactions were explored by utilizing STRING server, illustrated that CDK4 and E2F1 showed strong interaction with P16-INK4 and RB1 based on confidence score of 0.999 and 0.999 respectively. In order to facilitate a comprehensive understanding of the complex interactions between candidate genes with their functional interactors, GRAMM-X server was used. Protein-protein docking investigation of P16-INK4 revealed four ionic bonds illustrating Arg47, Arg80,Cys72 and Met1 residues as actively participating in interactions with CDK4 while docking results of RB1 showed four hydrogen bonds involving Glu864, Ser567, Asp36 and Arg861 residues which interact strongly with its respective functional interactor E2F1. Conclusion This research may provide a basis for understanding biological insights of P16-INK4 and RB1 proteins which will be helpful in future to design a suitable drug to inhibit the disease pathogenesis as we have determined the interacting amino acids which can be targeted in order to design a ligand in-vitro to propose a drug for clinical trials. Protein -protein docking of

Study of the magnetic interaction in nanocrystalline Pr-Fe-Co-Nb-B permanent magnets

Science.gov (United States)

Dospial, M.; Plusa, D.; Ślusarek, B.

2012-03-01

The magnetic properties of an isotropic, epoxy resin bonded magnets made from Pr-Fe-Co-Nb-B powder were investigated. The magnetization reversal process and magnetic parameters were examined by measurements of the initial magnetization curve, major and minor hysteresis loops and sets of recoil curves. From the initial magnetization curve and the field dependencies of the reversible and irreversible magnetization components derived from the recoil loops it was found that the magnetization reversal process is the combination of the nucleation of reversed domains and pinning of domain walls at the grain boundaries and the reversible rotation of magnetization vector in single domain grains. The interactions between grains were studied by means of δM plots. The nonlinear behavior of δM curve approve that the short range intergrain exchange coupling interactions are dominant in a field up to the sample coercivity. The interaction domains and fine magnetic structure were revealed as the evidence of exchange coupling between soft α-Fe and hard magnetic Nd2Fe14B grains.

Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis

DEFF Research Database (Denmark)

Collins, Ryan L; Hu, Ting; Wejse, Christian

2013-01-01

for this problem. The goal of the present study was to apply MDR to mining high-order epistatic interactions in a population-based genetic study of tuberculosis (TB). Results The study used a previously published data set consisting of 19 candidate single-nucleotide polymorphisms (SNPs) in 321 pulmonary TB cases...

Quantitative studies of antimicrobial peptide-lipid membrane interactions

DEFF Research Database (Denmark)

Kristensen, Kasper

antimicrobial peptides interact with phospholipid membranes. Motivated by that fact, the scope of this thesis is to study these antimicrobial peptide-lipid membrane interactions. In particular, we attempt to study these interactions with a quantitative approach. For that purpose, we consider the three...... a significant problem for quantitative studies of antimicrobial peptide-lipid membrane interactions; namely that antimicrobial peptides adsorb to surfaces of glass and plastic. Specifically, we demonstrate that under standard experimental conditions, this effect is significant for mastoparan X, melittin...... lead to inaccurate conclusions, or even completely wrong conclusions, when interpreting the FCS data. We show that, if all of the pitfalls are avoided, then FCS is a technique with a large potential for quantitative studies of antimicrobial peptide-induced leakage of fluorescent markers from large...

Interaction of Chelerythrine with Keyhole Limpet Hemocyanin: a Fluorescence Spectroscopy and Molecular Docking Study

Science.gov (United States)

Zhong, M.; Long, R. Q.; Wang, Y. H.; Chen, C. L.

2018-05-01

The quenching mechanism between chelerythrine (CHE) and keyhole limpet hemocyanin (KLH) was investigated using fluorescence spectroscopy and molecular docking. The experiments were conducted at three different temperatures (293, 298, and 303 K). The results revealed that the intrinsic fluorescence of KLH was strongly quenched by CHE through a static quenching mechanism. The thermodynamic parameters (ΔG, ΔH, and ΔS) of the interaction were calculated, indicating that the interaction between CHE and KLH was spontaneous and that van der Waals forces and hydrogen bond formation played major roles in the binding process. The intrinsic fluorescence of the tyrosine and tryptophan residues in KLH was studied by synchronous fluorescence, which suggested that CHE changed the conformation of KLH. Finally, molecular docking was used to obtain detailed information on the binding sites and binding affinities between CHE and KLH.

Interactions of coal gangue and pine sawdust during combustion of their blends studied using differential thermogravimetric analysis.

Science.gov (United States)

Zhang, Yuanyuan; Zhang, Zhezi; Zhu, Mingming; Cheng, Fangqin; Zhang, Dongke

2016-08-01

The interactions between coal gangue and pine sawdust during the combustion process were studied using thermogravimetric analysis. The effect of the blending ratio, oxygen concentration and heating rate on the weight loss (TG) and differential thermogravimetric (TGA) profiles was examined. The TG and DTG curves of the blends were not additives of those of the individual materials, suggesting that interactions between coal gangue and pine sawdust had occurred during the combustion, especially in the temperature range of 400-600°C. Kinetic analysis confirmed that the combustion of coal gangue, pine sawdust and their blends was chemical reaction controlled. Further analysis revealed that the interactions between coal gangue and pine sawdust were primarily due to thermal effects rather than structural changes, with the thermal inertia of coal gangue dominating over the behaviour of the blends. The interactions decreased with decreasing the coal gangue ratio in the blend, oxygen concentration and heating rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inhibition of thrombin by functionalized C60 nanoparticles revealed via in vitro assays and in silico studies.

Science.gov (United States)

Liu, Yanyan; Fu, Jianjie; Pan, Wenxiao; Xue, Qiao; Liu, Xian; Zhang, Aiqian

2018-01-01

The studies on the human toxicity of nanoparticles (NPs) are far behind the rapid development of engineered functionalized NPs. Fullerene has been widely used as drug carrier skeleton due to its reported low risk. However, different from other kinds of NPs, fullerene-based NPs (C 60 NPs) have been found to have an anticoagulation effect, although the potential target is still unknown. In the study, both experimental and computational methods were adopted to gain mechanistic insight into the modulation of thrombin activity by nine kinds of C 60 NPs with diverse surface chemistry properties. In vitro enzyme activity assays showed that all tested surface-modified C 60 NPs exhibited thrombin inhibition ability. Kinetic studies coupled with competitive testing using 3 known inhibitors indicated that six of the C 60 NPs, of greater hydrophobicity and hydrogen bond (HB) donor acidity or acceptor basicity, acted as competitive inhibitors of thrombin by directly interacting with the active site of thrombin. A simple quantitative nanostructure-activity relationship model relating the surface substituent properties to the inhibition potential was then established for the six competitive inhibitors. Molecular docking analysis revealed that the intermolecular HB interactions were important for the specific binding of C 60 NPs to the active site canyon, while the additional stability provided by the surface groups through van der Waals interaction also play a key role in the thrombin binding affinity of the NPs. Our results suggest that thrombin is a possible target of the surface-functionalized C 60 NPs relevant to their anticoagulation effect. Copyright © 2017. Published by Elsevier B.V.

Bronchodilation and smoking interaction in COPD: a cohort pilot study to assess cardiovascular risk.

Science.gov (United States)

van Dijk, Wouter D; Lenders, Jacques W M; Holtman, Joran; Grootens, Joke; Akkermans, Reinier; Heijdra, Yvonne; van Weel, Chris; Schermer, Tjard R J

2012-01-01

Smoking and bronchodilator treatment are both extensively studied as key elements in patients with chronic obstructive pulmonary disease. However, little is known about whether or not these elements interact in terms of developing cardiovascular diseases in patients with COPD. To explore to what extent the risk of developing ischemic cardiovascular disease in COPD patients is mediated by smoking status, use of bronchodilators and--specifically--their interaction. We performed an observational pilot study on a relatively healthy Dutch COPD cohort from a primary care diagnostic center database with full information on spirometry tests, smoking status, bronchodilator use and other prescribed medication. We defined first ischemic cardiovascular events as primary outcome, measured by first prescription of antiplatelet drugs and/or nitrates. Unadjusted analyses by Kaplan-Meier were followed by adjusted Cox' proportional hazards. 845 COPD patients, totaling 2,169 observation years, were included in the analyses. We observed an increased risk for nonfatal ischemic cardiovascular events by smoking (adjusted HR=3.58, p=0.001) and a protective effect of bronchodilators (adjusted HR=0.43, p=0.01). Although the protective effect of bronchodilators appears to be substantially minimized in patients that persist in smoking, we could not statistically confirm a hazardous interaction between bronchodilators and smoking (HR 2.50, p=0.21). Our study reveals bronchodilators may protect from ischemic cardiovascular events in a relatively 'healthy' COPD population. We did not confirm a hazardous interaction between bronchodilators and smoking, although we observed current smokers benefit substantially less from the protective effect of bronchodilators. Copyright © 2011 S. Karger AG, Basel.

Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion.

Science.gov (United States)

Rosenthal, Sara Brin; Twomey, Colin R; Hartnett, Andrew T; Wu, Hai Shan; Couzin, Iain D

2015-04-14

Coordination among social animals requires rapid and efficient transfer of information among individuals, which may depend crucially on the underlying structure of the communication network. Establishing the decision-making circuits and networks that give rise to individual behavior has been a central goal of neuroscience. However, the analogous problem of determining the structure of the communication network among organisms that gives rise to coordinated collective behavior, such as is exhibited by schooling fish and flocking birds, has remained almost entirely neglected. Here, we study collective evasion maneuvers, manifested through rapid waves, or cascades, of behavioral change (a ubiquitous behavior among taxa) in schooling fish (Notemigonus crysoleucas). We automatically track the positions and body postures, calculate visual fields of all individuals in schools of ∼150 fish, and determine the functional mapping between socially generated sensory input and motor response during collective evasion. We find that individuals use simple, robust measures to assess behavioral changes in neighbors, and that the resulting networks by which behavior propagates throughout groups are complex, being weighted, directed, and heterogeneous. By studying these interaction networks, we reveal the (complex, fractional) nature of social contagion and establish that individuals with relatively few, but strongly connected, neighbors are both most socially influential and most susceptible to social influence. Furthermore, we demonstrate that we can predict complex cascades of behavioral change at their moment of initiation, before they actually occur. Consequently, despite the intrinsic stochasticity of individual behavior, establishing the hidden communication networks in large self-organized groups facilitates a quantitative understanding of behavioral contagion.

Ghost-in-the-Machine reveals human social signals for human-robot interaction.

Science.gov (United States)

Loth, Sebastian; Jettka, Katharina; Giuliani, Manuel; de Ruiter, Jan P

2015-01-01

We used a new method called "Ghost-in-the-Machine" (GiM) to investigate social interactions with a robotic bartender taking orders for drinks and serving them. Using the GiM paradigm allowed us to identify how human participants recognize the intentions of customers on the basis of the output of the robotic recognizers. Specifically, we measured which recognizer modalities (e.g., speech, the distance to the bar) were relevant at different stages of the interaction. This provided insights into human social behavior necessary for the development of socially competent robots. When initiating the drink-order interaction, the most important recognizers were those based on computer vision. When drink orders were being placed, however, the most important information source was the speech recognition. Interestingly, the participants used only a subset of the available information, focussing only on a few relevant recognizers while ignoring others. This reduced the risk of acting on erroneous sensor data and enabled them to complete service interactions more swiftly than a robot using all available sensor data. We also investigated socially appropriate response strategies. In their responses, the participants preferred to use the same modality as the customer's requests, e.g., they tended to respond verbally to verbal requests. Also, they added redundancy to their responses, for instance by using echo questions. We argue that incorporating the social strategies discovered with the GiM paradigm in multimodal grammars of human-robot interactions improves the robustness and the ease-of-use of these interactions, and therefore provides a smoother user experience.

Ghost-in-the-Machine reveals human social signals for human–robot interaction

Science.gov (United States)

Loth, Sebastian; Jettka, Katharina; Giuliani, Manuel; de Ruiter, Jan P.

2015-01-01

We used a new method called “Ghost-in-the-Machine” (GiM) to investigate social interactions with a robotic bartender taking orders for drinks and serving them. Using the GiM paradigm allowed us to identify how human participants recognize the intentions of customers on the basis of the output of the robotic recognizers. Specifically, we measured which recognizer modalities (e.g., speech, the distance to the bar) were relevant at different stages of the interaction. This provided insights into human social behavior necessary for the development of socially competent robots. When initiating the drink-order interaction, the most important recognizers were those based on computer vision. When drink orders were being placed, however, the most important information source was the speech recognition. Interestingly, the participants used only a subset of the available information, focussing only on a few relevant recognizers while ignoring others. This reduced the risk of acting on erroneous sensor data and enabled them to complete service interactions more swiftly than a robot using all available sensor data. We also investigated socially appropriate response strategies. In their responses, the participants preferred to use the same modality as the customer’s requests, e.g., they tended to respond verbally to verbal requests. Also, they added redundancy to their responses, for instance by using echo questions. We argue that incorporating the social strategies discovered with the GiM paradigm in multimodal grammars of human–robot interactions improves the robustness and the ease-of-use of these interactions, and therefore provides a smoother user experience. PMID:26582998

cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici

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Huang Lili

2009-06-01

Full Text Available Abstract Background Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-AFLP. Results Of the total 54,912 transcript derived fragments (TDFs obtained using cDNA-AFLP with 64 primer pairs, 2,306 (4.2% displayed altered expression patterns after inoculation, of which 966 showed up-regulated and 1,340 down-regulated. 186 TDFs produced reliable sequences after sequencing of 208 TDFs selected, of which 74 (40% had known functions through BLAST searching the GenBank database. Majority of the latter group had predicted gene products involved in energy (13%, signal transduction (5.4%, disease/defence (5.9% and metabolism (5% of the sequenced TDFs. BLAST searching of the wheat stem rust fungus genome database identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were validated of the pathogen origin using PCR-based assays followed by sequencing confirmation. Of the 186 reliable TDFs, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR analyses. Results confirmed the altered expression patterns of 28 (96.5% genes revealed by the cDNA-AFLP technique. Conclusion The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the

Interaction of the Saccharomyces cerevisiae α-factor with phospholipid vesicles as revealed by proton and phosphorus NMR

International Nuclear Information System (INIS)

Jelicks, L.A.; Broido, M.S.; Becker, J.M.; Naider, F.R.

1989-01-01

Proton and phosphorus-31 nuclear magnetic resonance ( 1 H and 31 P NMR) studies of the interaction between a tridecapeptide pheromone, the α-factor of Saccharomyces cerevisiae, and sonicated lipid vesicles are reported. 31 P NMR studies demonstrate that there is interaction of the peptide with the phosphorus headgroups, and quasielastic light scattering (QLS) studies indicate that lipid vesicles increase in size upon addition of peptide. Previous solution (aqueous and DMSO) studies from this laboratory indicate that α-factor is highly flexible with only one long-lived identifiable structural feature, a type II β-turn spanning the central portion of the peptide. Two-dimensional (2D) 1 H nuclear Overhauser effect spectroscopy (NOESY) studies demonstrate a marked ordering of the peptide upon interaction with lipid, suggesting a compact N-terminus, in addition to a stabilized β-turn. In contrast to these results in both solution and lipid environment, Wakamatsu et al. proposed a lipid environment conformation, on the basis of one-dimensional transferred NOE studies in D 2 O, which does not include the β-turn

Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.

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Turner, Leslie M; Harr, Bettina

2014-12-09

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.

Topological surface states interacting with bulk excitations in the Kondo insulator SmB6 revealed via planar tunneling spectroscopy.

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Park, Wan Kyu; Sun, Lunan; Noddings, Alexander; Kim, Dae-Jeong; Fisk, Zachary; Greene, Laura H

2016-06-14

Samarium hexaboride (SmB6), a well-known Kondo insulator in which the insulating bulk arises from strong electron correlations, has recently attracted great attention owing to increasing evidence for its topological nature, thereby harboring protected surface states. However, corroborative spectroscopic evidence is still lacking, unlike in the weakly correlated counterparts, including Bi2Se3 Here, we report results from planar tunneling that unveil the detailed spectroscopic properties of SmB6 The tunneling conductance obtained on the (001) and (011) single crystal surfaces reveals linear density of states as expected for two and one Dirac cone(s), respectively. Quite remarkably, it is found that these topological states are not protected completely within the bulk hybridization gap. A phenomenological model of the tunneling process invoking interaction of the surface states with bulk excitations (spin excitons), as predicted by a recent theory, provides a consistent explanation for all of the observed features. Our spectroscopic study supports and explains the proposed picture of the incompletely protected surface states in this topological Kondo insulator SmB6.

Brain transcriptome-wide screen for HIV-1 Nef protein interaction partners reveals various membrane-associated proteins.

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Ellen C Kammula

Full Text Available HIV-1 Nef protein contributes essentially to the pathology of AIDS by a variety of protein-protein-interactions within the host cell. The versatile functionality of Nef is partially attributed to different conformational states and posttranslational modifications, such as myristoylation. Up to now, many interaction partners of Nef have been identified using classical yeast two-hybrid screens. Such screens rely on transcriptional activation of reporter genes in the nucleus to detect interactions. Thus, the identification of Nef interaction partners that are integral membrane proteins, membrane-associated proteins or other proteins that do not translocate into the nucleus is hampered. In the present study, a split-ubiquitin based yeast two-hybrid screen was used to identify novel membrane-localized interaction partners of Nef. More than 80% of the hereby identified interaction partners of Nef are transmembrane proteins. The identified hits are GPM6B, GPM6A, BAP31, TSPAN7, CYB5B, CD320/TCblR, VSIG4, PMEPA1, OCIAD1, ITGB1, CHN1, PH4, CLDN10, HSPA9, APR-3, PEBP1 and B3GNT, which are involved in diverse cellular processes like signaling, apoptosis, neurogenesis, cell adhesion and protein trafficking or quality control. For a subfraction of the hereby identified proteins we present data supporting their direct interaction with HIV-1 Nef. We discuss the results with respect to many phenotypes observed in HIV infected cells and patients. The identified Nef interaction partners may help to further elucidate the molecular basis of HIV-related diseases.

Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

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Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

2017-01-01

Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks

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Toni Vallès-Català

2016-03-01

Full Text Available In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs, a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.

Using interactive graphical and technological strategies for EFL reading comprehension: A case study involving engineering students

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Julia Valeska Barraza

2014-09-01

Full Text Available This qualitative study engaged a group of engineering students in the use of interactive graphical and technological strategies called IGOs (interactive, graphic organisers software in order to improve their level of EFL reading comprehension. The learners were asked to use three different types of IGOs, causes and effects, a sequence of events and pros and cons. Data was gathered through an opinion’s survey with the intention of collecting and evaluating the students’ perceptions on the use of the IGOs software. Findings revealed that most of the learners answered positively. Students also expressed they wanted more opportunities to use this software; because they not only could improve their scores but also, they enjoyed the experience they had using the new strategies software.

A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

Science.gov (United States)

Li, Yating; Wei, Haoran; Liu, Rutao

2014-03-01

Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.

Histone modifications influence mediator interactions with chromatin

Science.gov (United States)

Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.

2011-01-01

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760

Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

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Harvey, Ben P; Gwynn-Jones, Dylan; Moore, Pippa J

2013-01-01

Ocean acidification and warming are considered two of the greatest threats to marine biodiversity, yet the combined effect of these stressors on marine organisms remains largely unclear. Using a meta-analytical approach, we assessed the biological responses of marine organisms to the effects of ocean acidification and warming in isolation and combination. As expected biological responses varied across taxonomic groups, life-history stages, and trophic levels, but importantly, combining stressors generally exhibited a stronger biological (either positive or negative) effect. Using a subset of orthogonal studies, we show that four of five of the biological responses measured (calcification, photosynthesis, reproduction, and survival, but not growth) interacted synergistically when warming and acidification were combined. The observed synergisms between interacting stressors suggest that care must be made in making inferences from single-stressor studies. Our findings clearly have implications for the development of adaptive management strategies particularly given that the frequency of stressors interacting in marine systems will be likely to intensify in the future. There is now an urgent need to move toward more robust, holistic, and ecologically realistic climate change experiments that incorporate interactions. Without them accurate predictions about the likely deleterious impacts to marine biodiversity and ecosystem functioning over the next century will not be possible. PMID:23610641

A combined spectroscopic and molecular docking study on site selective binding interaction of Toluidine blue O with Human and Bovine serum albumins

Energy Technology Data Exchange (ETDEWEB)

Selva Sharma, Arumugam [Department of Chemistry, Bharathiar University, Coimbatore 641046 (India); Anandakumar, Shanmugam [Department of Bioinformatics, Bharathiar University, Coimbatore 641046 (India); Ilanchelian, Malaichamy, E-mail: chelian73@yahoo.com [Department of Chemistry, Bharathiar University, Coimbatore 641046 (India)

2014-07-01

In the present investigation the interaction of a biologically active photodynamic therapeutic agent Toluidine blue O (TBO) with Serum albumins viz Human serum albumin (HSA) and Bovine serum albumin (BSA) was studied using absorption, emission, circular dichroism spectroscopy and molecular docking experiments. The emission titration experiments between HSA/BSA and TBO revealed the existence of strong interactions between TBO and the proteins. The site competitive experiment of HSA and BSA showed that the primary binding site of TBO is located in site I of HSA/BSA involving hydrophobic, hydrogen bonding and electrostatic interaction. To ascertain the results of site competitive experiments, molecular docking was utilized to characterize the binding models of TBO–HSA/BSA complexes. From the molecular docking studies, free energy calculations were undertaken to examine the energy contributions and the role of various amino acid residues of HSA/BSA in TBO binding. The existence of Forster Resonance Energy Transfer (FRET) between the ligand and the protein was utilized to calculate the donor–acceptor distance of TBO and protein. The TBO induced conformational changes of HSA/BSA was established using synchronous emission, three dimensional emission and circular dichroism studies. - Highlights: • Site selective binding interaction of TBO with HSA and BSA were investigated. • TBO quenches the intrinsic fluorescence of HSA/BSA by static quenching process. • Computational studies of TBO with HSA/BSA substantiate the experimental findings. • 3D and CD spectral studies of TBO–HSA/BSA revealed structural changes in protein. • The distance (r) between TBO and HSA/BSA were estimated from FRET theory.

A Study on the Interaction Mechanism between Thermal Radiation and Materials

Institute of Scientific and Technical Information of China (English)

Dehong XIA; Tao YU; Chuangu WU; Qingqing CHANG; Honglei JIAO

2005-01-01

From the viewpoint of field synergy principle and dipole radiation theory, the interaction between the incident thermal radiation wave and materials is analyzed to reveal the mechanism of selective absorption of incident thermal radiation. It is shown that the frequency of the incident thermal radiation and the damping constant of damping oscillators in materials are of vital importance for the thermal radiation properties (reflectivity, absorptivity, transmissivity, etc.) of materials.

From Child-Robot Interaction to Child-Robot-Therapist Interaction: A Case Study in Autism

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I. Giannopulu

2012-01-01

Full Text Available Troubles in social communication as well as deficits in the cognitive treatment of emotions are supposed to be a fundamental part of autism. We present a case study based on multimodal interaction between a mobile robot and a child with autism in spontaneous, free game play. This case study tells us that the robot mediates the interaction between the autistic child and therapist once the robot-child interaction has been established. In addition, the child uses the robot as a mediator to express positive emotion playing with the therapist. It is thought that the three-pronged interaction i.e., child-robot-therapist could better facilitate the transfer of social and emotional abilities to real life settings. Robot therapy has a high potential to improve the condition of brain activity in autistic children.

Alecto 2 - interaction studies

International Nuclear Information System (INIS)

Brunet, J.P.; Clouet d'Orval, Ch.; Mougniot, J.C.; Penet, F.

1965-01-01

Weak interactions were experimentally studies with the tank of the critical assembly Alecto II and one, two or three bottles containing solutions of various concentrations. In particular, was studied the validity of certain classical assumptions, shielding effects, screening and semi-reflexion effects, importance of thermal coupling. The method of the 'k eff , solid angle' is shown to apply to such a system. The determination by divergence and pulsed neutron technique of the reactivity related to a millimeter of solution level affords the obtention of critical heights in terms of reactivity. (authors) [fr

NMR Studies of Protein Hydration and Protein-Ligand Interactions

Science.gov (United States)

Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

A map of directional genetic interactions in a metazoan cell.

Science.gov (United States)

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-03-06

Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

Social interaction in synthetic and natural microbial communities.

Science.gov (United States)

Xavier, Joao B

2011-04-12

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.

Simultaneous recordings from the primary visual cortex and lateral geniculate nucleus reveal rhythmic interactions and a cortical source for γ-band oscillations.

Science.gov (United States)

Bastos, Andre M; Briggs, Farran; Alitto, Henry J; Mangun, George R; Usrey, W Martin

2014-05-28

Oscillatory synchronization of neuronal activity has been proposed as a mechanism to modulate effective connectivity between interacting neuronal populations. In the visual system, oscillations in the gamma-frequency range (30-100 Hz) are thought to subserve corticocortical communication. To test whether a similar mechanism might influence subcortical-cortical communication, we recorded local field potential activity from retinotopically aligned regions in the lateral geniculate nucleus (LGN) and primary visual cortex (V1) of alert macaque monkeys viewing stimuli known to produce strong cortical gamma-band oscillations. As predicted, we found robust gamma-band power in V1. In contrast, visual stimulation did not evoke gamma-band activity in the LGN. Interestingly, an analysis of oscillatory phase synchronization of LGN and V1 activity identified synchronization in the alpha (8-14 Hz) and beta (15-30 Hz) frequency bands. Further analysis of directed connectivity revealed that alpha-band interactions mediated corticogeniculate feedback processing, whereas beta-band interactions mediated geniculocortical feedforward processing. These results demonstrate that although the LGN and V1 display functional interactions in the lower frequency bands, gamma-band activity in the alert monkey is largely an emergent property of cortex. Copyright © 2014 the authors 0270-6474/14/347639-06$15.00/0.

Social signal processing for studying parent-infant interaction

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Marie eAvril

2014-12-01

Full Text Available Studying early interactions is a core issue of infant development and psychopathology. Automatic social signal processing theoretically offers the possibility to extract and analyse communication by taking an integrative perspective, considering the multimodal nature and dynamics of behaviours (including synchrony. This paper proposes an explorative method to acquire and extract relevant social signals from a naturalistic early parent-infant interaction. An experimental setup is proposed based on both clinical and technical requirements. We extracted various cues from body postures and speech productions of partners using the IMI2S (Interaction, Multimodal Integration, and Social Signal Framework. Preliminary clinical and computational results are reported for two dyads (one pathological in a situation of severe emotional neglect and one normal control as an illustration of our cross-disciplinary protocol. The results from both clinical and computational analyses highlight similar differences: the pathological dyad shows dyssynchronic interaction led by the infant whereas the control dyad shows synchronic interaction and a smooth interactive dialog. The results suggest that the current method might be promising for future studies.

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

Science.gov (United States)

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

2016-01-01

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

Study of the interaction between two newly synthesized cyclometallated platinum (II) complexes and human serum albumin: Spectroscopic characterization and docking simulation

Energy Technology Data Exchange (ETDEWEB)

Yousefi, Reza, E-mail: ryousefi@shirazu.ac.ir [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Mohammadi, Roghayeh [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Taheri-Kafrani, Asghar [Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Bagher Shahsavani, Mohammad [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Dadkhah Aseman, Marzieh; Masoud Nabavizadeh, S.; Rashidi, Mehdi [Department of Chemistry, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Poursasan, Najmeh; Moosavi-Movahedi, Ali-Akbar [Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran (Iran, Islamic Republic of)

2015-03-15

This study describes HSA binding properties of two cyclometalated platinum (II) complexes with non-leaving lipophilic ligands; deprotonated 2-phenylpyridine (ppy): C{sub 1} and deprotonated benzo [h]quinolone (bhq): C{sub 2}, using UV–vis, fluorescence and circular dichroism (CD) spectroscopy. The absorption spectra of HSA decreased in the presence of increasing concentration of these complexes, reflecting HSA structural alteration after drug's binding. Also the thermodynamic parameters (ΔG, ΔH and ΔS) that obtained from Trp fluorescence study revealed that the interaction between these complexes and HSA were spontaneous. In addition, C{sub 1} with flexible chemical structure indicated significantly higher fluorescence quenching and binding affinity to HSA than C{sub 2} which possesses a higher structural rigidity. The ANS fluorescence results also indicated that two Pt (II) complexes were competing for binding to the hydrophobic regions of HSA. Moreover, CD results demonstrated that C{sub 2} complex induced alteration of HSA conformation to more significant extent compared to C{sub 1}. The molecular docking results revealed the involvement of π–π stacking and hydrophobic interaction between these complexes and the protein. Overall, this study may highlight the significance of structural flexibility in designing of future anticancer Pt (II) complexes with improved binding affinity for HSA. - Highlights: • HSA is a general transport carrier for a wide variety of ligands such as metabolites and pharmaceutical drugs. • The HSA binding properties of two structurally related cyclometallated platinum (II) complexes (C{sub 1} and C{sub 2}) were studied. • The complexes can bind to HSA and induce structural alteration in this protein. • The thermodynamic parameters revealed that the interactions were spontaneous and mainly hydrophobic driven. • C{sub 1} with flexible chemical structure indicated a higher binding affinity for HSA than C{sub 2}.

The interaction of new piroxicam analogues with lipid bilayers--a calorimetric and fluorescence spectroscopic study.

Science.gov (United States)

Maniewska, Jadwiga; Szczęśniak-Sięga, Berenika; Poła, Andrzej; Sroda-Pomianek, Kamila; Malinka, Wiesław; Michalak, Krystyna

2014-01-01

The purpose of the present paper was to assess the ability of new piroxicam analogues to interact with the lipid bilayers. The results of calorimetric and fluorescence spectroscopic experiments of two new synthesized analogues of piroxicam, named PR17 and PR18 on the phase behavior of phospholipid bilayers and fluorescence quenching of fluorescent probes (Laurdan and Prodan), which molecular location within membranes is known with certainty, are shown in present work. The presented results revealed that, depending on the details of chemical structure, the studied compounds penetrated the lipid bilayers.

Spectral long-range interaction of temporal incoherent solitons.

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Xu, Gang; Garnier, Josselin; Picozzi, Antonio

2014-02-01

We study the interaction of temporal incoherent solitons sustained by a highly noninstantaneous (Raman-like) nonlinear response. The incoherent solitons exhibit a nonmutual interaction, which can be either attractive or repulsive depending on their relative initial distance. The analysis reveals that incoherent solitons exhibit a long-range interaction in frequency space, which is in contrast with the expected spectral short-range interaction described by the usual approach based on the Raman-like spectral gain curve. Both phenomena of anomalous interaction and spectral long-range behavior of incoherent solitons are described in detail by a long-range Vlasov equation.

Factors Associated with Potential Food-Drug Interaction in Hospitalized Patients: A Cross-Sectional Study in Northeast Iran

Directory of Open Access Journals (Sweden)

Mostafa Abdollahi

2018-04-01

Full Text Available Background: The minimization of adverse food-drug interactions will improve patient care by optimizing the therapeutic effects and maintaining proper nutritional status. Aim: The aim of the present study was to find the main factors that may place the hospitalized patients at risk of potential food-drug interactions. Method: This cross-sectional, descriptive study was conducted on 400 inpatients admitted to the Department of Internal Medicine of a teaching hospital in Mashhad, Northeast Iran, within 20 March 2013 to 20 April 2013. The potential food-drug interactions were evaluated for 19 commonly prescribed medications. The main factors (e.g., age, gender, education level, number of medications, and duration of the disease that may place the patients at risk of potential food-drug interactions were analyzed for each patient. Results: Out of the 19 commonly prescribed medications, 17 drugs (89% were not properly used with respect to meal. Furthermore, 14 commonly prescribed drugs were found to have a high frequency (≥50% of potential food-drug interactions. Most of the patients (n=359, 89.8% consumed their medicines at inappropriate time with respect to meals. The results of a multiple logistic regression after adjustment for confounders revealed that the age [β=0.005, CI: 0.0-0.01; P=033], number of medications [β=0.1, CI: 0.083-0.117; P

In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop1[OPEN

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Shivhare, Devendra

2017-01-01

To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice (Oryza sativa) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca. Further mutational analysis suggested that Glu-217 restricts the flexibility of the α4-β4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function. PMID:28546437

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

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Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

Science.gov (United States)

Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

2018-02-01

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Azadirachtin(A) distinctively modulates subdomain 2 of actin - novel mechanism to induce depolymerization revealed by molecular dynamics study.

Science.gov (United States)

Pravin Kumar, R; Roopa, L; Sudheer Mohammed, M M; Kulkarni, Naveen

2016-12-01

Azadirachtin(A) (AZA), a potential insecticide from neem, binds to actin and induces depolymerization in Drosophila. AZA binds to the pocket same as that of Latrunculin A (LAT), but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP-ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA-induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilized the interactions between subdomain 2 of one actin and subdomains 1 and 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n + 2. However, the specific triggering point for the separation of the subunits was the destabilization of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n + 2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.

Alecto 2 - interaction studies; Alecto 2 - etudes d'interaction

Energy Technology Data Exchange (ETDEWEB)

Brunet, J P; Clouet d' Orval, Ch; Mougniot, J C; Penet, F [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1965-07-01

Weak interactions were experimentally studies with the tank of the critical assembly Alecto II and one, two or three bottles containing solutions of various concentrations. In particular, was studied the validity of certain classical assumptions, shielding effects, screening and semi-reflexion effects, importance of thermal coupling. The method of the 'k{sub eff}, solid angle' is shown to apply to such a system. The determination by divergence and pulsed neutron technique of the reactivity related to a millimeter of solution level affords the obtention of critical heights in terms of reactivity. (authors) [French] Une etude experimentale d'interactions faibles a ete faite entre la cuve de l'experience critique ALECTO II et une, deux ou trois bouteilles contenant des concentrations variees. On etudie, en particulier, la validite de certaines hypotheses classiques, effets d'ombre, d'ecrans, de semi-reflexion, importance du couplage thermique. On montre d'autre part que la methode du 'K{sub eff}, angle solide' peut s'appliquer a un tel systeme. La determination par divergence et neutrons pulses de la reactivite liee au millimetre de solution permet de traduire les hauteurs critiques obtenues, en terme de reactivite. (auteurs)

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells.

Directory of Open Access Journals (Sweden)

Krzysztof Poterlowicz

2017-09-01

Full Text Available Mammalian genomes contain several dozens of large (>0.5 Mbp lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene

A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions

Science.gov (United States)

Hostetler, Jessica B.; Sharma, Sumana; Bartholdson, S. Josefin; Wright, Gavin J.; Fairhurst, Rick M.; Rayner, Julian C.

2015-01-01

Background A vaccine targeting Plasmodium vivax will be an essential component of any comprehensive malaria elimination program, but major gaps in our understanding of P. vivax biology, including the protein-protein interactions that mediate merozoite invasion of reticulocytes, hinder the search for candidate antigens. Only one ligand-receptor interaction has been identified, that between P. vivax Duffy Binding Protein (PvDBP) and the erythrocyte Duffy Antigen Receptor for Chemokines (DARC), and strain-specific immune responses to PvDBP make it a complex vaccine target. To broaden the repertoire of potential P. vivax merozoite-stage vaccine targets, we exploited a recent breakthrough in expressing full-length ectodomains of Plasmodium proteins in a functionally-active form in mammalian cells and initiated a large-scale study of P. vivax merozoite proteins that are potentially involved in reticulocyte binding and invasion. Methodology/Principal Findings We selected 39 P. vivax proteins that are predicted to localize to the merozoite surface or invasive secretory organelles, some of which show homology to P. falciparum vaccine candidates. Of these, we were able to express 37 full-length protein ectodomains in a mammalian expression system, which has been previously used to express P. falciparum invasion ligands such as PfRH5. To establish whether the expressed proteins were correctly folded, we assessed whether they were recognized by antibodies from Cambodian patients with acute vivax malaria. IgG from these samples showed at least a two-fold change in reactivity over naïve controls in 27 of 34 antigens tested, and the majority showed heat-labile IgG immunoreactivity, suggesting the presence of conformation-sensitive epitopes and native tertiary protein structures. Using a method specifically designed to detect low-affinity, extracellular protein-protein interactions, we confirmed a predicted interaction between P. vivax 6-cysteine proteins P12 and P41, further

Study on competitive interaction models in Cayley tree

International Nuclear Information System (INIS)

Moreira, J.G.M.A.

1987-12-01

We propose two kinds of models in the Cayley tree to simulate Ising models with axial anisotropy in the cubic lattice. The interaction in the direction of the anisotropy is simulated by the interaction along the branches of the tree. The interaction in the planes perpendicular to the anisotropy direction, in the first model, is simulated by interactions between spins in neighbour branches of the same generation arising from same site of the previous generation. In the second model, the simulation of the interaction in the planes are produced by mean field interactions among all spins in sites of the same generation arising from the same site of the previous generations. We study these models in the limit of infinite coordination number. First, we analyse a situation with antiferromagnetic interactions along the branches between first neighbours only, and we find the analogous of a metamagnetic Ising model. In the following, we introduce competitive interactions between first and second neighbours along the branches, to simulate the ANNNI model. We obtain one equation of differences which relates the magnetization of one generation with the magnetization of the two previous generations, to permit a detailed study of the modulated phase region. We note that the wave number of the modulation, for one fixed temperature, changes with the competition parameter to form a devil's staircase with a fractal dimension which increases with the temperature. We discuss the existence of strange atractors, related to a possible caothic phase. Finally, we show the obtained results when we consider interactions along the branches with three neighbours. (author)

In vitro study on the interaction of 4,4-dimethylcurcumin with calf thymus DNA

Energy Technology Data Exchange (ETDEWEB)

Liu, Bing-Mi, E-mail: liubingmi@163.com [Department of Pharmacy, Liaoning University, Shenyang 110036 (China); Bai, Chong-Liang [Centre for Molecular Science and Engineering, Northeastern University, Shenyang 110819 (China); Zhang, Jun; Liu, Yang; Dong, Bo-Yang; Zhang, Yi-Tong [Department of Pharmacy, Liaoning University, Shenyang 110036 (China); Liu, Bin, E-mail: liubinzehao@163.com [Department of Pharmacy, Liaoning University, Shenyang 110036 (China)

2015-10-15

The interaction of 4,4-dimethylcurcumin (DMCU), a synthesized analog of curcumin, with calf-thymus DNA (ct-DNA) was investigated using fluorescence, absorption, and circular dichroism (CD) spectroscopy, coupled with viscosity measurements and molecular docking techniques. DMCU was found to bind to ct-DNA with moderate binding affinity through groove binding as evidenced by a decrease in the absorption intensity in combination with no obvious change in the relative specific viscosity of ct-DNA and the CD spectrum. Thermodynamic analysis of the fluorescence data obtained at different temperatures suggested that the binding process was spontaneous and was primarily driven by hydrogen bonding and van der Waals forces. Furthermore, competitive binding experiments with ethidium bromide and 4′,6-diamidino-2-phenylindole as probes showed that DMCU could preferentially bind in the minor groove of double-stranded DNA. The results obtained from the molecular docking studies were consistent with these experimental results. This study explored the potential applicability of the spectroscopic properties of DMCU for studying its interactions with relevant biological or biomimicking targets. - Highlights: • 4,4-dimethylcurcumin (DMCU) has strong fluorescence characteristics. • DMCU could bind to DNA through groove binding. • Docking studies revealed that DMCU bound to the A–T region in the minor groove.

Levels of Interaction Provided by Online Distance Education Models

Science.gov (United States)

Alhih, Mohammed; Ossiannilsson, Ebba; Berigel, Muhammet

2017-01-01

Interaction plays a significant role to foster usability and quality in online education. It is one of the quality standard to reveal the evidence of practice in online distance education models. This research study aims to evaluate levels of interaction in the practices of distance education centres. It is aimed to provide online distance…

A linguistic study of patient-centered interviewing: emergent interactional effects.

Science.gov (United States)

Hesson, Ashley M; Sarinopoulos, Issidoros; Frankel, Richard M; Smith, Robert C

2012-09-01

To evaluate interactional effects of patient-centered interviewing (PCI) compared to isolated clinician-centered interviewing (CCI). We conducted a pilot study comparing PCI (N=4) to CCI (N=4) for simulated new-patient visits. We rated interviews independently and measured patient satisfaction with the interaction via a validated questionnaire. We conducted interactional sociolinguistic analysis on the interviews and compared across three levels of analysis: turn, topic, and interaction. We found significant differences between PCI and CCI in physician responses to patients' psychosocial cues and concerns. The number and type of physician questions also differed significantly across PCI and CCI sets. Qualitatively, we noted several indicators of physician-patient attunement in the PCI interviews that were not present in the CCI interviews. They spanned diverse aspects of physician and patient speech, suggesting interactional accommodation on the part of both participants. This small pilot study highlights a variety of interactional variables that may underlie the effects associated with patient-centered interviewing (e.g., positive relationships, health outcomes). Question form, phonological accommodation processes, and use of stylistic markers are relatively unexplored in controlled studies of physician-patient interaction. This study characterizes several interactional variables for larger scale studies and contributes to models of patient-centeredness in practice. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Structural study of surfactant-dependent interaction with protein

Energy Technology Data Exchange (ETDEWEB)

Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India); Kohlbrecher, Joachim [Laboratory for Neutron Scattering, Paul Scherrer Institut, CH-5232 PSI Villigen (Switzerland)

2015-06-24

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds

Science.gov (United States)

Links, Matthew G; Demeke, Tigst; Gräfenhan, Tom; Hill, Janet E; Hemmingsen, Sean M; Dumonceaux, Tim J

2014-01-01

In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces. The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined. A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99–100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds. cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera. PMID:24444052

[Differential gene expression in incompatible interaction between Lilium regale Wilson and Fusarium oxysporum f. sp. lilii revealed by combined SSH and microarray analysis].

Science.gov (United States)

Rao, J; Liu, D; Zhang, N; He, H; Ge, F; Chen, C

2014-01-01

Fusarium wilt, caused by a soilborne pathogen Fusarium oxysporum f. sp. lilii, is the major disease of lily (Lilium L.). In order to isolate the genes differentially expressed in a resistant reaction to F. oxysporum in L. regale Wilson, a cDNA library was constructed with L. regale root during F. oxysporum infection using the suppression subtractive hybridization (SSH), and a total of 585 unique expressed sequence tags (ESTs) were obtained. Furthermore, the gene expression profiles in the incompatible interaction between L. regale and F. oxysporum were revealed by oligonucleotide microarray analysis of 585 unique ESTs comparison to the compatible interaction between a susceptible Lilium Oriental Hybrid 'Siberia' and F. oxysporum. The result of expression profile analysis indicated that the genes encoding pathogenesis-related proteins (PRs), antioxidative stress enzymes, secondary metabolism enzymes, transcription factors, signal transduction proteins as well as a large number of unknown genes were involved in early defense response of L. regale to F. oxysporum infection. Moreover, the following quantitative reverse transcription PCR (QRT-PCR) analysis confirmed reliability of the oligonucleotide microarray data. In the present study, isolation of differentially expressed genes in L. regale during response to F. oxysporum helped to uncover the molecular mechanism associated with the resistance of L. regale against F. oxysporum.

Kinesthetic Interaction

DEFF Research Database (Denmark)

Fogtmann, Maiken Hillerup; Fritsch, Jonas; Kortbek, Karen Johanne

2008-01-01

Within the Human-Computer Interaction community there is a growing interest in designing for the whole body in interaction design. The attempts aimed at addressing the body have very different outcomes spanning from theoretical arguments for understanding the body in the design process, to more...... practical examples of designing for bodily potential. This paper presents Kinesthetic Interaction as a unifying concept for describing the body in motion as a foundation for designing interactive systems. Based on the theoretical foundation for Kinesthetic Interaction, a conceptual framework is introduced...... to reveal bodily potential in relation to three design themes – kinesthetic development, kinesthetic means and kinesthetic disorder; and seven design parameters – engagement, sociality, movability, explicit motivation, implicit motivation, expressive meaning and kinesthetic empathy. The framework is a tool...

Study of 12C interactions at HISS

International Nuclear Information System (INIS)

Crawford, H.J.

1982-12-01

Single-particle inclusive measurements in high-energy nuclear physics have provided the foundation for a number of models of interacting nuclear fluids. Such measurements yield information on the endpoints of the evolution of highly excited nuclear systems. However, they suffer from the fact that observed particles can be formed in a large number of very different evolutionary paths. To learn more about how interactions proceed we have performed a series of experiments in which all fast nuclear fragments are analyzed for each individual interaction. These experiments were performed at the LBL Bevalac HISS (Heavy Ion Spectrometer System) facility where we studied the interaction of 1 GeV/nuc 12C nuclei with targets of C, CH 2 , Cu, and U. In this paper we describe HISS and present some preliminary results of the experiment

Valerian: No Evidence for Clinically Relevant Interactions

Directory of Open Access Journals (Sweden)

Olaf Kelber

2014-01-01

Full Text Available In recent popular publications as well as in widely used information websites directed to cancer patients, valerian is claimed to have a potential of adverse interactions with anticancer drugs. This questions its use as a safe replacement for, for example, benzodiazepines. A review on the interaction potential of preparations from valerian root (Valeriana officinalis L. root was therefore conducted. A data base search and search in a clinical drug interaction data base were conducted. Thereafter, a systematic assessment of publications was performed. Seven in vitro studies on six CYP 450 isoenzymes, on p-glycoprotein, and on two UGT isoenzymes were identified. However, the methodological assessment of these studies did not support their suitability for the prediction of clinically relevant interactions. In addition, clinical studies on various valerian preparations did not reveal any relevant interaction potential concerning CYP 1A2, 2D6, 2E1, and 3A4. Available animal and human pharmacodynamic studies did not verify any interaction potential. The interaction potential of valerian preparations therefore seems to be low and thereby without clinical relevance. We conclude that there is no specific evidence questioning their safety, also in cancer patients.

Changes in cerebro-cerebellar interaction during response inhibition after performance improvement.

Science.gov (United States)

Hirose, Satoshi; Jimura, Koji; Kunimatsu, Akira; Abe, Osamu; Ohtomo, Kuni; Miyashita, Yasushi; Konishi, Seiki

2014-10-01

It has been demonstrated that motor learning is supported by the cerebellum and the cerebro-cerebellar interaction. Response inhibition involves motor responses and the higher-order inhibition that controls the motor responses. In this functional MRI study, we measured the cerebro-cerebellar interaction during response inhibition in two separate days of task performance, and detected the changes in the interaction following performance improvement. Behaviorally, performance improved in the second day, compared to the first day. The psycho-physiological interaction (PPI) analysis revealed the interaction decrease from the right inferior frontal cortex (rIFC) to the cerebellum (lobule VII or VI). It was also revealed that the interaction increased from the same cerebellar region to the primary motor area. These results suggest the involvement of the cerebellum in response inhibition, and raise the possibility that the performance improvement was supported by the changes in the cerebro-cerebellar interaction. Copyright © 2014 Elsevier Inc. All rights reserved.

Light and noise pollution interact to disrupt interspecific interactions.

Science.gov (United States)

McMahon, Taegan A; Rohr, Jason R; Bernal, Ximena E

2017-05-01

Studies on the consequences of urbanization often examine the effects of light, noise, and heat pollution independently on isolated species providing a limited understanding of how these combined stressors affect species interactions. Here, we investigate how these factors interact to affect parasitic frog-biting midges (Corethrella spp.) and their túngara frog (Engystomops pustulosus) hosts. A survey of túngara frog calling sites revealed that frog abundance was not significantly correlated with urbanization, light, noise, or temperature. In contrast, frog-biting midges were sensitive to light pollution and noise pollution. Increased light intensity significantly reduced midge abundance at low noise levels. At high noise intensity, there were no midges regardless of light level. Two field experiments controlling light and noise levels to examine attraction of the midges to their host and their feeding behavior confirmed the causality of these field patterns. These findings demonstrate that both light and noise pollution disrupt this host-parasite interaction and highlight the importance of considering interactions among species and types of pollutants to accurately assess the impacts of urbanization on ecological communities. © 2017 by the Ecological Society of America.

Nano Cu interaction with single amino acid tyrosine derived self-assemblies; study through XRD, AFM, confocal Raman microscopy, SERS and DFT methods

Science.gov (United States)

Govindhan, Raman; Karthikeyan, Balakrishnan

2017-12-01

3,5-Bis(trifluoromethyl)benzylamine derivatives of single amino acid tyrosine produced self-assembled nanotubes (BTTNTs) as simple Phe-Phe. It has been observed that tyrosine derivative gives exclusively micro and nano tubes irrespective of the concentration of the precursor monomer. However, the introduced xenobiotic trifluoromethyl group (TFM) present in key backbone positionsof the self assembly gives the specific therapeutic function has been highlighted. Herein this work study of such self assembled nanotubes were studied through experimental and theoretical methods. The interaction of nanocopper cluster with the nanotubes (Cu@BTTNTs) were extensively studied by various methods like XRD, AFM, confocal Raman microscopy, SERS and theoretical methods like Mulliken's atomic charge analysis. SERS reveals that the interactions of Cu cluster with NH2, OH, NH and phenyl ring π-electrons system of BTTNTs. DFT studies gave the total dipole moment values of Cu@BTTNTs and explained the nature of interaction.

β-Lactam antibiotics epitope mapping with STD NMR spectroscopy: a study of drug-human serum albumin interaction

International Nuclear Information System (INIS)

Milagre, Cintia D. F.; Cabeca, Luis F.; Almeida, Wanda P.; Marsaioli, Anita J.

2012-01-01

Molecular recognition events are key issues in many biological processes. STD NMR (saturation transfer difference nuclear magnetic resonance spectroscopy) is one of the techniques used to understand such biological interactions. Herein, we have investigated the interactions of four β-lactam antibiotics belonging to two classes (cephalosporins and penicillins) with human serum albumin (HSA) by 1 H STD NMR revealing that the interaction between the aromatic moiety and HSA is responsible for the binding efficiency. Thus, the structural differences from the five to six-membered thio ring in penicillins and cephalosporins do not seem to influence antibiotic albumin interactions. (author)

Who is the competent physics student? A study of students' positions and social interaction in small-group discussions

Science.gov (United States)

Due, Karin

2014-06-01

This article describes a study which explored the social interaction and the reproduction and challenge of gendered discourses in small group discussions in physics. Data for the study consisted of video recordings of eight upper secondary school groups solving physics problems and 15 audiotaped individual interviews with participating students. The analysis was based on gender theory viewing gender both as a process and a discourse. Specifically discursive psychology analysis was used to examine how students position themselves and their peers within discourses of physics and gender. The results of the study reveal how images of physics and of "skilled physics student" were constructed in the context of the interviews. These discourses were reconstructed in the students' discussions and their social interactions within groups. Traditional gendered positions were reconstructed, for example with boys positioned as more competent in physics than girls. These positions were however also resisted and challenged.

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

Science.gov (United States)

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

Directory of Open Access Journals (Sweden)

Qianqian Yin

2014-11-01

Full Text Available Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.

Interactions of carbon dioxide with model organic molecules: A comparative theoretical study

Science.gov (United States)

Trung, Nguyen Tien; Nguyen, Minh Tho

2013-08-01

Interaction energies obtained using CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ computations including both ZPE and BSSE corrections range from -2.9 to -14.2 kJ mol-1. While formic acid forms the most stable complex with CO2, formaldehyde yields the least stable complex. Lewis acid-base interaction such as C-N⋯C(CO2), Cdbnd O⋯C(CO2), which overcomes C-H⋯O blue-shifting hydrogen bond, plays a significant role in stabilizing most complexes. However, the strength of (HCOOH, CO2) is mainly determined by O-H⋯O red-shifting hydrogen bond. The C-H⋯O blue-shifting hydrogen bond is revealed upon complexation of CH3OH, HCHO, HCOOH, CH3COCH3 and HCOOCH3 with CO2. Remarkably, existence of weak hydrogen bonded C-H⋯O interaction is not found in the (CH3OCH3, CO2) and (CH3NH2, CO2) pairs.

Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age.

Science.gov (United States)

Murfin, Kristen E; Dillman, Adler R; Foster, Jeremy M; Bulgheresi, Silvia; Slatko, Barton E; Sternberg, Paul W; Goodrich-Blair, Heidi

2012-08-01

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

International Nuclear Information System (INIS)

Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

2014-01-01

Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

A case-only genome-wide association study for assessing gene-sex interaction in Allergic rhinitis

DEFF Research Database (Denmark)

Mohammadnejad, Afsaneh; Brasch-Andersen, Charlotte; Haagerup, Annette

-value = 2.8 × 10−5) sits in C5orf66 gene on 5q31. Poster abstract 2 Discussion: Our study was able to detect a significant SNP rs4251459 mapping to IRAK4 gene on 12q12 locus which appeared to increase the risk of AR in females than males. This gene has previously been reported to have a sex dependent effect...... on AR. C5orf66 loci might also be an interesting candidate for AR, but its role warrants further validations. Additionally, pathway analysis from GSEA identified a pathway related to immune system which is biologically meaningful and supportive. In conclusion, our study revealed the gene-sex interaction...

Size-dependent physicochemical and mechanical interactions in battery paste anodes of Si-microwires revealed by Fast-Fourier-Transform Impedance Spectroscopy

Science.gov (United States)

Hansen, Sandra; Quiroga-González, Enrique; Carstensen, Jürgen; Adelung, Rainer; Föll, Helmut

2017-05-01

Perfectly aligned silicon microwire arrays show exceptionally high cycling stability with record setting (high) areal capacities of 4.25 mAh cm-2. Those wires have a special, modified length and thickness in order to perform this good. Geometry and sizes are the most important parameters of an anode to obtain batteries with high cycling stability without irreversible losses. The wires are prepared with a unique etching fabrication method, which allows to fabricate wires of very precise sizes. In order to investigate how good randomly oriented silicon wires perform in contrast to the perfect order of the array, the wires are embedded in a paste. This study reveals the fundamental correlation between geometry, mechanics and charge transfer kinetics of silicon electrodes. Using a suitable RC equivalent circuit allows to evaluate data from cyclic voltammetry and simultaneous FFT-Impedance Spectroscopy (FFT-IS), yielding in time-resolved resistances, time constants, and their direct correlation to the phase transformations. The change of the resistances during lithiation and delithiation correlates to kinetics and charge transfer mechanisms. This study demonstrates how the mechanical and physiochemical interactions at the silicon/paste interface inside the paste electrodes lead to void formation around silicon and with it to material loss and capacity fading.

Experimental studies of oxidic molten corium-vessel steel interaction

International Nuclear Information System (INIS)

Bechta, S.V.; Khabensky, V.B.; Vitol, S.A.; Krushinov, E.V.; Lopukh, D.B.; Petrov, Yu.B.; Petchenkov, A.Yu.; Kulagin, I.V.; Granovsky, V.S.; Kovtunova, S.V.; Martinov, V.V.; Gusarov, V.V.

2001-01-01

The experimental results of molten corium-steel specimen interaction with molten corium on the 'Rasplav-2' test facility are presented. In the experiments, cooled vessel steel specimens positioned on the molten pool bottom and uncooled ones lowered into the molten pool were tested. Interaction processes were studied for different corium compositions, melt superheating and in alternative (inert and air) overlying atmosphere. Hypotheses were put forward explaining the observed phenomena and interaction mechanisms. The studies presented in the paper were aimed at the detection of different corium-steel interaction mechanisms. Therefore certain identified phenomena are more typical of the ex-vessel localization conditions than of the in-vessel corium retention. Primarily, this can be referred to the phenomena of low-temperature molten corium-vessel steel interaction in oxidizing atmosphere

Experimental studies of oxidic molten corium-vessel steel interaction

Energy Technology Data Exchange (ETDEWEB)

Bechta, S.V. E-mail: niti-npc@sbor.net; Khabensky, V.B.; Vitol, S.A.; Krushinov, E.V.; Lopukh, D.B.; Petrov, Yu.B.; Petchenkov, A.Yu.; Kulagin, I.V.; Granovsky, V.S.; Kovtunova, S.V.; Martinov, V.V.; Gusarov, V.V

2001-12-01

The experimental results of molten corium-steel specimen interaction with molten corium on the 'Rasplav-2' test facility are presented. In the experiments, cooled vessel steel specimens positioned on the molten pool bottom and uncooled ones lowered into the molten pool were tested. Interaction processes were studied for different corium compositions, melt superheating and in alternative (inert and air) overlying atmosphere. Hypotheses were put forward explaining the observed phenomena and interaction mechanisms. The studies presented in the paper were aimed at the detection of different corium-steel interaction mechanisms. Therefore certain identified phenomena are more typical of the ex-vessel localization conditions than of the in-vessel corium retention. Primarily, this can be referred to the phenomena of low-temperature molten corium-vessel steel interaction in oxidizing atmosphere.

Interaction and miscibility study of fumarate-based macromers with chitosan

International Nuclear Information System (INIS)

Hashemi Doulabi, Azadehsadat; Mirzadeh, Hamid; Imani, Mohammad

2013-01-01

This work is aimed to prepare Chitosan/Poly(ethylene glycol fumarate) (Ch/PEGF) blend films and to determine blend miscibility of the two polymers as a function of molecular interactions between Ch and PEGF. The blend films are prepared in various ratios (0/100 to 100/0) by the conventional solution-casting method. Interactions occurring in the blends are investigated and probed by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and dynamic mechanical thermal analysis (DMTA). FTIR and XRD analyses reveal the existence of newly-formed hydrogen bond interactions between Ch and PEGF. The influence of Ch/PEGF blend ratio on thermal properties of the blend systems is discussed especially considering thermal stability. The results indicate that both melting point and crystallinity of PEGF component in the blends depend on the composition of the blends. The obtained results of FTIR, DSC, and XRD analyses suggest that the partially protonated amine groups of Ch interacts with the hydroxyl groups of PEGF and thus partial miscibility are occurred. The results are confirmed with polarized microscopy observations. It is shown that although weak hydrogen bonding exists between the polymers functional groups; the blends are partially miscible. Highlights: ► Miscibility of Ch/PEGF blends is evaluated as a function of molecular interactions. ► We explore the relationship between blend ratio of films and miscibility behavior. ► Chitosan chains can affect and disturb original crystalline structures of PEGF. ► Thermal stability of the blend films is discussed. ► These analyses suggest the blends are partially miscible

Spectral studies of Lanthanide interactions with membrane surfaces

Energy Technology Data Exchange (ETDEWEB)

Karukstis, K.K.; Kao, M.Y.; Savin, D.A.; Bittker, R.A.; Kaphengst, K.J.; Emetarom, C.M.; Naito, N.R.; Takamoto, D.Y. [Harvey Mudd College, Claremont, CA (United States)

1995-03-23

We have monitored the interactions of the series of trivalent lanthanide cations with the thylakoid membrane surface of spinach chloroplasts using two complementary spectral techniques. Measurements of the fluorescence emission of the extrinsic probe 2-p-toluidinonaphthalene-6-sulfonate (TNS) and the absorbance of the intrinsic chromophore chlorophyll provide two sensitive means of characterizing the dependence of the cation-membrane interaction on the nature of the cation. In these systems, added lanthanide cations adsorb onto the membrane surface to neutralize exposed segments of membrane-embedded protein complexes. The lanthanide-induced charge neutralization increases the proximity of added TNS anion to the membrane surface as evidenced by variations in the TNS fluorescence level and wavelength of maximum emission. Our results reveal a strong dependence of TNS fluorescence parameters on both lanthanide size and total orbital angular momentum L value. Lanthanides with greater charge density (small size and/or low L value) enhance the TNS fluorescence level to a greater extent. A possible origin for the lanthanide-dependent TNS fluorescence levels is suggested in terms of a heterogeneity in the number and type of TNS binding sites. The data are consistent with the proposal that larger lanthanides with smaller enthalpies of hydration induce more significant membrane appression. 59 refs., 9 figs., 2 tabs.

The pragmatics of therapeutic interaction: an empirical study.

Science.gov (United States)

Lepper, Georgia

2009-10-01

The research reported in this article aims to demonstrate a method for the systematic study of the therapist/patient interaction in psychoanalytic psychotherapy, drawing upon the tradition and methods of 'pragmatics'--the study of language in interaction. A brief introduction to the discipline of pragmatics demonstrates its relevance to the contemporary focus of clinical theory on the here-and-now dynamics of the relationship between analyst and patient. This is followed by a detailed study of five segments from the transcript of a therapeutic dialogue, drawn from a brief psychoanalytic psychotherapy, in which therapist and patient negotiate the meaning of the patient's symptom: Is it psychosomatic? The research seeks to show how the therapeutic process can be observed and studied as an interactional achievement, grounded in general and well-studied procedures through which meaning is intersubjectively developed and shared. Implications of the analysis for clinical theory and practice, and further research, are discussed.

Dynamics of urokinase receptor interaction with Peptide antagonists studied by amide hydrogen exchange and mass spectrometry

DEFF Research Database (Denmark)

Jørgensen, Thomas J D; Gårdsvoll, Henrik; Danø, Keld

2004-01-01

Using amide hydrogen exchange combined with electrospray ionization mass spectrometry, we have in this study determined the number of amide hydrogens on several peptides that become solvent-inaccessible as a result of their high-affinity interaction with the urokinase-type plasminogen activator...... receptor (uPAR). These experiments reveal that at least six out of eight amide hydrogens in a synthetic nine-mer peptide antagonist (AE105) become sequestered upon engagement in uPAR binding. Various uPAR mutants with decreased affinity for this peptide antagonist gave similar results, thereby indicating...... that deletion of the favorable interactions involving the side chains of these residues in uPAR does not affect the number of hydrogen bonds established by the main chain of the peptide ligand. The isolated growth factor-like domain (GFD) of the cognate serine protease ligand for uPAR showed 11 protected amide...

Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices

International Nuclear Information System (INIS)

Lee, P.-F.; Yeh, Alvin T.; Bayless, Kayla J.

2009-01-01

The interactions between endothelial cells (ECs) and the extracellular matrix (ECM) are fundamental in mediating various steps of angiogenesis, including cell adhesion, migration and sprout formation. Here, we used a noninvasive and non-destructive nonlinear optical microscopy (NLOM) technique to optically image endothelial sprouting morphogenesis in three-dimensional (3D) collagen matrices. We simultaneously captured signals from collagen fibers and endothelial cells using second harmonic generation (SHG) and two-photon excited fluorescence (TPF), respectively. Dynamic 3D imaging revealed EC interactions with collagen fibers along with quantifiable alterations in collagen matrix density elicited by EC movement through and morphogenesis within the matrix. Specifically, we observed increased collagen density in the area between bifurcation points of sprouting structures and anisotropic increases in collagen density around the perimeter of lumenal structures, but not advancing sprout tips. Proteinase inhibition studies revealed membrane-associated matrix metalloproteinase were utilized for sprout advancement and lumen expansion. Rho-associated kinase (p160ROCK) inhibition demonstrated that the generation of cell tension increased collagen matrix alterations. This study followed sprouting ECs within a 3D matrix and revealed that the advancing structures recognize and significantly alter their extracellular environment at the periphery of lumens as they progress

The study of ethnic attitudes during interactions with avatars in virtual environments

Directory of Open Access Journals (Sweden)

Galina Ya. Menshikova

2018-03-01

the direction of mutual gaze. Results. The results showed that participants preferred to keep closer interpersonal distances from the avatars of the same ethnic group as their own. During interaction with avatars belonging to another ethnic group, significantly larger interpersonal distances were preferred. A significant correlation between the interpersonal distance and the PConclusion. Virtual reality technology provides a unique and valuable tool for social researchers, including in ethnic attitude studies. A complex method of measuring interpersonal distances and the Presence Effect allows us to assess the main variables during social interaction with high accuracy. The virtual environments designed for this study can be applied successfully not only for studying proxemic behavior, but also for accomplishing other tasks, such as developing communication skills and forming positive attitudes towards ethnic out-groups.resence Effect was also revealed.

Flow motifs reveal limitations of the static framework to represent human interactions

Science.gov (United States)

Rocha, Luis E. C.; Blondel, Vincent D.

2013-04-01

Networks are commonly used to define underlying interaction structures where infections, information, or other quantities may spread. Although the standard approach has been to aggregate all links into a static structure, some studies have shown that the time order in which the links are established may alter the dynamics of spreading. In this paper, we study the impact of the time ordering in the limits of flow on various empirical temporal networks. By using a random walk dynamics, we estimate the flow on links and convert the original undirected network (temporal and static) into a directed flow network. We then introduce the concept of flow motifs and quantify the divergence in the representativity of motifs when using the temporal and static frameworks. We find that the regularity of contacts and persistence of vertices (common in email communication and face-to-face interactions) result on little differences in the limits of flow for both frameworks. On the other hand, in the case of communication within a dating site and of a sexual network, the flow between vertices changes significantly in the temporal framework such that the static approximation poorly represents the structure of contacts. We have also observed that cliques with 3 and 4 vertices containing only low-flow links are more represented than the same cliques with all high-flow links. The representativity of these low-flow cliques is higher in the temporal framework. Our results suggest that the flow between vertices connected in cliques depend on the topological context in which they are placed and in the time sequence in which the links are established. The structure of the clique alone does not completely characterize the potential of flow between the vertices.

Landmark Study Reveals Antarctic Glacier's Long History of Retreat

OpenAIRE

Kuska, Dale M.

2016-01-01

Faculty Showcase Archive Article Approved for public release; distribution is unlimited. A major study, released in late November in the journal “Nature,” reveals the history of retreat of the massive Pine Island Glacier (PIG) in western Antarctica, widely considered one of the largest contributors to global sea-level rise.

[Role of food interaction pharmacokinetic studies in drug development. Food interaction studies of theophylline and nifedipine retard and buspirone tablets].

Science.gov (United States)

Drabant, S; Klebovich, I; Gachályi, B; Renczes, G; Farsang, C

1998-09-01

Due to several mechanism, meals may modify the pharmacokinetics of drug products, thereby eliciting to clinically significant food interaction. Food interactions with the drug substance and with the drug formulation should be distinguished. Food interaction of different drug products containing the same active ingredient can be various depending on the pharmaceutical formulation technology. Particularly, in the case of modified release products, the food/formulation interaction can play an important role in the development of food interaction. Well known example, that bioavailability of theophylline can be influenced in different way (either increased, decreased or unchanged) by concomitant intake of food in the case of different sustained release products. The role and methods of food interaction studies in the different kinds of drug development (new chemical entity, modified release products, generics) are reviewed. Prediction of food effect response on the basis of the physicochemical and pharmacokinetic characteristics of the drug molecule or formulations is discussed. The results of three food interaction studies carried out the products of EGIS Pharmaceuticals Ltd. are also reviewed. The pharmacokinetic parameters of theophyllin 400 mg retard tablet were practically the same in both fasting condition and administration after consumption of a high fat containing standard breakfast. The ingestion of a high fat containing breakfast, increased the AUC of nifedipine from 259.0 +/- 101.2 ng h/ml to 326.7 +/- 122.5 ng h/ml and Cmax from 34.5 +/- 15.9 ng/ml to 74.3 +/- 23.9 ng/ml in case of nifedipine 20 mg retard tablet, in agreement with the data of literature. The statistical evaluation indicated significant differences between the pharmacokinetic parameters in the case of two administrations (before and after meal). The effect of a high fat containing breakfast for a generic version of buspiron 10 mg tablet and the bioequivalence after food consumption were

Experimental studies of pion-nucleus interactions at intermediate energies

International Nuclear Information System (INIS)

1991-01-01

This report summarizes the work on experimental research in intermediate energy nuclear physics carried out at New Mexico State University in 1991 under a great from the US Department of Energy. Most of these studies have involved investigations of various pion-nucleus interactions. The work has been carried out both with the LAMPF accelerator at the Los Alamos National Laboratory and with the cyclotron at the Paul Scherrer Institute (PSI) near Zurich, Switzerland. Part of the experimental work involves measurements of new data on double-charge-exchange scattering, using facilities at LAMPF which we helped modify, and on pion absorption, using a new detector system at PSI that covers nearly the full solid-angle region which we helped construct. Other work involved preparation for future experiments using polarized nuclear targets and a new high-resolution spectrometer system for detecting π 0 mesons. We also presented several proposals for works to be done in future years, involving studies related to pi-mesonic atoms, fundamental pion-nucleon interactions, studies of the difference between charged and neutral pion interactions with the nucleon, studies of the isospin structure of pion-nucleus interactions, and pion scattering from polarized 3 He targets. This work is aimed at improving our understanding of the pion-nucleon interaction, of the pion-nucleus interaction mechanism, and of nuclear structure

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Directory of Open Access Journals (Sweden)

David eBerry

2014-05-01

Full Text Available Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well networks reveal the underlying interactions, and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

Science.gov (United States)

Berry, David; Widder, Stefanie

2014-01-01

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

Why do interracial interactions impair executive function? A resource depletion account.

Science.gov (United States)

Richeson, Jennifer A; Trawalter, Sophie

2005-06-01

Three studies investigated the veracity of a resource depletion account of the impairment of inhibitory task performance after interracial contact. White individuals engaged in either an interracial or same-race interaction, then completed an ostensibly unrelated Stroop color-naming test. In each study, the self-regulatory demands of the interaction were either increased (Study 1) or decreased (Studies 2 and 3). Results revealed that increasing the self-regulatory demands of an interracial interaction led to greater Stroop interference compared with control, whereas reducing self-regulatory demands led to less Stroop interference. Manipulating self-regulatory demands did not affect Stroop performance after same-race interactions. Taken together, the present studies point to resource depletion as the likely mechanism underlying the impairment of cognitive functioning after interracial dyadic interactions.

Differential proteomics reveals novel insights into Nosema-honey bee interactions.

Science.gov (United States)

Kurze, Christoph; Dosselli, Ryan; Grassl, Julia; Le Conte, Yves; Kryger, Per; Baer, Boris; Moritz, Robin F A

2016-12-01

Host manipulation is a common strategy by parasites to reduce host defense responses, enhance development, host exploitation, reproduction and, ultimately, transmission success. As these parasitic modifications can reduce host fitness, increased selection pressure may result in reciprocal adaptations of the host. Whereas the majority of studies on host manipulation have explored resistance against parasites (i.e. ability to prevent or limit an infection), data describing tolerance mechanisms (i.e. ability to limit harm of an infection) are scarce. By comparing differential protein abundance, we provide evidence of host-parasite interactions in the midgut proteomes of N. ceranae-infected and uninfected honey bees from both Nosema-tolerant and Nosema-sensitive lineages. We identified 16 proteins out of 661 protein spots that were differentially abundant between experimental groups. In general, infections of Nosema resulted in an up-regulation of the bee's energy metabolism. Additionally, we identified 8 proteins that were differentially abundant between tolerant and sensitive honey bees regardless of the Nosema infection. Those proteins were linked to metabolism, response to oxidative stress and apoptosis. In addition to bee proteins, we also identified 3 Nosema ceranae proteins. Interestingly, abundance of two of these Nosema proteins were significantly higher in infected Nosema-sensitive honeybees relative to the infected Nosema-tolerant lineage. This may provide a novel candidate for studying the molecular interplay between N. ceranae and its honey bee host in more detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding.

Science.gov (United States)

Tollington, Simon; Greenwood, Andrew; Jones, Carl G; Hoeck, Paquita; Chowrimootoo, Aurélie; Smith, Donal; Richards, Heather; Tatayah, Vikash; Groombridge, Jim J

2015-07-01

Infectious diseases are widely recognized to have substantial impact on wildlife populations. These impacts are sometimes exacerbated in small endangered populations, and therefore, the success of conservation reintroductions to aid the recovery of such species can be seriously threatened by outbreaks of infectious disease. Intensive management strategies associated with conservation reintroductions can further compound these negative effects in such populations. Exploring the sublethal effects of disease outbreaks among natural populations is challenging and requires longitudinal, individual life-history data on patterns of reproductive success and other indicators of individual fitness. Long-term monitoring data concerning detailed reproductive information of the reintroduced Mauritius parakeet (Psittacula echo) population collected before, during and after a disease outbreak was investigated. Deleterious effects of an outbreak of beak and feather disease virus (BFDV) were revealed on hatch success, but these effects were remarkably short-lived and disproportionately associated with breeding pairs which took supplemental food. Individual BFDV infection status was not predicted by any genetic, environmental or conservation management factors and was not associated with any of our measures of immune function, perhaps suggesting immunological impairment. Experimental immunostimulation using the PHA (phytohaemagglutinin assay) challenge technique did, however, provoke a significant cellular immune response. We illustrate the resilience of this bottlenecked and once critically endangered, island-endemic species to an epidemic outbreak of BFDV and highlight the value of systematic monitoring in revealing inconspicuous but nonetheless substantial ecological interactions. Our study demonstrates that the emergence of such an infectious disease in a population ordinarily associated with increased susceptibility does not necessarily lead to deleterious impacts on population

Revealing Partons in Hadrons: From the ISR to the SPS Collider

CERN Document Server

Darriulat, Pierre

2015-01-01

Our understanding of the structure of hadrons has developed during the seventies and early eighties from a few vague ideas to a precise theory, Quantum Chromodynamics, that describes hadrons as made of elementary partons (quarks and gluons). Deep inelastic scattering of electrons and neutrinos on nucleons and electron–positron collisions have played a major role in this development. Less well known is the role played by hadron collisions in revealing the parton structure, studying the dynamic of interactions between partons and offering an exclusive laboratory for the direct study of gluon interactions. The present article recalls the decisive contributions made by the CERN Intersecting Storage Rings and, later, the proton–antiproton SPS Collider to this chapter of physics.

Study of the magnetic interaction in nanocrystalline Pr–Fe–Co–Nb–B permanent magnets

International Nuclear Information System (INIS)

Dospial, M.; Plusa, D.; Ślusarek, B.

2012-01-01

The magnetic properties of an isotropic, epoxy resin bonded magnets made from Pr–Fe–Co–Nb–B powder were investigated. The magnetization reversal process and magnetic parameters were examined by measurements of the initial magnetization curve, major and minor hysteresis loops and sets of recoil curves. From the initial magnetization curve and the field dependencies of the reversible and irreversible magnetization components derived from the recoil loops it was found that the magnetization reversal process is the combination of the nucleation of reversed domains and pinning of domain walls at the grain boundaries and the reversible rotation of magnetization vector in single domain grains. The interactions between grains were studied by means of δM plots. The nonlinear behavior of δM curve approve that the short range intergrain exchange coupling interactions are dominant in a field up to the sample coercivity. The interaction domains and fine magnetic structure were revealed as the evidence of exchange coupling between soft α-Fe and hard magnetic Nd 2 Fe 14 B grains. - Highlights: ► Coercivity of the Pr–Fe–Co–Nb–B magnet is determined by the pinning of domain walls at the grain boundaries. ► Rotation of magnetization vector and domain walls bowing also give the contribution to the initial and demagnetization process. ► δM behavior shows that the dominant interaction is the short range exchange one among soft magnetic α-Fe and hard magnetic Pr 2 Fe 14 B grains.

Multi-spectroscopic studies on the interaction of human serum albumin with astilbin: Binding characteristics and structural analysis

Energy Technology Data Exchange (ETDEWEB)

Wang, Jin; Li, Shuang; Peng, Xialian; Yu, Qing [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Department Chemistry and Chemical Engineering, Guangxi Normal University, Ministry of Education of China, Guilin 541004 (China); Bian, Hedong, E-mail: gxnuchem312@yahoo.com.cn [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Department Chemistry and Chemical Engineering, Guangxi Normal University, Ministry of Education of China, Guilin 541004 (China); Huang, Fuping [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Department Chemistry and Chemical Engineering, Guangxi Normal University, Ministry of Education of China, Guilin 541004 (China); Liang, Hong, E-mail: lianghongby@yahoo.com.cn [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Department Chemistry and Chemical Engineering, Guangxi Normal University, Ministry of Education of China, Guilin 541004 (China)

2013-04-15

Five spectroscopic techniques were used to investigate the interaction of astilbin (ASN) with human serum albumin (HSA). UV–vis absorption measurements prove that ASN–HSA complex can be formed. The analysis of fluorescence spectra reveal that in the presence of ASN, quenching mechanism of HSA is considered as static quenching. The quenching rate constant k{sub q}, K{sub SV} and the binding constant K were estimated. According to the van't Hoff equation, the thermodynamic parameters enthalpy change (ΔΗ) and entropy change (ΔS) were calculated to be −12.94 kJ mol{sup −1} and 35.92 J mol{sup −1} K{sup −1}, respectively. These indicate that the hydrophobic interaction is the major forces between ASN and HSA, but the hydrogen bond interaction cannot be excluded. The changes in the secondary structure of HSA which was induced by ASN were determined by circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and Raman spectroscopy. -- Graphical abstract: In this paper, the interaction of HSA with ASN was systematically studied under simulated physiological conditions by using UV–vis absorption, CD, FT-IR, fluorescence and Raman spectroscopic approaches. The quenching constant k{sub q}, K{sub SV} and the binding constant K were estimated. The changes in the secondary structure of HSA were studied by Circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and Raman spectroscopy. The UV–visible absorption spectra of HSA in the absence and presence of different concentration of ASN (1) and fluorescence spectra of HSA in the absence and the presence of ASN (2). Highlights: ► Interaction of ASN and HSA has been studied by five spectroscopic techniques. ► Hydrophobic interaction is the major forces between ASN and HSA. ► Binding of ASN induced the changes in the secondary structure of HSA.

Contribution to the study of the interactions between residual stresses and oxygen dissolution in a reactive deformable solid

International Nuclear Information System (INIS)

Raceanu, Laura

2011-01-01

The aim of this PhD work is to highlight the interactions between the mechanical stress and the chemical composition within diffusion of matter process for a reactive solid. The chronological evolution of our work goes from a parametric numerical study to an experimental study and reveals the role of mechanical stresses on the oxygen diffusion process. Different origins of mechanical stress were first numerically analysed from the point of view of their impacts on the process of oxygen diffusion into a metal (Zr) or a ceramic (UO 2 ) subjected to an oxidizing environment. This approach allowed us: - to identify a surface treatment (shot-peening) able to generate a residual specific stress field, as a starting point for an experimental study implementation in order to validate the numerical study conclusions; - to highlight the ability of the stress field on the stabilisation of the morphology of an undulated metal/oxide interface (case of Zr). In the experimental approach, different techniques were used to characterize the material (GDOS, SEM, TGA, hole-drilling method, micro-hardness tests). They permitted the detection of a strong influence of shot-peening on the oxidation rate. The comparison of experimental and numerical simulation results reveals strong interactions between stress and compositions fields induced by the different treatments (shot-peening and/or pre-oxidation). This study opens up many opportunities in the understanding of multi-physics coupling effects being very useful for the optimization of mechanical and chemical surface-treatments, able furthermore to favour the diffusion (nitriding, cementation) or to slow it down (corrosion). (author) [fr

A comparative study of polymer-dye interaction

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Nandini R.

2009-08-01

Full Text Available The interaction between an anionic dye Methyl Orange and two poly cations namely, Poly (N-vinyl-4-methylpyridiniumiodide, (PC1 & Poly (vinylbenzyltriphenylphosphoniumchloride, (PC2 has been investigated by spectrophotometric method. The polymers are observed to induce metachromasy in the dye as evidenced from the considerable blue shift in the absorption maximum of the dye. The interaction constant and thermodynamic parameters of interaction have been determined by absorbance measurements at the metachromatic band. The effect of additives such as ionic salts, alcohols, urea and polyelectrolytes on the reversal of metachromasy has been studied and used to determine the stability of the metachromatic complex and to understand the nature of binding.

Studying physician effects on patient outcomes: physician interactional style and performance on quality of care indicators.

Science.gov (United States)

Franks, Peter; Jerant, Anthony F; Fiscella, Kevin; Shields, Cleveland G; Tancredi, Daniel J; Epstein, Ronald M

2006-01-01

Many prior studies which suggest a relationship between physician interactional style and patient outcomes may have been confounded by relying solely on patient reports, examining very few patients per physician, or not demonstrating evidence of a physician effect on the outcomes. We examined whether physician interactional style, measured both by patient report and objective encounter ratings, is related to performance on quality of care indicators. We also tested for the presence of physician effects on the performance indicators. Using data on 100 US primary care physician (PCP) claims data on 1,21,606 of their managed care patients, survey data on 4746 of their visiting patients, and audiotaped encounters of 2 standardized patients with each physician, we examined the relationships between claims-based quality of care indicators and both survey-derived patient perceptions of their physicians and objective ratings of interactional style in the audiotaped standardized patient encounters. Multi-level models examined whether physician effects (variance components) on care indicators were mediated by patient perceptions or objective ratings of interactional style. We found significant physician effects associated with glycohemoglobin and cholesterol testing. There was also a clinically significant association between better patient perceptions of their physicians and more glycohemoglobin testing. Multi-level analyses revealed, however, that the physician effect on glycohemoglobin testing was not mediated by patient perceived physician interaction style. In conclusion, similar to prior studies, we found evidence of an apparent relationship between patient perceptions of their physician and patient outcomes. However, the apparent relationships found in this study between patient perceptions of their physicians and patient care processes do not reflect physician style, but presumably reflect unmeasured patient confounding. Multi-level modeling may contribute to better

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds.

Science.gov (United States)

Boast, Alexander P; Weyrich, Laura S; Wood, Jamie R; Metcalf, Jessica L; Knight, Rob; Cooper, Alan

2018-02-13

Over the past 50,000 y, biotic extinctions and declines have left a legacy of vacant niches and broken ecological interactions across global terrestrial ecosystems. Reconstructing the natural, unmodified ecosystems that preceded these events relies on high-resolution analyses of paleoecological deposits. Coprolites are a source of uniquely detailed information about trophic interactions and the behaviors, gut parasite communities, and microbiotas of prehistoric animal species. Such insights are critical for understanding the legacy effects of extinctions on ecosystems, and can help guide contemporary conservation and ecosystem restoration efforts. Here we use high-throughput sequencing (HTS) of ancient eukaryotic DNA from coprolites to reconstruct aspects of the biology and ecology of four species of extinct moa and the critically endangered kakapo parrot from New Zealand (NZ). Importantly, we provide evidence that moa and prehistoric kakapo consumed ectomycorrhizal fungi, suggesting these birds played a role in dispersing fungi that are key to NZ's natural forest ecosystems. We also provide the first DNA-based evidence that moa frequently supplemented their broad diets with ferns and mosses. Finally, we also find parasite taxa that provide insight into moa behavior, and present data supporting the hypothesis of coextinction between moa and several parasite species. Our study demonstrates that HTS sequencing of coprolites provides a powerful tool for resolving key aspects of ancient ecosystems and may rapidly provide information not obtainable by conventional paleoecological techniques, such as fossil analyses.

STUDY OF INTERACTION BETWEEN LEAD AND GASTRIC MUCOSAL PROTEIN OF RATS WITH FORENSIC TOXICOLOGY APPROACH

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Iwan Aflanie

2017-09-01

Full Text Available Abstract: Recently, forensic toxicology has been an interesting concern, especially in exposing the phenomena associated with the law. Using the forensic toxicology approach, several cases of lead (Pb poisoning have been widely revealed. In this present study will be investigate the interaction between Pb and amino acid gastric mucosal constituent proteins, especially cysteine and tyrosine groups. This research is a pure experimental research with posttest control group design, which is divided into 4 groups with 6 rats (Rattus novergicus in each group. Treatment in each group as follows; P0 was control group were given 2 ml of distilled water; P1 = administration of Pb 0.1 g/L; P2 = Pb administration of 1 mg/L; and P3 = Pb administration of 10 g/L for 4 weeks repectively. According to the results, it can be concluded that Pb-Protein interaction tends to binding of Pb-Cysteine rather than Pb-Tyrosine

Experimental Studies of Thermal Interactions at AEE Winfrith

International Nuclear Information System (INIS)

Briggs, A.J.

1976-01-01

Assessment of the consequences of very severe reactor accidents in which fuel is melted involves evaluation of the nature of any thermal interaction between molten fuel or cladding and the reactor coolant. Work on these problems has been pursued in many countries, both experimentally and theoretically, but although much progress has been made there is as yet no well established theoretical description of large scale efficient thermal interactions. The need for further experimental data in this area was one of the main reasons for establishing a new range of experimental facilities at Winfrith which provide the ability to carry out experiments involving explosions under safe conditions. Experiments are set up inside a strong test cell situated in the centre of a 200 m exclusion area. Instrumentation is provided for transient measurements of pressure and strain, and for high speed cine photography. The first part of this programme started early in 1975, and is concerned with the propagation of thermal interaction through a metal/water system. This programme is not yet complete but some results of interest have been obtained. The first part of this paper will describe these experiments and discuss the significance of the results currently available. Such studies of large scale metal/water interactions should help to provide an improved understanding of the way in which propagation might occur in the reactor case, but must be complemented by experiments using reactor materials. The second stage of the Winfrith programme will study the UO 2 /Na system directly. Facilities for the production of pure uranium burning thermite charges will be commissioned early in 1976. This chemical technique for producing molten UO 2 will be used in two main types of experiment. Firstly the interaction of a two phase bubble of UO 2 with a surrounding pool of Na will be studied, extending the investigations of this kind started at AWRE Foulness. Secondly, the heat transfer rate from UO 2

Gene-based testing of interactions in association studies of quantitative traits.

Directory of Open Access Journals (Sweden)

Li Ma

Full Text Available Various methods have been developed for identifying gene-gene interactions in genome-wide association studies (GWAS. However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene-gene interaction (GGG tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein-protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies.

The dynamic multisite interactions between two intrinsically disordered proteins

KAUST Repository

Wu, Shaowen

2017-05-11

Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a structured protein, while the Interaction between two IDPs is poorly understood. In this study, we combined NMR, smFRET, and molecular dynamics (MD) simulation to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by MD and mutagenesis studies. Our study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.

ISOLTRAP Mass Measurements for Weak-Interaction Studies

International Nuclear Information System (INIS)

Kellerbauer, A.; Delahaye, P.; Herlert, A.; Audi, G.; Guenaut, C.; Lunney, D.; Beck, D.; Herfurth, F.; Kluge, H.-J.; Mukherjee, M.; Rodriguez, D.; Weber, C.; Yazidjian, C.; Blaum, K.; Bollen, G.; Schwarz, S.; George, S.; Schweikhard, L.

2006-01-01

The conserved-vector-current (CVC) hypothesis of the weak interaction and the unitarity of the Cabibbo-Kobayashi-Maskawa (CKM) matrix are two fundamental postulates of the Standard Model. While existing data on CVC supports vector current conservation, the unitarity test of the CKM matrix currently fails by more than two standard deviations. High-precision mass measurements performed with the ISOLTRAP experiment at ISOLDE/CERN provide crucial input for these fundamental studies by greatly improving our knowledge of the decay energy of super-allowed β decays. Recent results of mass measurements on the β emitters 18Ne, 22Mg, 34Ar, and 74Rb as pertaining to weak-interaction studies are presented

FTIR Drug-Polymer Interactions Studies of Perindopril Erbumine

International Nuclear Information System (INIS)

Modni, A.; Ahmad, S.; Din, I.; Hussain, Z.

2014-01-01

The present study was carried out to prepare different combinations of Perindopril Erbumine with different polymers like Hydroxy propyl methyl cellulose, Hydroxy propyl methyl cellulose K4M, Hydroxy propyl methyl cellulose K15M, Xanthan gum and Ethyl cellulose, thereby to determine any possible interactions between Perindopril erbumine and polymers. The analytical technique Fourier Transform Infrared (FTIR) spectroscopy was used to take spectra of individual drug, polymers and combination of drug with polymers. The results were analyzed to find out any interactions of Perindopril erbumine and polymers. From this study it was concluded that there were no any significant changes in characteristic peaks of drug after combinations with polymers which indicated no interaction between Perindopril erbumine and polymers. (author)

Interactions of acetylated histones with DNA as revealed by UV laser induced histone-DNA crosslinking

International Nuclear Information System (INIS)

Stefanovsky, V.Yu.; Dimitrov, S.I.; Angelov, D.; Pashev, I.G.

1989-01-01

The interaction of acetylated histones with DNA in chromatin has been studied by UV laser-induced crosslinking histones to DNA. After irradiation of the nuclei, the covalently linked protein-DNA complexes were isolated and the presence of histones in them demonstrated immunochemically. When chromatin from irradiated nuclei was treated with clostripain, which selectively cleaved the N-terminal tails of core histones, no one of them was found covalently linked to DNA, thus showing that crosslinking proceeded solely via the N-terminal regions. However, the crosslinking ability of the laser was preserved both upon physiological acetylation of histones, known to be restricted to the N-terminal tails, and with chemically acetylated chromatin. This finding is direct evidence that the postsynthetic histone acetylation does not release the N-terminal tails from interaction with DNA

Microstructure, interparticle interactions and magnetotransport of manganite-polyaniline nanocomposites

Energy Technology Data Exchange (ETDEWEB)

Romero, Mariano; Faccio, Ricardo; Pardo, Helena [Centro NanoMat/Cryssmat Lab, DETEMA, Facultad de Química, Universidad de la República (Uruguay); Centro Interdisciplinario de Nanotecnología, Química y Física de Materiales, Espacio Interdisciplinario, Universidad de la República (Uruguay); Tumelero, Milton A. [Laboratorio de filmes finos e superficies, Departamento de Física, Universidad Federal de Santa Catarina, Florianópolis (Brazil); Campos Plá Cid, Cristiani [Laboratorio Central de Microscopia Electronica, Universidad Federal de Santa Catarina, Florianópolis (Brazil); Pasa, André A. [Laboratorio de filmes finos e superficies, Departamento de Física, Universidad Federal de Santa Catarina, Florianópolis (Brazil); Laboratorio Central de Microscopia Electronica, Universidad Federal de Santa Catarina, Florianópolis (Brazil); Mombrú, Álvaro W., E-mail: amombru@fq.edu.uy [Centro NanoMat/Cryssmat Lab, DETEMA, Facultad de Química, Universidad de la República (Uruguay); Centro Interdisciplinario de Nanotecnología, Química y Física de Materiales, Espacio Interdisciplinario, Universidad de la República (Uruguay)

2016-03-01

In this report, we present the study on the microstructure and interparticle interactions of manganite-polyaniline nanocomposites using grazing incidence small angle X-ray scattering (SAXS). In order to determine the nanoparticles mean diameter and correlation distances, data analysis was performed using the Guinier and Beaucage fits, in good agreement with transmission electron microscopy and X-ray diffraction analysis. The analysis of the interference functions revealed the existence of attractive interactions between nanoparticles. The nanocomposites with higher manganite concentration showed best fitting using the sticky hard sphere approximation. A weakening in the attractive interaction with increasing the dilution of nanoparticles in the polymer matrix was observed until a critical volume fraction (ϕ{sub c} ∼ 0.4) is reached, upon which the hard sphere approximation showed best fitting. The interaction potentials were estimated at room temperature revealing a decrease in the depth and width of the square well with increasing nanoparticle dilution. Coercive field and remanent magnetization showed a decrease with increasing polymer addition suggesting the declining of dipole–dipole interactions, in agreement with SAXS analysis. Magnetoresistance also showed an enhancement that could be probably associated to the decrease in the dipole–dipole interactions between ferromagnetic La{sub 2/3}Sr{sub 1/3}MnO{sub 3} (LSMO) nanoparticles at a critical separation distance in these nanocomposites. - Highlights: • A SAXS study on the microstructure of manganite-polyaniline nanocomposites is reported. • We report the presence of attractive interactions for the composites with higher concentration in manganite. • Interparticle dipole–dipole interactions were estimated by means of the SAXS interference function. • Coercive field and remanent magnetization studies showed agreement with SAXS analysis. • Magnetotransport showed an enhancement in relation to

Positive expectations encourage generalization from a positive intergroup interaction to outgroup attitudes.

Science.gov (United States)

Deegan, Matthew P; Hehman, Eric; Gaertner, Samuel L; Dovidio, John F

2015-01-01

The current research reveals that while positive expectations about an anticipated intergroup interaction encourage generalization of positive contact to outgroup attitudes, negative expectations restrict the effects of contact on outgroup attitudes. In Study 1, when Blacks and Whites interacted with positive expectations, interaction quality predicted outgroup attitudes to a greater degree than when groups interacted with negative expectations. When expectations (Studies 2 and 3) and the actual interaction quality (Study 4) were manipulated orthogonally, negative expectations about the interaction predicted negative outgroup attitudes, regardless of actual interaction quality. By contrast, participants holding positive expectations who experienced a positive interaction expressed positive outgroup attitudes, whereas when they experienced a negative interaction, they expressed outgroup attitudes as negative as those with negative expectations. Across all four studies, positive expectations encouraged developing outgroup attitudes consistent with interaction quality. © 2014 by the Society for Personality and Social Psychology, Inc.

Theoretical studies of molecular interactions

Energy Technology Data Exchange (ETDEWEB)

Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

1993-12-01

This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

Initial Development and Pilot Study Design of Interactive Lecture Demonstrations for ASTRO 101

Science.gov (United States)

Schwortz, Andria C.; French, D. A; Gutierrez, Joseph V; Sanchez, Richard L; Slater, Timothy F.; Tatge, Coty

2014-06-01

Interactive lecture demonstrations (ILDs) have repeatedly shown to be effective tools for improving student achievement in the context of learning physics. As a first step toward systematic development of interactive lecture demonstrations in ASTRO 101, the introductory astronomy survey course, a systematic review of education research, describing educational computer simulations (ECSs) reveals that initial development requires a targeted study of how ASTRO 101 students respond to ECSs in the non-science majoring undergraduate lecture setting. In this project we have adopted the process by which ILDs were designed, pilot-tested, and successfully implemented in the context of physics teaching (Sokoloff & Thornton, 1997; Sokoloff & Thornton, 2004). We have designed the initial pilot-test set of ASTRO 101 ILD instructional materials relying heavily on ECSs. Both an instructor’s manual and a preliminary classroom-ready student workbook have been developed, and we are implementing a pilot study to explore their effectiveness in communicating scientific content, and the extent to which they might enhance students’ knowledge of and perception about astronomy and science in general. The study design uses a pre-/post-test quasi-experimental study design measuring students’ normalized gain scores, calculated as per Hake (1998) and Prather (2009), using a slightly modified version of S. Slater’s (2011) Test Of Astronomy STandards TOAST combined with other instruments. The results of this initial study will guide the iterative development of ASTRO 101 ILDs that are intended to both be effective at enhancing student achievement and easy for instructors to successfully implement.

A Usability Study of Interactive Web-Based Modules

Science.gov (United States)

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…

Molecular interaction studies of acetylcholinesterase with potential acetylcholinesterase inhibitors from the root of Rhodiola crenulata using molecular docking and isothermal titration calorimetry methods.

Science.gov (United States)

Li, Fa-Jie; Liu, Yuan; Yuan, Yuan; Yang, Bin; Liu, Zhen-Ming; Huang, Lu-Qi

2017-11-01

(-)-Epicatechin gallate ((-)-ECG), 1,2,3,4,6-O-pentagalloylglucose (PGG), rhodionin, herbacetin and rhodiosin isolated from the root of Rhodiola crenulata exhibited potent, dose-dependent inhibitory effects on acetylcholinesterase (AChE) with IC 50 ranged from 57.50±5.83 to 2.43±0.34μg/mL. With the aim of explaining the differences in activity of these active ingredients and clarifying how they inhibit AChE, the AChE-inhibitor interactions were further explored using molecular docking and isothermal titration calorimetry (ITC) methods in the present study. Molecular docking studies revealed that all compounds except PGG showed binding energy values ranging from -10.30 to -8.00kcal/mol while the binding energy of galantamine, a known AChE inhibitor, was -9.53kcal/mol; they inhibited the AChE by binding into the ligand pocket with the similar binding pattern to that of galantamine by interacting with Glu199 of AChE. Inhibition constant of these active ingredients had a positive correlation with binding energy. The interaction between AChE and PGG was further evaluated with the ITC method and the results indicated that the PGG-AChE interaction was relevant to AChE concentration. The results revealed a possible mechanism for the AChE inhibition activity of these bioactive ingredients, which may provide some help in lead compounds optimization in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Snapshots of an Engineered Cystathionine-γ-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site

Energy Technology Data Exchange (ETDEWEB)

Yan, Wupeng; Stone, Everett; Zhang, Yan Jessie

2017-02-01

Enzyme therapeutics that can degrade l-methionine (l-Met) are of great interest as numerous malignancies are exquisitely sensitive to l-Met depletion. To exhaust the pool of methionine in human serum, we previously engineered an l-Met-degrading enzyme based on the human cystathionine-γ-lyase scaffold (hCGL-NLV) to circumvent immunogenicity and stability issues observed in the preclinical application of bacterially derived methionine-γ-lyases. To gain further insights into the structure–activity relationships governing the chemistry of the hCGL-NLV lead molecule, we undertook a biophysical characterization campaign that captured crystal structures (2.2 Å) of hCGL-NLV with distinct reaction intermediates, including internal aldimine, substrate-bound, gem-diamine, and external aldimine forms. Curiously, an alternate form of hCGL-NLV that crystallized under higher-salt conditions revealed a locally unfolded active site, correlating with inhibition of activity as a function of ionic strength. Subsequent mutational and kinetic experiments pinpointed that a salt bridge between the phosphate of the essential cofactor pyridoxal 5'-phosphate (PLP) and residue R62 plays an important role in catalyzing β- and γ-eliminations. Our study suggests that solvent ions such as NaCl disrupt electrostatic interactions between R62 and PLP, decreasing catalytic efficiency.

Immunohistochemical study of epithelial-myofibroblast interaction in Barrett metaplasia

Directory of Open Access Journals (Sweden)

Ochicha O

2010-04-01

Full Text Available Context: Sub-epithelial myofibroblasts are known to influence the biology (proliferation, differentiation and apoptosis of overlying epithelia. In the intestine, myofibroblasts have been demonstrated to be essential for epithelial differentiation. It is therefore hypothesized that myofibroblasts may also be involved in intestinal metaplasia that is characteristic of Barrett esophagus. Objective: This study endeavors to immunohistologically evaluate epithelial-myofibroblast interaction in Barrett′s metaplasia. Materials and Methods: Nineteen archival esophageal endoscopic biopsies of Barrett′s metaplasia were immune-phenotyped for the following epithelial and myofibroblast antigens - cytokeratins (CK 8, 13, 18, CDX2 (Caudal type homeobox 2, a-smooth muscle actin (SMA. Results: α-SMA immunostaining revealed close association between myofibroblasts and metaplastic Barrett′s epithelium but not with normal esophageal squamous epithelium. Myofibroblasts were more prominent in dysplastic than in non-dysplastic Barrett metaplasia. CDX2 and CK 8/18, indicators of intestinal differentiation were expressed in Barrett metaplasia but not normal esophageal squamous epithelium, while the reverse was the case for CK 13, which only stained normal esophageal squamous epithelium. Conclusion: Although their precise role is yet to be clearly defined, sub-epithelial myofibroblasts are very likely involved in the pathogenesis of Barrett′s metaplasia.

Study on the Interaction between Two Hydrokinetic Savonius Turbines

Directory of Open Access Journals (Sweden)

Kailash Golecha

2012-01-01

Full Text Available Savonius turbine is simple in design and easy to fabricate at a lower cost. The drag is the basic driving force for Savonius turbine. Savonius turbines are mainly used for the small-scale electricity generation in remote areas. In real life, multiple Savonius turbines are to be arranged to form a farm to scale up the electricity generation. So, it is important to study the interaction among them to avoid the power loss due to negative interaction between turbines. The purpose of this investigation is to examine closely the effect of interaction between two Savonius turbines arranged in line. Experimental investigations are carried out to study the mutual interaction between turbines with water as the working medium at a Reynolds number of 1.2×105 based on the diameter of the turbine. Influence of separation gap between the two Savonius turbines is studied by varying the separation gap ratio (/ from 3 to 8. As the separation gap ratio increases from 3 to 8, becomes lesser the mutual interaction between the turbines. Results conclude that two turbines placed at a separation gap ratio of 8 performed independently without affecting the performance of each other.

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.

Directory of Open Access Journals (Sweden)

Jens Christian Claussen

2017-06-01

Full Text Available The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.

Case-only study of interactions between metabolic enzymes and smoking in colorectal cancer

International Nuclear Information System (INIS)

Fan, Chunhong; Jin, Mingjuan; Chen, Kun; Zhang, Yongjing; Zhang, Shuangshuang; Liu, Bing

2007-01-01

Gene-gene and gene-environment interactions involved in the metabolism of carcinogens may increase the risk of cancer. Our objective was to measure the interactions between common polymorphisms of P450 (CYP1A2, CYP1B1, CYP2E1), GSTM1 and T1, SULT1A1 and cigarette smoking in colorectal cancer (CRC). A case-only design was conducted in a Chinese population including 207 patients with sporadic CRC. Unconditional logistic regression analysis was performed adjusting for age, gender, alcohol consumption, and cigarette smoking. The interaction odds ratio (COR) for the gene-gene interaction between CYP1B1 1294G and SULT1A1 638A allele was 2.68 (95% CI: 1.16–6.26). The results of the gene-environment analyses revealed that an interaction existed between cigarette smoking and the CYP1B1 1294G allele for CRC (COR = 2.62, 95%CI: 1.01–6.72), the COR for the interaction of CYP1B1 1294G and smoking history > 35 pack-years was 3.47 (95%CI: 1.12–10.80). No other significant gene-gene and gene-environment interactions were observed. Our results showed that the interaction between polymorphisms in CYP1B1 1294G and SULT1A1*2 may play a significant role on CRC in the Chinese population. Also, it is suggested that the association between cigarette smoking and CRC could be differentiated by the CYP1B1 1294G allele

Vibrational, calorimetric, and molecular conformational study on calcein interaction with model lipid membrane

International Nuclear Information System (INIS)

Maherani, Behnoush; Arab-Tehrany, Elmira; Rogalska, Ewa; Korchowiec, Beata; Kheirolomoom, Azadeh; Linder, Michel

2013-01-01

Nanoliposomes are commonly used as a carrier in controlled release drug delivery systems. Controlled release formulations can be used to reduce the amount of drug necessary to cause the same therapeutic effect in patients. One of the most noticeable factors in release profiles is the strength of the drug-carrier interaction. To adjust the pharmacokinetic and pharmacodynamic properties of therapeutic agents, it is necessary to optimize the drug-carrier interaction. To get a better understanding of this interaction, large unilamellar liposomes containing calcein were prepared using 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1,2-palmitoyl-sn-glycero-3-phosphocholine, and a mixture of them; calcein was chosen as a model polar molecule of biological interest. The thermodynamic changes induced by calcein and its location in lipid bilayers were determined by differential scanning calorimetry and Raman spectroscopy, respectively. The results reveal that calcein has no significant influence on thermotropic properties of the lipid membrane, but causing the abolition of pre-transition. The decreasing of the pre-transition can be ascribed to the presence of calcein near the hydrophilic cooperative zone of the bilayer. The change in intensity of the Raman peaks represents the interaction of calcein with choline head groups. Moreover, the impact of calcein on phosphoglyceride Langmuir layers spread at the air–water interface was studied using surface pressure-area and surface potential-area isotherms, as well as polarization-modulation infrared reflection–absorption spectroscopy and Brewster angle microscopy. The results obtained indicate that calcein introduce no major modification on the systems prepared with pure lipids

Mental health and social networks in early adolescence: a dynamic study of objectively-measured social interaction behaviors.

Science.gov (United States)

Pachucki, Mark C; Ozer, Emily J; Barrat, Alain; Cattuto, Ciro

2015-01-01

How are social interaction dynamics associated with mental health during early stages of adolescence? The goal of this study is to objectively measure social interactions and evaluate the roles that multiple aspects of the social environment--such as physical activity and food choice--may jointly play in shaping the structure of children's relationships and their mental health. The data in this study are drawn from a longitudinal network-behavior study conducted in 2012 at a private K-8 school in an urban setting in California. We recruited a highly complete network sample of sixth-graders (n = 40, 91% of grade, mean age = 12.3), and examined how two measures of distressed mental health (self-esteem and depressive symptoms) are positionally distributed in an early adolescent interaction network. We ascertained how distressed mental health shapes the structure of relationships over a three-month period, adjusting for relevant dimensions of the social environment. Cross-sectional analyses of interaction networks revealed that self-esteem and depressive symptoms are differentially stratified by gender. Specifically, girls with more depressive symptoms have interactions consistent with social inhibition, while boys' interactions suggest robustness to depressive symptoms. Girls higher in self-esteem tended towards greater sociability. Longitudinal network behavior models indicate that gender similarity and perceived popularity are influential in the formation of social ties. Greater school connectedness predicts the development of self-esteem, though social ties contribute to more self-esteem improvement among students who identify as European-American. Cross-sectional evidence shows associations between distressed mental health and students' network peers. However, there is no evidence that connected students' mental health status becomes more similar in their over time because of their network interactions. These findings suggest that mental health during early

XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation

DEFF Research Database (Denmark)

Mortuza, Gulnahar B; Cavazza, Tommaso; Garcia-Mayoral, Maria Flor

2014-01-01

215 (chTOG), dissecting the mechanism by which their interaction promotes microtubule elongation during spindle assembly. Using SAXS, we show that the TACC domain (TD) is an elongated structure that mediates the interaction with the C terminus of XMAP215. Our data suggest that one TD and two XMAP215...... molecules associate to form a four-helix coiled-coil complex. A hybrid methods approach was used to define the precise regions of the TACC heptad repeat and the XMAP215 C terminus required for assembly and functioning of the complex. We show that XTACC3 can induce the recruitment of larger amounts of XMAP...

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

Science.gov (United States)

Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

2011-02-01

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

Comparison of multivariate methods for studying the G×E interaction

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Deoclécio Domingos Garbuglio

2015-12-01

Full Text Available The objective of this work was to evaluate three statistical multivariate methods for analyzing adaptability and environmental stratification simultaneously, using data from maize cultivars indicated for planting in the State of Paraná-Brazil. Under the FGGE and GGE methods, the genotypic effect adjusts the G×E interactions across environments, resulting in a high percentage of explanation associated with a smaller number of axes. Environmental stratification via the FGGE and GGE methods showed similar responses, while the AMMI method did not ensure grouping of environments. The adaptability analysis revealed low divergence patterns of the responses obtained through the three methods. Genotypes P30F35, P30F53, P30R50, P30K64 and AS 1570 showed high yields associated with general adaptability. The FGGE method allowed differences in yield responses in specific regions and the impact in locations belonging to the same environmental group (through rE to be associated with the level of the simple portion of the G×E interaction.

Neutron Scattering Studies of Nano-Scale Wood-Water Interactions

Science.gov (United States)

Plaza Rodriguez, Nayomi Z.

Understanding and controlling water in wood is critical to both improving forest products moisture durability and developing new sustainable forest products-based technologies. While wood is known to be hygroscopic, there is still a lack of understanding on the nanoscale wood-water interactions necessary for increased moisture-durability and dimensional stability. My PhD thesis focuses on the development and implementation of neutron scattering methods that can provide insight on both the structural and dynamical changes associated with these interactions so that products with improved moisture durability can be developed efficiently. Using small angle neutron scattering (SANS) and a custom-built in situ relative humidity chamber I studied the anisotropic moisture-induced swelling of wood nanostructure. First, I studied the effects of sample preparation by comparing SANS patterns of wiley milled wood and intact latewood cell walls, and found that scattering from intact wood provide more information about the spatial arrangement of the wood nanostructures inside the cell wall. Comparisons between SANS patterns from earlywood and latewood, also showed that the higher cell wall density of latewood cell walls results in patterns with more pronounced anisotropic features. Then, by measuring latewood loblolly pine sections obtained from the same growth ring and prepared in each of the primary wood planes, I tracked the cellulose elementary fibril spacing as a function of humidity in both intact and partially cut cell walls. These studies showed that even though swelling at the elementary fibril spacing is responsible for the majority of the transverse swelling observed at the S2 level, it is not primary plane dependent. Additionally, there were no differences in the elementary fibril spacing between partially-cut and intact cell walls, except at high humidity where the spacing in partially-cut cells was higher. SANS was also used to study the effects of two chemical

In vivo Host-Pathogen Interaction as Revealed by Global Proteomic Profiling of Zebrafish Larvae

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Francisco Díaz-Pascual

2017-07-01

Full Text Available The outcome of a host-pathogen interaction is determined by the conditions of the host, the pathogen, and the environment. Although numerous proteomic studies of in vitro-grown microbial pathogens have been performed, in vivo proteomic approaches are still rare. In addition, increasing evidence supports that in vitro studies inadequately reflect in vivo conditions. Choosing the proper host is essential to detect the expression of proteins from the pathogen in vivo. Numerous studies have demonstrated the suitability of zebrafish (Danio rerio embryos as a model to in vivo studies of Pseudomonas aeruginosa infection. In most zebrafish-pathogen studies, infection is achieved by microinjection of bacteria into the larvae. However, few reports using static immersion of bacterial pathogens have been published. In this study we infected 3 days post-fertilization (DPF zebrafish larvae with P. aeruginosa PAO1 by immersion and injection and tracked the in vivo immune response by the zebrafish. Additionally, by using non-isotopic (Q-exactive metaproteomics we simultaneously evaluated the proteomic response of the pathogen (P. aeruginosa PAO1 and the host (zebrafish. We found some zebrafish metabolic pathways, such as hypoxia response via HIF activation pathway, were exclusively enriched in the larvae exposed by static immersion. In contrast, we found that inflammation mediated by chemokine and cytokine signaling pathways was exclusively enriched in the larvae exposed by injection, while the integrin signaling pathway and angiogenesis were solely enriched in the larvae exposed by immersion. We also found important virulence factors from P. aeruginosa that were enriched only after exposure by injection, such as the Type-III secretion system and flagella-associated proteins. On the other hand, P. aeruginosa proteins involved in processes like biofilm formation, and cellular responses to antibiotic and starvation were enriched exclusively after exposure by

In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies.

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Abo Dena, Ahmed S; Abdel Gaber, Sara A

2017-06-15

Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1 HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV. Copyright © 2017 Elsevier B.V. All rights reserved.

In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies

Science.gov (United States)

Abo Dena, Ahmed S.; Abdel Gaber, Sara A.

2017-06-01

Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV.

Ab initio study of interaction of helium with edge and screw dislocations in tungsten

Energy Technology Data Exchange (ETDEWEB)

Bakaev, Alexander, E-mail: bakaev_vic@mail.ru [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation); Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden (Germany); Terentyev, Dmitry [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Grigorev, Petr [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation); Ghent University, Applied Physics EA17 FUSION-DC, St. Pietersnieuwstraat, 41 B4, B-9000 Gent (Belgium); Posselt, Matthias [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden (Germany); Zhurkin, Evgeny E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation)

2017-02-15

Highlights: • Both screw (SD) and edge dislocations (ED) offer trapping sites for He in tungsten. • He atom is attracted to SD and ED with the interaction energy of ~1.3 and ~3.0 eV, respectively. • The attraction of He to dislocations can contribute to the nucleation of He clusters at high T. - Abstract: The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of −1.3 and −3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.

Ab initio study of interaction of helium with edge and screw dislocations in tungsten

International Nuclear Information System (INIS)

Bakaev, Alexander; Terentyev, Dmitry; Grigorev, Petr; Posselt, Matthias; Zhurkin, Evgeny E.

2017-01-01

Highlights: • Both screw (SD) and edge dislocations (ED) offer trapping sites for He in tungsten. • He atom is attracted to SD and ED with the interaction energy of ~1.3 and ~3.0 eV, respectively. • The attraction of He to dislocations can contribute to the nucleation of He clusters at high T. - Abstract: The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of −1.3 and −3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.

A computational study of anion-modulated cation-π interactions.

Science.gov (United States)

Carrazana-García, Jorge A; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M

2012-05-24

The interaction of anions with cation-π complexes formed by the guanidinium cation and benzene was thoroughly studied by means of computational methods. Potential energy surface scans were performed in order to evaluate the effect of the anion coming closer to the cation-π pair. Several structures of guanidinium-benzene complexes and anion approaching directions were examined. Supermolecule calculations were performed on ternary complexes formed by guanidinium, benzene, and one anion and the interaction energy was decomposed into its different two- and three-body contributions. The interaction energies were further dissected into their electrostatic, exchange, repulsion, polarization and dispersion contributions by means of local molecular orbital energy decomposition analysis. The results confirm that, besides the electrostatic cation-anion attraction, the effect of the anion over the cation-π interaction is mainly due to polarization and can be rationalized following the changes in the anion-π and the nonadditive (three-body) terms of the interaction. When the cation and the anion are on the same side of the π system, the three-body interaction is anticooperative, but when the anion and the cation are on opposite sides of the π system, the three-body interaction is cooperative. As far as we know, this is the first study where this kind of analysis is carried out with a structured cation as guanidinium with a significant biological interest.

Exploring the interaction between Salvia miltiorrhiza and human serum albumin: Insights from herb-drug interaction reports, computational analysis and experimental studies

Science.gov (United States)

Shao, Xin; Ai, Ni; Xu, Donghang; Fan, Xiaohui

2016-05-01

Human serum albumin (HSA) binding is one of important pharmacokinetic properties of drug, which is closely related to in vivo distribution and may ultimately influence its clinical efficacy. Compared to conventional drug, limited information on this transportation process is available for medicinal herbs, which significantly hampers our understanding on their pharmacological effects, particularly when herbs and drug are co-administrated as polytherapy to the ailment. Several lines of evidence suggest the existence of Salvia miltiorrhiza-Warfarin interaction. Since Warfarin is highly HSA bound in the plasma with selectivity to site I, it is critical to evaluate the possibility of HSA-related herb-drug interaction. Herein an integrated approach was employed to analyze the binding of chemicals identified in S. miltiorrhiza to HSA. Molecular docking simulations revealed filtering criteria for HSA site I compounds that include docking score and key molecular determinants for binding. For eight representative ingredients from the herb, their affinity and specificity to HSA site I was measured and confirmed fluorometrically, which helps to improve the knowledge of interaction mechanisms between this herb and HSA. Our results indicated that several compounds in S. miltiorrhiza were capable of decreasing the binding constant of Warfarin to HSA site I significantly, which may increase free drug concentration in vivo, contributing to the herb-drug interaction observed clinically. Furthermore, the significance of HSA mediated herb-drug interactions was further implied by manual mining on the published literatures on S. miltiorrhiza.

The Clopidogrel-PPI Interaction

DEFF Research Database (Denmark)

Juel, Jacob; Pareek, Manan; Jensen, Svend Eggert

2014-01-01

the potential for PPIs, especially omeprazole, to decrease the efficacy of clopidogrel, and both the U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) have issued warnings regarding the concomitant use of these medications. A review of the literature revealed that the pharmacodynamic...... studies support an interaction, whereas the clinical evidence, which is mainly based on nonrandomized, observational studies and secondary analyses of randomized trials, is conflicting. We conclude that PPIs should be prescribed together with DAPT for patients in whom they are recommended according...

Studies on the interaction of the food colorant tartrazine with double stranded deoxyribonucleic acid.

Science.gov (United States)

Basu, Anirban; Suresh Kumar, Gopinatha

2016-05-01

Interaction of the food additive tartrazine with double-stranded DNA was studied by spectroscopic and calorimetric techniques. Absorbance studies revealed that tartrazine exhibited hypochromism in the presence of DNA without any bathochromic effects. Minor groove displacement assay of DAPI and Hoechst 33258 suggested that tartrazine binds in the minor groove of DNA. The complexation was predominantly entropy driven with a smaller but favorable enthalpic contribution to the standard molar Gibbs energy. The equilibrium constant was evaluated to be (3.68 ± .08) × 10(4) M(-1) at 298.15 K. The negative standard molar heat capacity value along with an enthalpy-entropy compensation phenomenon proposed the involvement of dominant hydrophobic forces in the binding process. Tartrazine enhanced the thermal stability of DNA by 7.53 K under saturation conditions.

Interweaving interactions in virtual worlds: a case study.

Science.gov (United States)

Cantamesse, Matteo; Galimberti, Carlo; Giacoma, Gianandrea

2011-01-01

The aim of this study was to examine the effect of playing the online game World of Warcraft (WoW), both on adolescent's (effective) social interaction and on the competence they developed on it. Social interactions within the game environment have been investigated by integrating qualitative and quantitative methods: conversation analysis and social network analysis (SNA). From a psychosocial point of view, the in-game interactions, and in particular conversational exchanges, turn out to be a collaborative path of the joint definition of identities and social ties, with reflection on in-game processes and out-game relationship.

Culture matters : a study on presence in an interactive movie

NARCIS (Netherlands)

Hu, J.; Bartneck, C.

2008-01-01

A cross cultural study was conducted to test the influences of different cultural backgrounds on the user's presence experience in interacting with a distributed interactive movie. The effects of embodied interaction on presence were also investigated because embodiment is often used to enrich the

Interaction effect study on stress reaction and job burnout, personality, self-esteem in radiological medical personnel

International Nuclear Information System (INIS)

Li Linlin; Feng Liyun; Yang Yanyan; Wu Di

2009-01-01

Objective: To explore interaction effect between stress reaction and job burnout, personality, self-esteem in radiological medical personnel with path analysis. Methods: 728 radiological medical personnels were investigated with Maslach burnout Inventory-General Survey (MBI-GS), Chinese Perceived Stress Scale (CPSS), Eysenck Personality Questionnaire (EPQ) and Self-esteem Scale. Results: Multiple regression and path analysis revealed that there were statistically significant relation between stress reaction and job burnout, Personality and self-esteem. Conclusion: Psychological stress is a complicated and multiple interaction of psychological stress related factors. (authors)

Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics

DEFF Research Database (Denmark)

Yang, Fen; Braga, Marcella Nunes de Melo; Larsen, Martin Røssel

2013-01-01

The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat-S. tritici interaction, we performed a time-course study of S. tritici infection...... in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during...... compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger...

Revealing molecular mechanisms by integrating high-dimensional functional screens with protein interaction data.

Directory of Open Access Journals (Sweden)

Angela Simeone

2014-09-01

Full Text Available Functional genomics screens using multi-parametric assays are powerful approaches for identifying genes involved in particular cellular processes. However, they suffer from problems like noise, and often provide little insight into molecular mechanisms. A bottleneck for addressing these issues is the lack of computational methods for the systematic integration of multi-parametric phenotypic datasets with molecular interactions. Here, we present Integrative Multi Profile Analysis of Cellular Traits (IMPACT. The main goal of IMPACT is to identify the most consistent phenotypic profile among interacting genes. This approach utilizes two types of external information: sets of related genes (IMPACT-sets and network information (IMPACT-modules. Based on the notion that interacting genes are more likely to be involved in similar functions than non-interacting genes, this data is used as a prior to inform the filtering of phenotypic profiles that are similar among interacting genes. IMPACT-sets selects the most frequent profile among a set of related genes. IMPACT-modules identifies sub-networks containing genes with similar phenotype profiles. The statistical significance of these selections is subsequently quantified via permutations of the data. IMPACT (1 handles multiple profiles per gene, (2 rescues genes with weak phenotypes and (3 accounts for multiple biases e.g. caused by the network topology. Application to a genome-wide RNAi screen on endocytosis showed that IMPACT improved the recovery of known endocytosis-related genes, decreased off-target effects, and detected consistent phenotypes. Those findings were confirmed by rescreening 468 genes. Additionally we validated an unexpected influence of the IGF-receptor on EGF-endocytosis. IMPACT facilitates the selection of high-quality phenotypic profiles using different types of independent information, thereby supporting the molecular interpretation of functional screens.

The influence of interactive technology on student performance in an Oklahoma secondary Biology I program

Science.gov (United States)

Feltman, Vallery

Over the last decade growth in technologies available to teach students and enhance curriculum has become an important consideration in the educational system. The profile of today's secondary students have also been found to be quite different than those of the past. Their learning styles and preferences are issues that should be addressed by educators. With the growth and availability of new technologies students are increasingly expecting to use these as learning tools in their classrooms. This study investigates how interactive technology may impact student performance. This study specifically focuses on the use of the Apple Ipad in 4 Biology I classrooms. This study used an experimental mixed method design to examine how using Ipads for learning impacted student achievement, motivation to learn, and learning strategies. Qualitatively the study examined observed student behaviors and student perceptions regarding the use of interactive technologies. Data was analyzed using descriptive statistics, t-tests, 2-way ANOVAs, and qualitative analysis. Quantitatively the results revealed no significant difference between students who used the interactive technology to learn and those who did not. Qualitative data revealed behaviors indicative of being highly engaged with the subject matter and the development of critical thinking skills which may improve student performance. Student perceptions also revealed overall positive experiences with using interactive technology in the classroom. It is recommended that further studies be done to look at using interactive technologies for a longer period of time using multiple subjects areas. This would provide a more in-depth exploration of interactive technologies on student achievement.

Host-guest interaction of styrene and ethylbenzene in MIL-53 studied by solid-state NMR.

Science.gov (United States)

Li, Shenhui; Li, Jing; Tang, Jing; Deng, Feng

Solid-state NMR was utilized to explore the host-guest interaction between adsorbate and adsorbent at atomic level to understand the separation mechanism of styrene (St) and ethylbenzene (EB) in MIL-53(Al). 13 C- 27 Al double-resonance NMR experiments revealed that the host-guest interaction between St and MIL-53 was much stronger than that of EB adsorption. In addition, 13 C DIPSHIFT experiments suggested that the adsorbed St was less mobile than EB confined inside the MIL-53 pore. Furthermore, the host-guest interaction model between St, EB and MIL-53 was established on the basis of the spatial proximities information extracted from 2D 1 H- 1 H homo-nuclear correlation NMR experiments. According to the experimental observation from solid-state NMR, it was found that the presence of π-π interaction between St and MIL-53 resulted in the stronger host-guest interaction and less mobility of St. This work provides direct experimental evidence for understanding the separation mechanism of St and EB using MIL-53 as an adsorbent. Copyright © 2017 Elsevier Inc. All rights reserved.

Virtually naked: virtual environment reveals sex-dependent nature of skin disclosure.

Directory of Open Access Journals (Sweden)

Anna M Lomanowska

Full Text Available The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings.

Using interactive video technology in nursing education: a pilot study.

Science.gov (United States)

Zerr, Daria M; Pulcher, Karen L

2008-02-01

A pilot study was conducted to analyze the benefits of using interactive technology with external assessors and graduating senior nursing students during Senior Nurse Leadership Assessment Day at the University of Central Missouri. The primary aim was to determine whether videoconferencing technology would promote recruitment and retention of professional nurse external assessors without compromising student learning. Among the issues discussed are the advantages and disadvantages of using interactive videoconferencing technology in education and the influence of external assessors in nursing education. The study results indicate that interactive videoconferencing is an effective, accepted format for educational opportunities such as Senior Nurse Leadership Assessment Day, based on the lived experiences of the study participants. In addition, the results demonstrate that interactive videoconferencing does not compromise student learning or assessment by external assessors.

Antagonistic studies and hyphal interactions of the new antagonist Aspergillus piperis against some phytopathogenic fungi in vitro in comparison with Trichoderma harzianum.

Science.gov (United States)

El-Debaiky, Samah A

2017-12-01

The present study represents, for the first time, the detailed studies about the hyphal interactions of Aspergillus piperis, as a new antagonist, against some isolated plant pathogenic fungi (Alternaria alternata, Alternaria solani, Botrytis cinerea, Sclerotium cepivorum and Sclerotinia sclerotiorum) in vitro. The bio-controlling capability of A. piperis against the tested phytopathogens was tested using the dual culture method. This experiment revealed that A. piperis had antagonistic activity and reduced the growth of the tested phytopathogens and grew over their mycelia in the paired plates. Also, several antagonistic mechanisms were recorded, in this study, between A. piperis and the tested phytopathogens using the microscopic examination. The bio-controlling activity and the antagonistic mechanisms exhibited by the new antagonist, A. piperis were compared with those obtained by the common antagonist, Trichoderma harzianum against the same phytopathogens. The obtained results showed that, A. piperis was more effective than T. harzianum in inhibiting all the tested species in the dual culture plates. The best result was 81.85% inhibition percentage against S. sclerotiorum by A. piperis while, T. harzianum exhibits only 45.18%. Moreover, several antagonistic mechanisms and hyphal interactions were investigated among the hyphae of both A.piperis and T. harzianum and the hyphae of the tested phytopathogens. These mechanisms were summarized as; mycoparasitism (coiling and penetration of the hyphae) and antibiosis in the form of lysis of the hyphal cells and spores, denaturation and breaking of the hyphae. The indirect interaction (antibiosis) and the direct mycoparasitism were observed by A. piperis against all the tested phytopathogens, but it attacked the hyphae and conidiophores of A. alternata by only the antibiosis interaction. The microscopic examination revealed also that T. harzianum attacked the tested phytopathogens by both antibiosis and mycoparasitism

Context and Crossmodal Interactions: An ERP Study

Directory of Open Access Journals (Sweden)

Beatriz R Sarmiento

2011-10-01

Full Text Available In a previous behavioural study, we reported that a particular context of stimulus congruency influenced audiovisual interactions. In particular, audiovisual interaction, measured in terms of congruency effect, was reduced when a high proportion of incongruent trials was presented. We argued that this modulation was due to changes in participants' control set as a function of the context of congruency, with greater control applied when most of the trials were incongruent. Since behavioural data do not allow to specify the level at which control was affecting audiovisual interaction, we conducted an event-related potentials (ERPs study to further investigate each context of audiovisual congruency. Participants performed an audiovisual congruency task, where the stimulus onset could be present on two different contexts mixed at random: a high proportion congruent context and a low proportion congruent context. The context manipulation was found to modulate brain ERPs related to perceptual and response selection processes, ie, the N2 and P3 components. The N2 amplitude was larger for the less common trials on both high and low congruent proportion contexts, while the P3 amplitude and latency were differentially modulated by incongruent trials on the two contexts.

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

Science.gov (United States)

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

2015-11-03

Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Analysis of a summary network of co-infection in humans reveals that parasites interact most via shared resources

OpenAIRE

Griffiths, Emily C; Pedersen, Amy B; Fenton, Andy; Petchey, Owen L

2014-01-01

Simultaneous infection by multiple parasite species (viruses, bacteria, helminths, protozoa or fungi) is commonplace. Most reports show co-infected humans to have worse health than those with single infections. However, we have little understanding of how co-infecting parasites interact within human hosts. We used data from over 300 published studies to construct a network that offers the first broad indications of how groups of co-infecting parasites tend to interact. The network had three l...

Physiologically-Relevant Modes of Membrane Interactions by the Human Antimicrobial Peptide, LL-37, Revealed by SFG Experiments

Science.gov (United States)

Ding, Bei; Soblosky, Lauren; Nguyen, Khoi; Geng, Junqing; Yu, Xinglong; Ramamoorthy, Ayyalusamy; Chen, Zhan

2013-05-01

Antimicrobial peptides (AMPs) could become the next generation antibiotic compounds which can overcome bacterial resistance by disrupting cell membranes and it is essential to determine the factors underlying its mechanism of action. Although high-resolution NMR and other biological studies have provided valuable insights, it has been a major challenge to follow the AMP-membrane interactions at physiologically-relevant low peptide concentrations. In this study, we demonstrate a novel approach to overcome this major limitation by performing Sum Frequency Generation (SFG) vibrational spectroscopic experiments on lipid bilayers containing an AMP, LL-37. Our results demonstrate the power of SFG to study non-linear helical peptides and also infer that lipid-peptide interaction and the peptide orientation depend on the lipid membrane composition. The observed SFG signal changes capture the aggregating process of LL-37 on membrane. In addition, our SFG results on cholesterol-containing lipid bilayers indicate the inhibition effect of cholesterol on peptide-induced membrane permeation process.

Study of the interaction between fluoxetine hydrochloride and bovine serum albumin in the imitated physiological conditions by multi-spectroscopic methods

International Nuclear Information System (INIS)

Katrahalli, Umesha; Jaldappagari, Seetharamappa; Kalanur, Shankara S.

2010-01-01

The mechanism of interaction of an antidepressant, fluoxetine hydrochloride (FLX) with bovine serum albumin (BSA) has been studied by different spectroscopic techniques under physiological conditions. FLX was found to quench the intrinsic fluorescence of protein by static quenching mechanism. The binding constant 'K' was found to be 7.06x10 3 M -1 at 296 K. The value of 'n' close to unity revealed that the BSA has a single class of binding site for FLX. Based on thermodynamic parameters, hydrogen bonding and van der Waals forces were proposed to operate between BSA and FLX. The change in conformation of protein was noticed upon its interaction with the drug. From displacement studies it was concluded that the FLX bound to protein at site I. The effects of various common metals ions on the binding were also investigated.

Comparative Interactions of Dihydroquinazolin Derivatives with Human Serum Albumin Observed via Multiple Spectroscopy

Directory of Open Access Journals (Sweden)

Yi Wang

2017-02-01

Full Text Available The interactions of dihydroquinazolines with human serum albumin (HSA were studied in pH 7.4 aqueous solution via fluorescence, circular dichroism (CD and Fourier transform infrared (FTIR spectroscopic techniques. In this work, 6-chloro-1-(3,3-dimethyl-butanoyl-2(unsubstitutedphenyl-2,3-dihydroquinazolin-4(1H-one (PDQL derivatives were designed and synthesized to study the impact of five similar substituents (methyl, methoxy, cyano, trifluoromethyl and isopropyl on the interactions between PDQL and HSA using a comparative methodology. The results revealed that PDQL quenched the intrinsic fluorescence of HSA through a static quenching process. Displacement experiments with site-specific markers revealed that PDQL binds to HSA at site II (subdomain IIIA and that there may be only one binding site for PDQL on HSA. The thermodynamic parameters indicated that hydrophobic interactions mainly drove the interactions between PDQL and HSA. The substitution using five similar groups in the benzene ring could increase the interactions between PDQL and HSA to some extent through the van der Waals force or hydrogen bond effects in the proper temperature range. Isopropyl substitution could particularly enhance the binding affinity, as observed via comparative studies

Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel.

Science.gov (United States)

Cieslak, John A; Focia, Pamela J; Gross, Adrian

2010-02-23

Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that (31)P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the (31)P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.

Interaction studies of resistomycin from Streptomyces aurantiacus AAA5 with calf thymus DNA and bovine serum albumin

Science.gov (United States)

Vijayabharathi, R.; Sathyadevi, P.; Krishnamoorthy, P.; Senthilraja, D.; Brunthadevi, P.; Sathyabama, S.; Priyadarisini, V. Brindha

2012-04-01

Resistomycin, a secondary metabolite produced by Streptomyces aurantiacus AAA5. The binding interaction of resistomycin with calf thymus DNA (CT DNA) and bovine serum albumin (BSA) was investigated by spectrophotometry, spectrofluorimetry, circular dichroism (CD) and synchronous fluorescence techniques under physiological conditions in vitro. Absorption spectral studies along with the fluorescence competition with ethidium bromide measurements and circular dichroism clearly suggest that the resistomycin bind with CT DNA relatively strong via groove binding. BSA interaction results revealed that the drug was found to quench the fluorescence intensity of the protein through a static quenching mechanism. The number of binding sites 'n' and apparent binding constant 'K' calculated according to the Scatchard equation exhibit a good binding property to bovine serum albumin protein. In addition, the results observed from synchronous fluorescence measurements clearly demonstrate the occurrence of conformational changes of BSA upon addition of the test compound.

DFT study of the interaction between DOTA chelator and competitive alkali metal ions.

Science.gov (United States)

Frimpong, E; Skelton, A A; Honarparvar, B

2017-09-01

1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetracetic acid (DOTA) is an important chelator for radiolabeling of pharmaceuticals. The ability of alkali metals found in the body to complex with DOTA and compete with radio metal ions can alter the radiolabeling process. Non-covalent interactions between DOTA complexed with alkali metals Li + , Na + , K + and Rb + , are investigated with density functional theory using B3LYP and ωB97XD functionals. Conformational possibilities of DOTA were explored with a varying number of carboxylic pendant arms of DOTA in close proximity to the ions. It is found that the case in which four arms of DOTA are interacting with ions is more stable than other conformations. The objective of this study is to explore the electronic structure properties upon complexation of alkali metals Li + Na + , K + and Rb + with a DOTA chelator. Interaction energies, relaxation energies, entropies, Gibbs free energies and enthalpies show that the stability of DOTA, complexed with alkali metals decreases down the group of the periodic table. Implicit water solvation affects the complexation of DOTA-ions leading to decreases in the stability of the complexes. NBO analysis through the natural population charges and the second order perturbation theory, revealed a charge transfer between DOTA and alkali metals. Conceptual DFT-based properties such as HOMO/LUMO energies, ΔE HOMO-LUMO and chemical hardness and softness indicated a decrease in the chemical stability of DOTA-alkali metal complexes down the alkali metal series. This study serves as a guide to researchers in the field of organometallic chelators, particularly, radiopharmaceuticals in finding the efficient optimal match between chelators and various metal ions. Copyright © 2017 Elsevier Inc. All rights reserved.

A Study of Interaction Patterns and Awareness Design Elements in a Massively Multiplayer Online Game

Directory of Open Access Journals (Sweden)

Tiffany Y. Tang

2008-01-01

Full Text Available Massively multiplayer online games (MMOGs have been known to create rich and versatile social worlds for thousands of millions of players to participate. As such, various game elements and advance technologies such as artificial intelligence have been applied to encourage and facilitate social interactions in these online communities, the key to the success of MMOGs. However, there is a lack of studies addressing the usability of these elements in games. In this paper, we look into interaction patterns and awareness design elements that support the awareness in LastWorld and FairyLand. Experimental results obtained through both in-game experiences and player interviews reveal that not all awareness tools (e.g., an in-game map have been fully exploited by players. In addition, those players who are aware of these tools are not satisfied with them. Our findings suggest that awareness-oriented tools/channels should be easy to interpret and rich in conveying “knowledge” so as to reduce players-cognitive overload. These findings of this research recommend considerations of early stage MMOG design.

A new computational method for studies of 3-D dislocation-precipitate interactions in reactor steels

International Nuclear Information System (INIS)

Takahashi, A.; Gohniem, N.M.

2008-01-01

To enable computational design of advanced steels for reactor pressure vessels and core structural components, we present a new computational method for studies of the interaction between dislocations and precipitates. The method is based on three-dimensional parametric dislocation dynamics, Eshelby's inclusion and inhomogeneity solutions, and boundary and volume element numerical models. Results from this new method are successfully compared to recent molecular dynamics (MD) simulation results, and show good agreement with atomistic simulations. Then the method is first applied to the investigation of the critical shear stress (CSS) of precipitates sheared by successive dislocation cuttings. The simulations reveal that the CSS is reduced when dislocations cut precipitates, and that it can be as low as half the original value for a completely sheared precipitate. The influence of precipitate geometry and the ratio of precipitate-to-matrix elastic shear modulus on the CSS is presented, and the dependence of the interaction stress between dislocations and precipitates on their relative geometry is discussed. Finally an extension of the method to incorporate the dislocation core contribution to the CSS is highlighted. (author)

Energetic studies on DNA-peptide interaction in relation to the enthalpy-entropy compensation paradox.

Science.gov (United States)

Yang, Robin C K; Huang, Jonathan T B; Chien, Shih-Chuan; Huang, Roy; Jeng, Kee-Ching G; Chen, Yen-Chung; Liao, Mokai; Wu, Jia-Rong; Hung, Wei-Kang; Hung, Chia-Chun; Chen, Yu-Ling; Waring, Michael J; Sheh, Leung

2013-01-07

This study aims to interpret the energetic basis of complex DNA-peptide interactions according to a novel allosteric interaction network approach. In common with other designed peptides, five new conjugates incorporating the XPRK or XHypRK motif (Hyp = hydroxyproline) attached to a N-methylpyrrole (Py) tract with a basic tail have been found to display cooperative binding to DNA involving multiple monodentate as well as interstrand bidentate interactions. Using quantitative DNase I footprinting it appears that allosteric communication via cooperative binding to multiple sites on complementary DNA strands corresponds to two different types of DNA-peptide interaction network. Temperature variation experiments using a dodecapeptide RY-12 show that lower temperature (25 °C) favor a circuit type of allosteric interaction network, whereas higher temperatures (31 and 37 °C) afford only a partial-circuit type of network. Circular dichroism studies show that our five peptides induce significant local conformational changes in DNA via the minor groove, with apparently dimeric binding stoichiometry. Isothermal titration calorimetry reveals that these peptides, together with another seven for comparison, are strongly exothermic upon binding to a model 13-mer DNA duplex, characterized by ΔH ranging from -14.7 to -74.4 kcal mol(-1), and also high TΔS ranging from -6.5 to -65.9 kcal mol(-1). Multiple monodentate and bidentate interactions, as well as ionic forces that mediate positive cooperativity in sequence recognition, are consistent with a dramatic decrease in entropy and a 'tightening' effect of DNA conformation. Distinctive enthalpy-entropy compensation (EEC) relationships are demonstrated for the interaction of all twelve designed peptides with DNA, affording a straight line of slope close to unity when ΔH is plotted versus TΔS, with a y-axis intercept (average ΔG) corresponding to -8.5 kcal mol(-1), while the observed ΔG ranges from -8.2 to -9.1 kcal mol(-1) for

A rice kinase-protein interaction map.

Science.gov (United States)

Ding, Xiaodong; Richter, Todd; Chen, Mei; Fujii, Hiroaki; Seo, Young Su; Xie, Mingtang; Zheng, Xianwu; Kanrar, Siddhartha; Stevenson, Rebecca A; Dardick, Christopher; Li, Ying; Jiang, Hao; Zhang, Yan; Yu, Fahong; Bartley, Laura E; Chern, Mawsheng; Bart, Rebecca; Chen, Xiuhua; Zhu, Lihuang; Farmerie, William G; Gribskov, Michael; Zhu, Jian-Kang; Fromm, Michael E; Ronald, Pamela C; Song, Wen-Yuan

2009-03-01

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

A conceptual framework for studying the strength of plant-animal mutualistic interactions.

Science.gov (United States)

Vázquez, Diego P; Ramos-Jiliberto, Rodrigo; Urbani, Pasquinell; Valdovinos, Fernanda S

2015-04-01

The strength of species interactions influences strongly the structure and dynamics of ecological systems. Thus, quantifying such strength is crucial to understand how species interactions shape communities and ecosystems. Although the concepts and measurement of interaction strength in food webs have received much attention, there has been comparatively little progress in the context of mutualism. We propose a conceptual scheme for studying the strength of plant-animal mutualistic interactions. We first review the interaction strength concepts developed for food webs, and explore how these concepts have been applied to mutualistic interactions. We then outline and explain a conceptual framework for defining ecological effects in plant-animal mutualisms. We give recommendations for measuring interaction strength from data collected in field studies based on a proposed approach for the assessment of interaction strength in plant-animal mutualisms. This approach is conceptually integrative and methodologically feasible, as it focuses on two key variables usually measured in field studies: the frequency of interactions and the fitness components influenced by the interactions. © 2015 John Wiley & Sons Ltd/CNRS.

The feedback in the studies of interpersonal interaction

Directory of Open Access Journals (Sweden)

N V Amyaga

2014-12-01

Full Text Available The article examines the problem of interpreting and studying the feedback in interpersonal interaction as a result of some reflective position. A scientist interested in the feedback has to study the reflective positions as well and to consider their ‘second order’, i. e. to identify the object of his research as a certain number of direct and reverse processes together with their possible subjective representation. Considering the interaction of the sociologist with his customer, this means the necessity to correctly understand and reflect the goals, interests and negotiating tools of the other party that determine the success of negotiations.

Interactions of PLGA nanoparticles with blood components: protein adsorption, coagulation, activation of the complement system and hemolysis studies.

Science.gov (United States)

Fornaguera, Cristina; Calderó, Gabriela; Mitjans, Montserrat; Vinardell, Maria Pilar; Solans, Conxita; Vauthier, Christine

2015-04-14

The intravenous administration of poly(lactic-co-glycolic) acid (PLGA) nanoparticles has been widely reported as a promising alternative for delivery of drugs to specific cells. However, studies on their interaction with diverse blood components using different techniques are still lacking. Therefore, in the present work, the interaction of PLGA nanoparticles with blood components was described using different complementary techniques. The influence of different encapsulated compounds/functionalizing agents on these interactions was also reported. It is worth noting that all these techniques can be simply performed, without the need for highly sophisticated apparatus or skills. Moreover, their transference to industries and application of quality control could be easily performed. Serum albumin was adsorbed onto all types of tested nanoparticles. The saturation concentration was dependent on the nanoparticle size. In contrast, fibrinogen aggregation was dependent on nanoparticle surface charge. The complement activation was also influenced by the nanoparticle functionalization; the presence of a functionalizing agent increased complement activation, while the addition of an encapsulated compound only caused a slight increase. None of the nanoparticles influenced the coagulation cascade at low concentrations. However, at high concentrations, cationized nanoparticles did activate the coagulation cascade. Interactions of nanoparticles with erythrocytes did not reveal any hemolysis. Interactions of PLGA nanoparticles with blood proteins depended both on the nanoparticle properties and the protein studied. Independent of their loading/surface functionalization, PLGA nanoparticles did not influence the coagulation cascade and did not induce hemolysis of erythrocytes; they could be defined as safe concerning induction of embolization and cell lysis.

Analytical techniques for the study of polyphenol-protein interactions.

Science.gov (United States)

Poklar Ulrih, Nataša

2017-07-03

This mini review focuses on advances in biophysical techniques to study polyphenol interactions with proteins. Polyphenols have many beneficial pharmacological properties, as a result of which they have been the subject of intensive studies. The most conventional techniques described here can be divided into three groups: (i) methods used for screening (in-situ methods); (ii) methods used to gain insight into the mechanisms of polyphenol-protein interactions; and (iii) methods used to study protein aggregation and precipitation. All of these methods used to study polyphenol-protein interactions are based on modifications to the physicochemical properties of the polyphenols or proteins after binding/complex formation in solution. To date, numerous review articles have been published in the field of polyphenols. This review will give a brief insight in computational methods and biosensors and cell-based methods, spectroscopic methods including fluorescence emission, UV-vis adsorption, circular dichroism, Fourier transform infrared and mass spectrometry, nuclear magnetic resonance, X-ray diffraction, and light scattering techniques including small-angle X-ray scattering and small-angle neutron scattering, and calorimetric techniques (isothermal titration calorimetry and differential scanning calorimetry), microscopy, the techniques which have been successfully used for polyphenol-protein interactions. At the end the new methods based on single molecule detection with high potential to study polyphenol-protein interactions will be presented. The advantages and disadvantages of each technique will be discussed as well as the thermodynamic, kinetic or structural parameters, which can be obtained. The other relevant biophysical experimental techniques that have proven to be valuable, such electrochemical methods, hydrodynamic techniques and chromatographic techniques will not be described here.

Gender interaction in coed physical education: a study in Turkey.

Science.gov (United States)

Koca, Canan

2009-01-01

Although there has been a long-standing debate about whether a single-sex or mixed-sex environment is better for students in many Western countries, coeducation is one of the taken-for-granted issues in the modern Turkish education system. This study examined commonly expressed concerns about gender equity in a mixed-sex environment within the context of physical education (PE) in Turkey. The purpose of the study was to examine teacher-student interaction in the coed PE classroom, focusing on gender-stereotyped beliefs. Participants consisted of two PE teachers and 37 eighth-grade students from a private school situated in suburban Ankara Turkey. The modified observational instrument with the combination of Teacher-Student Interaction (TSI) and Interactions for Sex Equity in Classroom Teaching Observation System (INTERSECT) was used to assess teacher-student interaction in the classroom. In order to understand students' and teachers' gender-stereotyped beliefs, individual interviews were also conducted. The findings of this study indicated that both male and female PE teachers interact more frequently with boys, and this interaction was influenced by gender-stereotyped beliefs of both teachers and students. In sum, similar to many other western countries, the movement toward coeducation in Turkey has not automatically brought equal opportunities for girls or boys in PE.

An Oral Contraceptive Drug Interaction Study

Science.gov (United States)

Bradstreet, Thomas E.; Panebianco, Deborah L.

2004-01-01

This article focuses on a two treatment, two period, two treatment sequence crossover drug interaction study of a new drug and a standard oral contraceptive therapy. Both normal theory and distribution-free statistical analyses are provided along with a notable amount of graphical insight into the dataset. For one of the variables, the decision on…

Omega-3 Fatty acids and inflammation: novel interactions reveal a new step in neutrophil recruitment.

Directory of Open Access Journals (Sweden)

Samantha P Tull

2009-08-01

only revealed an unsuspected level of regulation in the migration of inflammatory leukocytes, it also contributes to our understanding of the interactions of this bioactive lipid with the inflammatory system. Moreover, it indicates the potential for novel therapeutics that target the inflammatory system with greater affinity and/or specificity than supplementing the diet with n-3-PUFAs.

77 FR 9946 - Draft Guidance for Industry on Drug Interaction Studies-Study Design, Data Analysis, Implications...

Science.gov (United States)

2012-02-21

... industry entitled ``Drug Interaction Studies--Study Design, Data Analysis, Implications for Dosing, and... data analysis in the context of identifying potential drug interactions. The guidance also addresses... Studies--Study Design, Data Analysis, and Implications for Dosing and Labeling.'' Comments were received...

Spectroscopic studies on the interaction of europium(III) and curium(III) with components of the human mucosa

Energy Technology Data Exchange (ETDEWEB)

Wilke, Claudia; Barkleit, Astrid [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Chemistry of the F-Elements

2016-07-01

To evaluate the health risks of lanthanides (Ln) and radiotoxic actinides (An) in case of ingestion accidents etc., investigations into the chemical reactions of these metals in the human gastrointestinal tract are necessary. Our previous study revealed that mucin, an important part of the protective mucosa layer in the digestive system, shows a strong interaction with Eu(III). Based on these results, the present study focuses on the components of this glycoprotein and identified N-acetylneuraminic acid (NANA) as the dominant binding carbohydrate of mucin. TRLFS measurements suggest the formation of a 1: 1 complex with log β of 3.2 ± 0.1 for Eu(III) and 3.3 ± 0.1 for Cm(III), respectively.

A Study of Multiplicities in Hadronic Interactions

Energy Technology Data Exchange (ETDEWEB)

Estrada Tristan, Nora Patricia; /San Luis Potosi U.

2006-02-01

Using data from the SELEX (Fermilab E781) experiment obtained with a minimum-bias trigger, we study multiplicity and angular distributions of secondary particles produced in interactions in the experimental targets. We observe interactions of {Sigma}{sup -}, proton, {pi}{sup -}, and {pi}{sup +}, at beam momenta between 250 GeV/c and 650 GeV/c, in copper, polyethylene, graphite, and beryllium targets. We show that the multiplicity and angular distributions for meson and baryon beams at the same momentum are identical. We also show that the mean multiplicity increases with beam momentum, and presents only small variations with the target material.

The geometric framework for nutrition reveals interactions between protein and carbohydrate during larval growth in honey bees

Directory of Open Access Journals (Sweden)

Bryan R. Helm

2017-06-01

Full Text Available In holometabolous insects, larval nutrition affects adult body size, a life history trait with a profound influence on performance and fitness. Individual nutritional components of larval diets are often complex and may interact with one another, necessitating the use of a geometric framework for elucidating nutritional effects. In the honey bee, Apis mellifera, nurse bees provision food to developing larvae, directly moderating growth rates and caste development. However, the eusocial nature of honey bees makes nutritional studies challenging, because diet components cannot be systematically manipulated in the hive. Using in vitro rearing, we investigated the roles and interactions between carbohydrate and protein content on larval survival, growth, and development in A. mellifera. We applied a geometric framework to determine how these two nutritional components interact across nine artificial diets. Honey bees successfully completed larval development under a wide range of protein and carbohydrate contents, with the medium protein (∼5% diet having the highest survival. Protein and carbohydrate both had significant and non-linear effects on growth rate, with the highest growth rates observed on a medium-protein, low-carbohydrate diet. Diet composition did not have a statistically significant effect on development time. These results confirm previous findings that protein and carbohydrate content affect the growth of A. mellifera larvae. However, this study identified an interaction between carbohydrate and protein content that indicates a low-protein, high-carb diet has a negative effect on larval growth and survival. These results imply that worker recruitment in the hive would decline under low protein conditions, even when nectar abundance or honey stores are sufficient.

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

Directory of Open Access Journals (Sweden)

Mohan Babu

2014-02-01

Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

Plasma-Oxygen Interaction During Thin Films Deposition by Laser ...

African Journals Online (AJOL)

In this contribution we study the effect of the oxygen pressure on the plasma dynamics during the ablation of oxides materials into an oxygen gas. The study was done using fast imaging and ion probe techniques. Both techniques revealed that a threshold oxygen pressure is needed to initiate the plume oxygen interaction.

CUSTOMER INTERACTION ON DIGITAL ECONOMY: A CASE STUDY

Directory of Open Access Journals (Sweden)

Mateus Tavares da Silva Cozer

2007-10-01

Full Text Available On a digital economy context, customer interaction is fundamental to any company to provide competitive advantage. This research intends to give concrete answers for the sea of information complexity which is the Internet. The main case is to build a model of digital customer interaction. Customization extends beyond targeted media to include the design and delivery of the product itself. Venkatraman (1998 defines dynamic customization based on three principles: modularity, intelligence and organization. The research is based on Interaction Model and its variables are: Products, Modularity, Artificial Intelligence, Market driven organization, and virtual communities. Two organizations were studied, one with physical product and another with virtual product, and the results were shown from a qualitative research.

Studies on melt-water-structure interaction during severe accidents

International Nuclear Information System (INIS)

Sehgal, B.R.; Dinh, T.N.; Okkonen, T.J.; Bui, V.A.; Nourgaliev, R.R.; Andersson, J.

1996-10-01

Results of a series of studies, on melt-water-structure interactions which occur during the progression of a core melt-down accident, are described. The emphasis is on the in-vessel interactions and the studies are both experimental and analytical. Since, the studies performed resulted in papers published in proceedings of the technical meetings, and in journals, copies of a set of selected papers are attached to provide details. A summary of the results obtained is provided for the reader who does not, or cannot, venture into the perusal of the attached papers. (au)

Studies on melt-water-structure interaction during severe accidents

Energy Technology Data Exchange (ETDEWEB)

Sehgal, B.R.; Dinh, T.N.; Okkonen, T.J.; Bui, V.A.; Nourgaliev, R.R.; Andersson, J. [Royal Inst. of Technology, Div. of Nucl. Power Safety, Stockholm (Sweden)

1996-10-01

Results of a series of studies, on melt-water-structure interactions which occur during the progression of a core melt-down accident, are described. The emphasis is on the in-vessel interactions and the studies are both experimental and analytical. Since, the studies performed resulted in papers published in proceedings of the technical meetings, and in journals, copies of a set of selected papers are attached to provide details. A summary of the results obtained is provided for the reader who does not, or cannot, venture into the perusal of the attached papers. (au).

Game theory and experimental games the study of strategic interaction

CERN Document Server

Colman, Andrew M

1982-01-01

Game Theory and Experimental Games: The Study of Strategic Interaction is a critical survey of the essential ideas of game theory and the findings of empirical research on strategic interaction. Some experiments using lifelike simulations of familiar kinds of strategic interactions are presented, and applications of game theory to the study of voting, the theory of evolution, and moral philosophy are discussed.Comprised of 13 chapters, this volume begins with an informal definition of game theory and an outline of the types of social situations to which it applies. Games of skill, games of cha

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

LENUS (Irish Health Repository)

Casey, Fergal

2011-08-22

Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

Electron Tomography Reveals the Active Phase–Support Interaction in Sulfidic Hydroprocessing Catalysts

NARCIS (Netherlands)

Eijsbouts, Sonja; Li, Xuang; Juan-Alcaniz, Jana; van den Oetelaar, Leon C A; Bergwerff, Jaap; Loos, Joachim; Carlsson, Anna; Vogt, E.T.C.

2017-01-01

Conventional two-dimensional (2D) transmission electron microscopy of sulfidic hydroprocessing catalysts can be deceiving and give the impression that parts of the support are overloaded with active phase. High-angle annular dark field scanning transmission electron microscopy tomography reveals

Fibronectin-cell interactions

DEFF Research Database (Denmark)

Couchman, J R; Austria, M R; Woods, A

1990-01-01

Fibronectins are widespread extracellular matrix and body fluid glycoproteins, capable of multiple interactions with cell surfaces and other matrix components. Their structure at a molecular level has been resolved, yet there are still many unanswered questions regarding their biologic activity...... in vivo. Much data suggests that fibronectins may promote extracellular matrix assembly, and cell adhesion to those matrices. However, one outstanding enigma is that fibronectins may, under different circumstances, promote both cell migration and anchorage. An analysis of the interaction of fibroblasts...... with proteolytically derived and purified domains of plasma fibronectin revealed that the type of adhesion and the correlated cytoskeletal organization depended on multiple interactions of fibronectin domains with the cell surface. Human dermal fibroblasts were capable of interacting with the integrin-binding domain...

Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction.

Science.gov (United States)

Hasanzadeh, Mohammad; Shadjou, Nasrin

2016-04-01

Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparative study of the interactions between bisphenol-A and its endocrine disrupting analogues with bovine serum albumin using multi-spectroscopic and molecular docking studies.

Science.gov (United States)

Ikhlas, Shoeb; Usman, Afia; Ahmad, Masood

2018-04-24

Interaction studies of bisphenol analogues; biphenol-A (BPA), bisphenol-B (BPB), and bisphenol-F (BPF) with bovine serum albumin (BSA) were performed using multi-spectroscopic and molecular docking studies at the protein level. The mechanism of binding of bisphenols with BSA was dynamic in nature. SDS refolding experiments demonstrated no stabilization of BSA structure denatured by BPB, however, BSA denatured by BPA and BPF was found to get stabilized. Also, CD spectra and molecular docking studies revealed that BPB bound more strongly and induced more conformational changes in BSA in comparison to BPA. Hence, this study throws light on the replacement of BPA by its analogues and whether the replacement is associated with a possible risk, raising a doubt that perhaps BPB is not a good substitute of BPA.

Circular dichroism study of the interaction between mutagens and bilirubin bound to different binding sites of serum albumins

Science.gov (United States)

Orlov, Sergey; Goncharova, Iryna; Urbanová, Marie

Although recent investigations have shown that bilirubin not only has a negative role in the organism but also exhibits significant antimutagenic properties, the mechanisms of interactions between bilirubin and mutagens are not clear. In this study, interaction between bilirubin bound to different binding sites of mammalian serum albumins with structural analogues of the mutagens 2-aminofluorene, 2,7-diaminofluorene and mutagen 2,4,7-trinitrofluorenone were investigated by circular dichroism and absorption spectroscopy. Homological human and bovine serum albumins were used as chiral matrices, which preferentially bind different conformers of bilirubin in the primary binding sites and make it observable by circular dichroism. These molecular systems approximated a real system for the study of mutagens in blood serum. Differences between the interaction of bilirubin bound to primary and to secondary binding sites of serum albumins with mutagens were shown. For bilirubin bound to secondary binding sites with low affinity, partial displacement and the formation of self-associates were observed in all studied mutagens. The associates of bilirubin bound to primary binding sites of serum albumins are formed with 2-aminofluorene and 2,4,7-trinitrofluorenone. It was proposed that 2,7-diaminofluorene does not interact with bilirubin bound to primary sites of human and bovine serum albumins due to the spatial hindrance of the albumins binding domains. The spatial arrangement of the bilirubin bound to serum albumin along with the studied mutagens was modelled using ligand docking, which revealed a possibility of an arrangement of the both bilirubin and 2-aminofluorene and 2,4,7-trinitrofluorenone in the primary binding site of human serum albumin.

Vortex dynamics during blade-vortex interactions

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Peng, Di; Gregory, James W.

2015-05-01

Vortex dynamics during parallel blade-vortex interactions (BVIs) were investigated in a subsonic wind tunnel using particle image velocimetry (PIV). Vortices were generated by applying a rapid pitch-up motion to an airfoil through a pneumatic system, and the subsequent interactions with a downstream, unloaded target airfoil were studied. The blade-vortex interactions may be classified into three categories in terms of vortex behavior: close interaction, very close interaction, and collision. For each type of interaction, the vortex trajectory and strength variation were obtained from phase-averaged PIV data. The PIV results revealed the mechanisms of vortex decay and the effects of several key parameters on vortex dynamics, including separation distance (h/c), Reynolds number, and vortex sense. Generally, BVI has two main stages: interaction between vortex and leading edge (vortex-LE interaction) and interaction between vortex and boundary layer (vortex-BL interaction). Vortex-LE interaction, with its small separation distance, is dominated by inviscid decay of vortex strength due to pressure gradients near the leading edge. Therefore, the decay rate is determined by separation distance and vortex strength, but it is relatively insensitive to Reynolds number. Vortex-LE interaction will become a viscous-type interaction if there is enough separation distance. Vortex-BL interaction is inherently dominated by viscous effects, so the decay rate is dependent on Reynolds number. Vortex sense also has great impact on vortex-BL interaction because it changes the velocity field and shear stress near the surface.

Interacting universes and the cosmological constant

International Nuclear Information System (INIS)

Alonso-Serrano, A.; Bastos, C.; Bertolami, O.; Robles-Pérez, S.

2013-01-01

In this Letter it is studied the effects that an interaction scheme among universes can have in the values of their cosmological constants. In the case of two interacting universes, the value of the cosmological constant of one of the universes becomes very close to zero at the expense of an increasing value of the cosmological constant of the partner universe. In the more general case of a chain of N interacting universes with periodic boundary conditions, the spectrum of the Hamiltonian splits into a large number of levels, each of them associated with a particular value of the cosmological constant, that can be occupied by single universes revealing a collective behavior that plainly shows that the multiverse is much more than the mere sum of its parts

Interacting universes and the cosmological constant

Energy Technology Data Exchange (ETDEWEB)

Alonso-Serrano, A. [Centro de Física “Miguel Catalán”, Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 121, 28006 Madrid (Spain); Estación Ecológica de Biocosmología, Pedro de Alvarado 14, 06411 Medellín (Spain); Bastos, C. [Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisboa (Portugal); Bertolami, O. [Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisboa (Portugal); Departamento de Física e Astronomia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Robles-Pérez, S., E-mail: salvarp@imaff.cfmac.csic.es [Centro de Física “Miguel Catalán”, Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 121, 28006 Madrid (Spain); Estación Ecológica de Biocosmología, Pedro de Alvarado 14, 06411 Medellín (Spain); Física Teórica, Universidad del País Vasco, Apartado 644, 48080 Bilbao (Spain)

2013-02-12

In this Letter it is studied the effects that an interaction scheme among universes can have in the values of their cosmological constants. In the case of two interacting universes, the value of the cosmological constant of one of the universes becomes very close to zero at the expense of an increasing value of the cosmological constant of the partner universe. In the more general case of a chain of N interacting universes with periodic boundary conditions, the spectrum of the Hamiltonian splits into a large number of levels, each of them associated with a particular value of the cosmological constant, that can be occupied by single universes revealing a collective behavior that plainly shows that the multiverse is much more than the mere sum of its parts.

Comparative study on collaborative interaction in non-immersive and immersive systems

Science.gov (United States)

Shahab, Qonita M.; Kwon, Yong-Moo; Ko, Heedong; Mayangsari, Maria N.; Yamasaki, Shoko; Nishino, Hiroaki

2007-09-01

This research studies the Virtual Reality simulation for collaborative interaction so that different people from different places can interact with one object concurrently. Our focus is the real-time handling of inputs from multiple users, where object's behavior is determined by the combination of the multiple inputs. Issues addressed in this research are: 1) The effects of using haptics on a collaborative interaction, 2) The possibilities of collaboration between users from different environments. We conducted user tests on our system in several cases: 1) Comparison between non-haptics and haptics collaborative interaction over LAN, 2) Comparison between non-haptics and haptics collaborative interaction over Internet, and 3) Analysis of collaborative interaction between non-immersive and immersive display environments. The case studies are the interaction of users in two cases: collaborative authoring of a 3D model by two users, and collaborative haptic interaction by multiple users. In Virtual Dollhouse, users can observe physics law while constructing a dollhouse using existing building blocks, under gravity effects. In Virtual Stretcher, multiple users can collaborate on moving a stretcher together while feeling each other's haptic motions.

SPS ionosphere/microwave beam interactions: Arecibo experimental studies

International Nuclear Information System (INIS)

Duncan, L.M.

1980-10-01

The purpose of this program is to determine the environmental impacts associated with the operation of the proposed SPS microwave power transmission system. It is expected that thermal effects will provide the dominant force driving the nonlinear ionosphere/microwave beam interactions. Collisional damping of radio waves, producing ohmic heating of the ionospheric plasma, depends inversely on the square of the radio wave frequency. Therefore, equivalent heating and equivalent thermal forces can be generated at lower radiated power densities by using lower radio wave frequencies. This principle is fundamental to a large part of the experimental program. An understanding of the physics of the specific interactions excited by the SPS microwave beam is also an important part of the assessment program. This program is designed to determine instability thresholds, the growth rates and spatial extent of the resultant ionospheric disturbances, and the frequency and power dependences of the interactions. How these interactions are affected by variations in the natural ionospheric conditions, how different instabilities occurring simultaneously may affect each other, and how distinct microwave beams might mutually interact are studied. Status of the program is described

Challenges and Opportunities in Genome-Wide Environmental Interaction (GWEI) studies

Science.gov (United States)

Aschard, Hugues; Lutz, Sharon; Maus, Bärbel; Duell, Eric J.; Fingerlin, Tasha; Chatterjee, Nilanjan; Kraft, Peter; Van Steen, Kristel

2012-01-01

The interest in performing gene-environment interaction studies has seen a significant increase with the increase of advanced molecular genetics techniques. Practically, it became possible to investigate the role of environmental factors in disease risk and hence to investigate their role as genetic effect modifiers. The understanding that genetics is important in the uptake and metabolism of toxic substances is an example of how genetic profiles can modify important environmental risk factors to disease. Several rationales exist to set up gene-environment interaction studies and the technical challenges related to these studies – when the number of environmental or genetic risk factors is relatively small – has been described before. In the post-genomic era, it is now possible to study thousands of genes and their interaction with the environment. This brings along a whole range of new challenges and opportunities. Despite a continuing effort in developing efficient methods and optimal bioinformatics infrastructures to deal with the available wealth of data, the challenge remains how to best present and analyze Genome-Wide Environmental Interaction (GWEI) studies involving multiple genetic and environmental factors. Since GWEIs are performed at the intersection of statistical genetics, bioinformatics and epidemiology, usually similar problems need to be dealt with as for Genome-Wide Association gene-gene Interaction (GWAI) studies. However, additional complexities need to be considered which are typical for large-scale epidemiological studies, but are also related to “joining” two heterogeneous types of data in explaining complex disease trait variation or for prediction purposes. PMID:22760307

A combination test for detection of gene-environment interaction in cohort studies.

Science.gov (United States)

Coombes, Brandon; Basu, Saonli; McGue, Matt

2017-07-01

Identifying gene-environment (G-E) interactions can contribute to a better understanding of disease etiology, which may help researchers develop disease prevention strategies and interventions. One big criticism of studying G-E interaction is the lack of power due to sample size. Studies often restrict the interaction search to the top few hundred hits from a genome-wide association study or focus on potential candidate genes. In this paper, we test interactions between a candidate gene and an environmental factor to improve power by analyzing multiple variants within a gene. We extend recently developed score statistic based genetic association testing approaches to the G-E interaction testing problem. We also propose tests for interaction using gene-based summary measures that pool variants together. Although it has recently been shown that these summary measures can be biased and may lead to inflated type I error, we show that under several realistic scenarios, we can still provide valid tests of interaction. These tests use significantly less degrees of freedom and thus can have much higher power to detect interaction. Additionally, we demonstrate that the iSeq-aSum-min test, which combines a gene-based summary measure test, iSeq-aSum-G, and an interaction-based summary measure test, iSeq-aSum-I, provides a powerful alternative to test G-E interaction. We demonstrate the performance of these approaches using simulation studies and illustrate their performance to study interaction between the SNPs in several candidate genes and family climate environment on alcohol consumption using the Minnesota Center for Twin and Family Research dataset. © 2017 WILEY PERIODICALS, INC.

Determinants of Internet Use for Interactive Learning: An Exploratory Study

Science.gov (United States)

Castaño, Jonatan; Duart, Josep M.; Sancho-Vinuesa, Teresa

2015-01-01

The use of the Internet in higher education teaching can facilitate the interactive learning process and thus improve educational outcomes. The aim of the study presented here is to explore which variables are linked to higher intensity of Internet-based interactive educational practices. The study is based on data obtained from an online survey…

Microstructural studies on chemical interactions in U-Mo with Al

International Nuclear Information System (INIS)

Martins, Ilson Carlos

2010-01-01

This research refers to the study of U-Mo alloy as an alternative material for producing nuclear fuel elements with high density of uranium, for research reactors of high performance. The international non-proliferation of nuclear weapons has enrichment level limited to 20% U 23 '5. U-Mo alloys with 6-10 wt% Mo can lead to a density up to 9 gU/cm 3 , inside the fuel core. The MTR fuel element plates are made from briquettes (U-Mo powder + Al) encapsulated in Al plates, then welded and rolled However, the U-Mo alloy is very reactive in the presence of Al. The reaction products of this interaction are undesirable from the standpoint of nuclear usage, since they cause a chemical interaction layer (IL) formed during thermal cycling and exposure to nuclear fission neutrons. As the IL has low thermal conductivity, they may cause structural failure in the fuel element during operation. The present study provides a new preparation technique for interdiffusion pairs made by hot rolling. The U-Mo alloy, in tablet format, is involved by matrix Al-plates, which is sealed and then hot rolled. This way to prepare the diffusion couples is an ideal condition to avoid the oxidation at the contact interface at U-Mo/Al. The hot rolling preparation also simulates the first reduction pass during MTR fuel plate manufacture. We chose to work with a Mo content of 10 wt% in U-Mo alloy to ensure greater phase formation, since this level favors a greater chemical stability in this phase. The Al alloy matrix was used as the AA1050 since it contains small impurity amounts. The interdiffusion couples U-10Mo/AA1050 were thermally treated in two temperature ranges (1500C and 5500C) and three soaking times (5h, 40h and 80h) to simulate the interdiffusion process and formation of chemical interaction layer. The analysis of the interaction layer U-10Mo/AA1050 was made by SEM/EDS and X-ray diffraction. It revealed a general trend of low interdiffusion of Al (about 8 atomic %) inside U-Mo. There was

Study of the Deformation/Interaction Model: How Interactions Increase the Reaction Barrier

Directory of Open Access Journals (Sweden)

Zhiling Liang

2018-01-01

Full Text Available The interactions (including weak interactions between dienophiles and dienes play an important role in the Diels-Alder reaction. To elucidate the influence of these interactions on the reactivity, a popular DFT functional and a variational DFT functional corrected with dispersion terms are used to investigate different substituent groups incorporated on the dienophiles and dienes. The bond order is used to track the trajectory of the cycloaddition reaction. The deformation/interaction model is used to obtain the interaction energy from the reactant complex to the inflection point until reaching the saddle point. The interaction energy initially increases with a decrease in the interatomic distance, reaching a maximum value, but then decreases when the dienophiles and dienes come closer. Reduced density gradient and chemical energy component analysis are used to analyse the interaction. Traditional transition state theory and variational transition state theory are used to obtain the reaction rates. The influence of tunneling on the reaction rate is also discussed.

Study of the interaction between fluoxetine hydrochloride and bovine serum albumin in the imitated physiological conditions by multi-spectroscopic methods

Energy Technology Data Exchange (ETDEWEB)

Katrahalli, Umesha [Department of Chemistry, Karnatak University, Dharwad 580 003 (India); Jaldappagari, Seetharamappa, E-mail: j_seetharam@rediffmail.co [Department of Chemistry, Karnatak University, Dharwad 580 003 (India); Kalanur, Shankara S. [Department of Chemistry, Karnatak University, Dharwad 580 003 (India)

2010-02-15

The mechanism of interaction of an antidepressant, fluoxetine hydrochloride (FLX) with bovine serum albumin (BSA) has been studied by different spectroscopic techniques under physiological conditions. FLX was found to quench the intrinsic fluorescence of protein by static quenching mechanism. The binding constant 'K' was found to be 7.06x10{sup 3} M{sup -1} at 296 K. The value of 'n' close to unity revealed that the BSA has a single class of binding site for FLX. Based on thermodynamic parameters, hydrogen bonding and van der Waals forces were proposed to operate between BSA and FLX. The change in conformation of protein was noticed upon its interaction with the drug. From displacement studies it was concluded that the FLX bound to protein at site I. The effects of various common metals ions on the binding were also investigated.

Proteomic Analysis of Interaction between a Plant Virus and Its Vector Insect Reveals New Functions of Hemipteran Cuticular Protein.

Science.gov (United States)

Liu, Wenwen; Gray, Stewart; Huo, Yan; Li, Li; Wei, Taiyun; Wang, Xifeng

2015-08-01

Numerous viruses can be transmitted by their corresponding vector insects; however, the molecular mechanisms enabling virus transmission by vector insects have been poorly understood, especially the identity of vector components interacting with the virus. Here, we used the yeast two-hybrid system to study proteomic interactions of a plant virus (Rice stripe virus, RSV, genus Tenuivirus) with its vector insect, small brown planthopper (Laodelphax striatellus). Sixty-six proteins of L. striatellus that interacted with the nucleocapsid protein (pc3) of RSV were identified. A virus-insect interaction network, constructed for pc3 and 29 protein homologs of Drosophila melanogaster, suggested that nine proteins might directly interact with pc3. Of the 66 proteins, five (atlasin, a novel cuticular protein, jagunal, NAC domain protein, and vitellogenin) were most likely to be involved in viral movement, replication, and transovarial transmission. This work also provides evidence that the novel cuticular protein, CPR1, from L. striatellus is essential for RSV transmission by its vector insect. CPR1 binds the nucleocapsid protein (pc3) of RSV both in vivo and in vitro and colocalizes with RSV in the hemocytes of L. striatellus. Knockdown of CPR1 transcription using RNA interference resulted in a decrease in the concentration of RSV in the hemolymph, salivary glands and in viral transmission efficiency. These data suggest that CPR1 binds RSV in the insect and stabilizes the viral concentration in the hemolymph, perhaps to protect the virus or to help move the virus to the salivary tissues. Our studies provide direct experimental evidence that viruses can use existing vector proteins to aid their survival in the hemolymph. Identifying these putative vector molecules should lead to a better understanding of the interactions between viruses and vector insects. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

An Activity Theoretical Approach to Social Interaction during Study Abroad

Science.gov (United States)

Shively, Rachel L.

2016-01-01

This case study examines how one study abroad student oriented to social interaction during a semester in Spain. Using an activity theoretical approach, the findings indicate that the student not only viewed social interaction with his Spanish host family and an expert-Spanish-speaking age peer as an opportunity for second language (L2) learning,…

In vitro study of interaction between quinine and Garcinia kola ...

African Journals Online (AJOL)

Purpose: To investigate the interaction between quinine and Garcinia kola using an in vitro adsorption study. Methods: In vitro interaction between quinine and G. kola was conducted at 37 ± 0.1 °C. Adsorption of quinine (2.5 - 40 μg/ml) to 2.5 % w/v G. kola suspension was studied. Thereafter, quinine desorption process ...

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

Science.gov (United States)

Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

2013-06-01

RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous 'polyamide amino acids' (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy-entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.

Spectroscopic study on the interaction of Bacillus subtilis α-amylase with cetyltrimethylammonium bromide

International Nuclear Information System (INIS)

Omidyan, R.; Kazemi, S.H.; Bordbar, A.K.; Zaynalpour, S.

2011-01-01

The interaction between α-amylase from Bacillus subtilis and cetyltrimethylammonium bromide (CTAB) has been investigated at various temperature conditions using fluorescence and circular dichroism (CD) spectroscopic methods. Fluorescence data revealed that the fluorescence quenching of α-amylase by CTAB is the result of complex formation between CTAB and α-amylase. The thermodynamic analysis on the binding interaction data shows that the interactions are strongly exothermic (ΔH o =-17.92 kJ mol -1 ) accompanied with increase in entropy (ΔS o between 109 to 135 J mol -1 K -1 ). Thus the binding of CTAB to α-amylase is both enthalpic and entropic driven, which represent the predominate role of both electrostatic and hydrophobic interactions in complex formation process. The values of 2.17x10 -3 M -1 and 1.30 have been obtained from associative binding constant (K a ) and stoichiometry of binding number (n), from analysis of fluorescence data, respectively. Circular dichroism spectra showed the substantial conformational changes in secondary structure of α-amylase due to binding of CTAB, which represents the complete destruction of both secondary and tertiary structure of α-amylase by CTAB. - Research highlights: → The Fluorescence quenching effect of α-amylase by CTAB is a consequence of formation α-amylase-CTAB complex. → The α-helical analyzing from the CD spectra in the various concentration of CTAB shows strongly deformation of α-amylase. → Thermodynamic analysis of quenching verify that the interactions are both enthalpy and entropic driven.

The roles of amensalistic and commensalistic interactions in large ecological network stability.

Science.gov (United States)

Mougi, Akihiko

2016-07-13

Ecological communities comprise diverse species and their interactions. Notably, ecological and evolutionary studies have revealed that reciprocal interactions such as predator-prey, competition, and mutualism, are key drivers of community dynamics. However, there is an argument that many species interactions are asymmetric, where one species unilaterally affects another species (amensalism or commensalism). This raises the unanswered question of what is the role of unilateral interactions in community dynamics. Here I use a theoretical approach to demonstrate that unilateral interactions greatly enhance community stability. The results suggested that amensalism and commensalism were more stabilizing than symmetrical interactions, such as competition and mutualism, but they were less stabilizing than an asymmetric antagonistic interaction. A mix of unilateral interactions increased stability. Furthermore, in communities with all interaction types, unilateral interactions tended to increase stability. This study suggests that unilateral interactions play a major role in maintaining communities, underlining the need to further investigate their roles in ecosystem dynamics.

Quantitative proteomic study of Aspergillus Fumigatus secretome revealed deamidation of secretory enzymes.

Science.gov (United States)

Adav, Sunil S; Ravindran, Anita; Sze, Siu Kwan

2015-04-24

Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated. The filamentous fungi play an essential role in lignocellulosic biomass recycling and fungal strains belonging to Aspergillus were also exploited as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. In this study, extracellular proteins secreted by thermophilic A. fumigatus when grown with cellulose, xylan and starch were profiled using isobaric tags for relative and absolute quantification (iTRAQ) by

Proteomic analysis reveals new cardiac-specific dystrophin-associated proteins.

Directory of Open Access Journals (Sweden)

Eric K Johnson

Full Text Available Mutations affecting the expression of dystrophin result in progressive loss of skeletal muscle function and cardiomyopathy leading to early mortality. Interestingly, clinical studies revealed no correlation in disease severity or age of onset between cardiac and skeletal muscles, suggesting that dystrophin may play overlapping yet different roles in these two striated muscles. Since dystrophin serves as a structural and signaling scaffold, functional differences likely arise from tissue-specific protein interactions. To test this, we optimized a proteomics-based approach to purify, identify and compare the interactome of dystrophin between cardiac and skeletal muscles from as little as 50 mg of starting material. We found selective tissue-specific differences in the protein associations of cardiac and skeletal muscle full length dystrophin to syntrophins and dystrobrevins that couple dystrophin to signaling pathways. Importantly, we identified novel cardiac-specific interactions of dystrophin with proteins known to regulate cardiac contraction and to be involved in cardiac disease. Our approach overcomes a major challenge in the muscular dystrophy field of rapidly and consistently identifying bona fide dystrophin-interacting proteins in tissues. In addition, our findings support the existence of cardiac-specific functions of dystrophin and may guide studies into early triggers of cardiac disease in Duchenne and Becker muscular dystrophies.

Observational study of drug-drug interactions in oncological inpatients

Directory of Open Access Journals (Sweden)

María Sacramento Díaz-Carrasco

2018-01-01

Full Text Available Objective: To determine the prevalence of potential clinically relevant drug- drug interactions in adult oncological inpatients, as well as to describe the most frequent interactions. A standard database was used. Method: An observational, transversal, and descriptive study including patients admitted to the Oncology Service of a reference hospital. All prescriptions were collected twice a week during a month. They were analysed using Lexicomp® database, recording all interactions classified with a level of risk: C, D or X. Results: A total of 1 850 drug-drug interactions were detected in 218 treatments. The prevalence of treatments with at least one clinically relevant interaction was 95%, being 94.5% for those at level C and 26.1% for levels D and X. The drugs most commonly involved in the interactions detected were opioid analgesics, antipsychotics (butyrophenones, benzodiazepines, pyrazolones, glucocorticoids and heparins, whereas interactions with antineoplastics were minimal, highlighting those related to paclitaxel and between metamizole and various antineoplastics. Conclusions: The prevalence of clinically relevant drug-drug interactions rate was very high, highlighting the high risk percentage of them related to level of risk X. Due to the frequency of onset and potential severity, highlighted the concomitant use of central nervous system depressants drugs with risk of respiratory depression, the risk of onset of anticholinergic symptoms when combining morphine or haloperidol with butylscopolamine, ipratropium bromide or dexchlorpheniramine and the multiple interactions involving metamizole.

Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic

Science.gov (United States)

Okumus, Burak; Wilson, Timothy J.; Lilley, David M. J.; Ha, Taekjip

2004-01-01

Single-molecule measurements have revealed that what were assumed to be identical molecules can differ significantly in their static and dynamic properties. One of the most striking examples is the hairpin ribozyme, which was shown to exhibit two to three orders of magnitude variation in folding kinetics between molecules. Although averaged behavior of single molecules matched the bulk solution data, it was not possible to exclude rigorously the possibility that the variations around the mean values arose from different ways of interacting with the surface environment. To test this, we minimized the molecules' interaction with the surface by encapsulating DNA or RNA molecules inside 100- to 200-nm diameter unilamellar vesicles, following the procedures described by Haran and coworkers. Vesicles were immobilized on a supported lipid bilayer via biotin-streptavidin linkages. We observed no direct binding of DNA or RNA on the supported bilayer even at concentrations exceeding 100 nM, indicating that these molecules do not bind stably on the membrane. Since the vesicle diameter is smaller than the resolution of optical microscopy, the lateral mobility of the molecules is severely constrained, allowing long observation periods. We used fluorescence correlation spectroscopy, nuclease digestion, and external buffer exchange to show that the molecules were indeed encapsulated within the vesicles. When contained within vesicles, the natural form of the hairpin ribozyme exhibited 50-fold variation in both folding and unfolding rates in 0.5 mM Mg2+, which is identical to what was observed from the molecules tethered directly on the surface. This strongly indicates that the observed heterogeneity in dynamic properties does not arise as an artifact of surface attachment, but is intrinsic to the nature of the molecules. PMID:15454471

Expressed proteins of Herbaspirillum seropedicae in maize (DKB240) roots-bacteria interaction revealed using proteomics.

Science.gov (United States)

Ferrari, Cibele Santos; Amaral, Fernanda Plucani; Bueno, Jessica Cavalheiro Ferreira; Scariot, Mirella Christine; Valentim-Neto, Pedro Alexandre; Arisi, Ana Carolina Maisonnave

2014-11-01

Several molecular tools have been used to clarify the basis of plant-bacteria interaction; however, the mechanism behind the association is still unclear. In this study, we used a proteomic approach to investigate the root proteome of Zea mays (cv. DKB240) inoculated with Herbaspirillum seropedicae strain SmR1 grown in vitro and harvested 7 days after inoculation. Eighteen differentially accumulated proteins were observed in root samples, ten of which were identified by MALDI-TOF mass spectrometry peptide mass fingerprint. Among the identified proteins, we observed three proteins present exclusively in inoculated root samples and six upregulated proteins and one downregulated protein relative to control. Differentially expressed maize proteins were identified as hypothetical protein ZEAMMB73_483204, hypothetical protein ZEAMMB73_269466, and tubulin beta-7 chain. The following were identified as H. seropedicae proteins: peroxiredoxin protein, EF-Tu elongation factor protein, cation transport ATPase, NADPH:quinone oxidoreductase, dinitrogenase reductase, and type III secretion ATP synthase. Our results presented the first evidence of type III secretion ATP synthase expression during H. seropedicae-maize root interaction.

NEW FORMS OF INTERACTION IN HIGHER EDUCATION

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Emanuela Maria AVRAM

2017-12-01

Full Text Available Interactivity in the academic environment is a key element of the communication policy of higher education institutions. In the teaching-learning process, mobile technology creates interactivity and offers the ability to access learning resources anywhere and anytime. The main objective of this study is to highlight the importance of mobile technology in the communication and learning process in academia. The results reveal that learning activities which are engaged in the university classroom could be continued and developed through mobile interaction which has become a great tool for the higher education institutions to communicate virtually with anyone despite physical distance. Mobile technologies offer new ways of creating and disseminating knowledge and can be used to improve the overall learning experience of students and teachers.

THE INTERACTION BETWEEN INSTITUTIONAL ENVIRONMENT AND INNOVATIVE ENTREPRENEURSHIP IN UKRAINE

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I. Prylutska

2014-09-01

Full Text Available The paper evaluates the interaction between institutional environment and innovative entrepreneurship in Ukraine. The factors which effect on its development are revealed. The study substantiates the most effective institutions on the development of the innovative entrepreneurship in Ukraine.

Interaction of human laminin receptor with Sup35, the [PSI⁺] prion-forming protein from S. cerevisiae: a yeast model for studies of LamR interactions with amyloidogenic proteins.

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Christine Pampeno

Full Text Available The laminin receptor (LamR is a cell surface receptor for extracellular matrix laminin, whereas the same protein within the cell interacts with ribosomes, nuclear proteins and cytoskeletal fibers. LamR has been shown to be a receptor for several bacteria and viruses. Furthermore, LamR interacts with both cellular and infectious forms of the prion protein, PrP(C and PrP(Sc. Indeed, LamR is a receptor for PrP(C. Whether LamR interacts with PrP(Sc exclusively in a capacity of the PrP receptor, or LamR specifically recognizes prion determinants of PrP(Sc, is unclear. In order to explore whether LamR has a propensity to interact with prions and amyloids, we examined LamR interaction with the yeast prion-forming protein, Sup35. Sup35 is a translation termination factor with no homology or functional relationship to PrP. Plasmids expressing LamR or LamR fused with the green fluorescent protein (GFP were transformed into yeast strain variants differing by the presence or absence of the prion conformation of Sup35, respectively [PSI⁺] and [psi⁻]. Analyses by immunoprecipitation, centrifugal fractionation and fluorescent microscopy reveal interaction between LamR and Sup35 in [PSI⁺] strains. The presence of [PSI⁺] promotes LamR co-precipitation with Sup35 as well as LamR aggregation. In [PSI⁺] cells, LamR tagged with GFP or mCherry forms bright fluorescent aggregates that co-localize with visible [PSI⁺] foci. The yeast prion model will facilitate studying the interaction of LamR with amyloidogenic prions in a safe and easily manipulated system that may lead to a better understanding and treatment of amyloid diseases.

Learning from tutorials: a qualitative study of approaches to learning and perceptions of tutorial interaction

DEFF Research Database (Denmark)

Herrmann, Kim Jesper

2014-01-01

This study examines differences in university students’ approaches to learning when attending tutorials as well as variation in students’ perceptions of tutorials as an educational arena. In-depth qualitative analysis of semi-structured interviews with undergraduates showed how surface and deep...... approaches to learning were revealed in the students’ note-taking, listening, and engaging in dialogue. It was also shown how variation in the students’ approaches to learning were coherent with variation in the students’ perceptions of the tutors’ pedagogical role, the value of peer interaction......, and the overall purpose of tutorials. The results are discussed regarding the paradox that students relying on surface approaches to learning seemingly are the ones least likely to respond to tutorials in the way they were intended....

Conflict interaction management as a cultural phenomenon

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Е L Ryabova

2009-12-01

Full Text Available The article provides the definition for the concept of conflict interaction culture, reveals its functions as well as the structure of its elements and components. Conflict interactions are also examined in the paper.

Small scale lithium-lead/water-interaction studies

International Nuclear Information System (INIS)

Kranert, O.; Kottowski, H.

1991-01-01

One current concept in fusion blanket design is to utilize water as the coolant and liquid lithium-lead as the breeding/neutron multiplier material. Considering the complex design of the blanket module, it is likely that a water leakage into the liquid alloy may occur due to a tube rupture provoking an intolerable pressure increase in the blanket module. The pressure increase is caused by the combined chemical and thermohydraulic reaction of lithium-lead with water. Experiments which simulate such a transient event are necessary to obtain information which is important for the blanket module design. The interaction has been investigated by conducting small-scale experiments at various injection pressures, alloy- and coolant temperatures. Besides using eutectic Li 17 Pb 83 , Li 7 Pb 2 , lithium and lead have been used. Among other results, the experiments indicate increasing chemical reaction with increasing lithium concentration. At the same time, the chemical reaction inhibits violent thermohydaulic reactions due to the attenuating effect of the hydrogen produced. The preliminary epxerimental results from Li 17 Pb 83 and Li 7 Pb 2 reveal that the pressure- and temperature transients caused by the chemical and thermohydraulic reactions lie within technically manageable limits. (orig.)

Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors

International Nuclear Information System (INIS)

Aghazadeh, Mustafa; Mirzaei, Mahmoud

2008-01-01

Hydrogen bond (HB) interactions are studied in the real crystalline structure of sulfamerazine by density functional theory (DFT) calculations of the electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (single) and four-molecule (cluster) models of sulfamerazine are created by available crystal coordinates and the EFG tensors are calculated in both models to indicate the influence of HB interactions on the tensors. Directly relate to the experiments, the calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant (qcc) and asymmetry parameter (η Q ). The evaluated NQR parameters reveal that due to contribution of the target molecule to N-H...N and N-H...O types of HB interactions, the EFG tensors at the sites of various nuclei are influenced from single model to the target molecule in cluster. Additionally, O2, N4, and H2 nuclei of the target molecule are significantly influenced by HB interactions, consequently, they have the major contributions to HB interactions in cluster model of sulfamerazine. The calculations are performed employing B3LYP method and 6-311++G** basis set using GAUSSIAN 98 suite of program

Interaction of magnetic resonators studied by the magnetic field enhancement

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Yumin Hou

2013-12-01

Full Text Available It is the first time that the magnetic field enhancement (MFE is used to study the interaction of magnetic resonators (MRs, which is more sensitive than previous parameters–shift and damping of resonance frequency. To avoid the coherence of lattice and the effect of Bloch wave, the interaction is simulated between two MRs with same primary phase when the distance is changed in the range of several resonance wavelengths, which is also compared with periodic structure. The calculated MFE oscillating and decaying with distance with the period equal to resonance wavelength directly shows the retardation effect. Simulation also shows that the interaction at normal incidence is sensitive to the phase correlation which is related with retardation effect and is ultra-long-distance interaction when the two MRs are strongly localized. When the distance is very short, the amplitude of magnetic resonance is oppressed by the strong interaction and thus the MFE can be much lower than that of single MR. This study provides the design rules of metamaterials for engineering resonant properties of MRs.

Utility of Interactional Strategies in the Study of Formal Operations Reasoning.

Science.gov (United States)

Siegler, Robert S.

This paper argues in favor of using interactional strategies in the study of formal operations reasoning. Interactional designs allow a convergent approach to specifying processes underlying the interaction of variables. In contrast, current methodologies contain two inherent disadvantages: they have limited utility in specifying the processes…

Organoid culture systems to study host-pathogen interactions

NARCIS (Netherlands)

Dutta, Devanjali; Clevers, Hans

2017-01-01

Recent advances in host-microbe interaction studies in organoid cultures have shown great promise and have laid the foundation for much more refined future studies using these systems. Modeling of Zika virus (ZIKV) infection in cerebral organoids have helped us understand its association with

Multiple analytical approaches reveal distinct gene-environment interactions in smokers and non smokers in lung cancer.

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Rakhshan Ihsan

Full Text Available Complex disease such as cancer results from interactions of multiple genetic and environmental factors. Studying these factors singularly cannot explain the underlying pathogenetic mechanism of the disease. Multi-analytical approach, including logistic regression (LR, classification and regression tree (CART and multifactor dimensionality reduction (MDR, was applied in 188 lung cancer cases and 290 controls to explore high order interactions among xenobiotic metabolizing genes and environmental risk factors. Smoking was identified as the predominant risk factor by all three analytical approaches. Individually, CYP1A1*2A polymorphism was significantly associated with increased lung cancer risk (OR = 1.69;95%CI = 1.11-2.59,p = 0.01, whereas EPHX1 Tyr113His and SULT1A1 Arg213His conferred reduced risk (OR = 0.40;95%CI = 0.25-0.65,p<0.001 and OR = 0.51;95%CI = 0.33-0.78,p = 0.002 respectively. In smokers, EPHX1 Tyr113His and SULT1A1 Arg213His polymorphisms reduced the risk of lung cancer, whereas CYP1A1*2A, CYP1A1*2C and GSTP1 Ile105Val imparted increased risk in non-smokers only. While exploring non-linear interactions through CART analysis, smokers carrying the combination of EPHX1 113TC (Tyr/His, SULT1A1 213GG (Arg/Arg or AA (His/His and GSTM1 null genotypes showed the highest risk for lung cancer (OR = 3.73;95%CI = 1.33-10.55,p = 0.006, whereas combined effect of CYP1A1*2A 6235CC or TC, SULT1A1 213GG (Arg/Arg and betel quid chewing showed maximum risk in non-smokers (OR = 2.93;95%CI = 1.15-7.51,p = 0.01. MDR analysis identified two distinct predictor models for the risk of lung cancer in smokers (tobacco chewing, EPHX1 Tyr113His, and SULT1A1 Arg213His and non-smokers (CYP1A1*2A, GSTP1 Ile105Val and SULT1A1 Arg213His with testing balance accuracy (TBA of 0.6436 and 0.6677 respectively. Interaction entropy interpretations of MDR results showed non-additive interactions of tobacco chewing with

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

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Oyang Yen-Jen

2010-10-01

Full Text Available Abstract 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.

A numerical study on ship-ship interaction in shallow and restricted waterway

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Sungwook Lee

2015-09-01

Full Text Available In the present study, a numerical prediction method on the hydrodynamic interaction force and moment between two ships in shallow and restricted waterway is presented. Especially, the present study proposes a methodology to overcome the limitation of the two dimensional perturbation method which is related to the moored-passing ship interaction. The validation study was performed and compared with the experiment, firstly. Afterward, in order to propose a methodology in terms with the moored-passing ship interaction, further studies were performed for the moored-passing ship case with a Reynolds Averaged Navier-Stokes (RANS calculation which is using OpenFOAM with Arbitrary Coupled Mesh Interface (ACMI technique and compared with the experiment result. Finally, the present study proposes a guide to apply the two dimensional perturbation method to the moored-passing ship interaction. In addition, it presents a possibility that the RANS calculation with ACMI can applied to the ship-ship interaction without using a overset moving grid technique.

A theoretical study of adsorbate-adsorbate interactions on Ru(0001)

DEFF Research Database (Denmark)

Mortensen, Jens Jørgen; Hammer, Bjørk; Nørskov, Jens Kehlet

1998-01-01

the barrier for dissociation, whereas S will increase it. The interaction with alkali atoms is mainly of an electrostatic nature. The poisoning by S is due to two kinds of repulsive interactions: a Pauli repulsion and a reduced covalent bond strength between the adsorbate and the surface d-electrons. In order...... to investigate these different interactions in more detail, we look at three different species (N atoms, and terminally bonded N(2) and CO) and use them as probes to study their interaction with two modifier atoms (Na and S). The two modifier atoms have very different properties, which allows us to decouple...

Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies.

Science.gov (United States)

Hüls, Anke; Krämer, Ursula; Carlsten, Christopher; Schikowski, Tamara; Ickstadt, Katja; Schwender, Holger

2017-12-16

Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. In such situations and in the presence of predominant marginal genetic effects, we have shown in a previous study that GRS with internal weights from marginal genetic effects ("GRS-marginal-internal") are a powerful and reliable alternative to single SNP approaches or the use of unweighted GRS. However, this approach might not be appropriate for detecting predominant interactions, i.e. interactions showing an effect stronger than the marginal genetic effect. In this paper, we present a weighting approach for such predominant interactions ("GRS-interaction-training") in which parts of the data are used to estimate the weights from the interaction terms and the remaining data are used to determine the GRS. We conducted a simulation study for the detection of GxE interactions in which we evaluated power, type I error and sign-misspecification. We compared this new weighting approach to the GRS-marginal-internal approach and to GRS with external weights. Our simulation study showed that in the absence of external weights and with predominant interaction effects, the highest power was reached with the GRS-interaction-training approach. If marginal genetic effects were predominant, the GRS-marginal-internal approach was more appropriate. Furthermore, the power to detect interactions reached by the GRS-interaction-training approach was only slightly lower than the power achieved by GRS with external weights. The power of the GRS-interaction-training approach was confirmed in a real data application to the Traffic, Asthma and Genetics (TAG) Study (N = 4465 observations). When appropriate external weights are unavailable, we

The Role of Chaperone-subunit Usher Domain Interactions in the Mechanism of Bacterial Pilus Biogenesis Revealed by ESI-MS*

Science.gov (United States)

Morrissey, Bethny; Leney, Aneika C.; Toste Rêgo, Ana; Phan, Gilles; Allen, William J.; Verger, Denis; Waksman, Gabriel; Ashcroft, Alison E.; Radford, Sheena E.

2012-01-01

The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species. PMID:22371487

The role of chaperone-subunit usher domain interactions in the mechanism of bacterial pilus biogenesis revealed by ESI-MS.

Science.gov (United States)

Morrissey, Bethny; Leney, Aneika C; Toste Rêgo, Ana; Phan, Gilles; Allen, William J; Verger, Denis; Waksman, Gabriel; Ashcroft, Alison E; Radford, Sheena E

2012-07-01

The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species.

Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses

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Hong Li

2017-05-01

Full Text Available Many plant pathogens secrete virulence effectors into host cells to target important proteins in host cellular network. However, the dynamic interactions between effectors and host cellular network have not been fully understood. Here, an integrative network analysis was conducted by combining Arabidopsis thaliana protein–protein interaction network, known targets of Pseudomonas syringae and Hyaloperonospora arabidopsidis effectors, and gene expression profiles in the immune response. In particular, we focused on the characteristic network topology of the effector targets and differentially expressed genes (DEGs. We found that effectors tended to manipulate key network positions with higher betweenness centrality. The effector targets, especially those that are common targets of an individual effector, tended to be clustered together in the network. Moreover, the distances between the effector targets and DEGs increased over time during infection. In line with this observation, pathogen-susceptible mutants tended to have more DEGs surrounding the effector targets compared with resistant mutants. Our results suggest a common plant–pathogen interaction pattern at the cellular network level, where pathogens employ potent local impact mode to interfere with key positions in the host network, and plant organizes an in-depth defense by sequentially activating genes distal to the effector targets.

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

Science.gov (United States)

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Flow cytometry approach for studying the interaction between ...

African Journals Online (AJOL)

Flow cytometry approach for studying the interaction between Bacillus mojavensis and Alternaria alternata. Asma Milet, Noreddine Kacem Chaouche, Laid Dehimat, Asma Ait Kaki, Mounira Kara Ali, Philippe Thonart ...

Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

Science.gov (United States)

Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

2018-05-19

Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA.

Science.gov (United States)

Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

2018-03-15

Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 10 3 M -1 , which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) were -63.19kJ mol -1 and -141.92J mol -1 K -1 , indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Study of the interaction of cysteamine and cystamine with the dipalmitoyl phosphatidylcholine

International Nuclear Information System (INIS)

Berleur, F.; Roman, V.; Jaskierowicz, D.; Audet, M.; Fatome, M.

1984-10-01

The thermodynamic study of the liposome-radioprotector system brings information on this interaction. The interaction is essentially electrostatic between the phosphate sites and the radioprotector cationic groups and this study could bring further information about the interaction between cysteamine and polyelectrolytic structures, DNA for example, and about the radioprotective properties of this drug [fr

In Situ Tagged nsp15 Reveals Interactions with Coronavirus Replication/Transcription Complex-Associated Proteins

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Jeremiah Athmer

2017-01-01

Full Text Available Coronavirus (CoV replication and transcription are carried out in close proximity to restructured endoplasmic reticulum (ER membranes in replication/transcription complexes (RTC. Many of the CoV nonstructural proteins (nsps are required for RTC function; however, not all of their functions are known. nsp15 contains an endoribonuclease domain that is conserved in the CoV family. While the enzymatic activity and crystal structure of nsp15 are well defined, its role in replication remains elusive. nsp15 localizes to sites of RNA replication, but whether it acts independently or requires additional interactions for its function remains unknown. To begin to address these questions, we created an in situ tagged form of nsp15 using the prototypic CoV, mouse hepatitis virus (MHV. In MHV, nsp15 contains the genomic RNA packaging signal (P/S, a 95-bp RNA stem-loop structure that is not required for viral replication or nsp15 function. Utilizing this knowledge, we constructed an internal hemagglutinin (HA tag that replaced the P/S. We found that nsp15-HA was localized to discrete perinuclear puncta and strongly colocalized with nsp8 and nsp12, both well-defined members of the RTC, but not the membrane (M protein, involved in virus assembly. Finally, we found that nsp15 interacted with RTC-associated proteins nsp8 and nsp12 during infection, and this interaction was RNA independent. From this, we conclude that nsp15 localizes and interacts with CoV proteins in the RTC, suggesting it plays a direct or indirect role in virus replication. Furthermore, the use of in situ epitope tags could be used to determine novel nsp-nsp interactions in coronaviruses.

Studies on the interaction between nanodiamond and human hemoglobin by surface tension measurement and spectroscopy methods.

Science.gov (United States)

Pishkar, Leila; Taheri, Saba; Makarem, Somayeh; Alizadeh Zeinabad, Hojjat; Rahimi, Arash; Saboury, Ali Akbar; Falahati, Mojtaba

2017-02-01

In this study, a novel method to probe molecular interactions and binding of human hemoglobin (Hb) with nanodiamond (ND) was introduced based on the surface tension measurement. This method complements conventional techniques, which are basically done by zeta potential and dynamic light scattering (DLS) measurements, near and far circular dichroism (CD) spectroscopy, intrinsic and extrinsic fluorescence spectroscopy. Addition of ND to Hb solution increased the surface tension value of Hb-ND complex relative to those of Hb and ND molecules. The zeta potential values reveled that Hb and ND provide identical charge distribution at pH 7.5. DLS measurements demonstrated that Hb, ND, and ND-Hb complex have hydrodynamic radiuses of 98.37 ± 4.57, 122.07 ± 7.88 nm and 62.27 ± 3.70 at pH of 7.5 respectively. Far and near UV-CD results indicated the loss of α-helix structure and conformational changes of Hb, respectively. Intrinsic fluorescence data demonstrated that the fluorescence quenching of Hb by ND was the result of the static quenching. The hydrophobic interaction plays a pivotal role in the interaction of ND with Hb. Fluorescence intensity changes over time revealed conformational change of Hb continues after the mixing of the components (Hb-ND) till 15 min, which is indicative of the denaturation of the Hb relative to the protein control. Extrinsic fluorescence data showed a considerable enhancement of the ANS fluorescence intensity of Hb-ND system relative to the Hb till 60 nM of ND, likely persuaded by greater exposure of nonpolar residues of Hb hydrophobic pocket. The remarkable decrease in T m value of Hb in Hb-ND complex exhibits interaction of Hb with ND conducts to conformational changes of Hb. This study offers consequential discrimination into the interaction of ND with proteins, which may be of significance for further appeal of these nanoparticles in biotechnology prosecution.

Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study.

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Melinda C Aldrich

Full Text Available BACKGROUND: Smoking tobacco reduces lung function. African Americans have both lower lung function and decreased metabolism of tobacco smoke compared to European Americans. African ancestry is also associated with lower pulmonary function in African Americans. We aimed to determine whether African ancestry modifies the association between smoking and lung function and its rate of decline in African Americans. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated a prospective ongoing cohort of 1,281 African Americans participating in the Health, Aging, and Body Composition (Health ABC Study initiated in 1997. We also examined an ongoing prospective cohort initiated in 1985 of 1,223 African Americans in the Coronary Artery Disease in Young Adults (CARDIA Study. Pulmonary function and tobacco smoking exposure were measured at baseline and repeatedly over the follow-up period. Individual genetic ancestry proportions were estimated using ancestry informative markers selected to distinguish European and West African ancestry. African Americans with a high proportion of African ancestry had lower baseline forced expiratory volume in one second (FEV₁ per pack-year of smoking (-5.7 ml FEV₁/ smoking pack-year compared with smokers with lower African ancestry (-4.6 ml in FEV₁/ smoking pack-year (interaction P value  = 0.17. Longitudinal analyses revealed a suggestive interaction between smoking, and African ancestry on the rate of FEV(1 decline in Health ABC and independently replicated in CARDIA. CONCLUSIONS/SIGNIFICANCE: African American individuals with a high proportion of African ancestry are at greater risk for losing lung function while smoking.

A Tendon Cell Specific RNAi Screen Reveals Novel Candidates Essential for Muscle Tendon Interaction.

Directory of Open Access Journals (Sweden)

Prabhat Tiwari

Full Text Available Tendons are fibrous connective tissue which connect muscles to the skeletal elements thus acting as passive transmitters of force during locomotion and provide appropriate body posture. Tendon-derived cues, albeit poorly understood, are necessary for proper muscle guidance and attachment during development. In the present study, we used dorsal longitudinal muscles of Drosophila and their tendon attachment sites to unravel the molecular nature of interactions between muscles and tendons. We performed a genetic screen using RNAi-mediated knockdown in tendon cells to find out molecular players involved in the formation and maintenance of myotendinous junction and found 21 candidates out of 2507 RNAi lines screened. Of these, 19 were novel molecules in context of myotendinous system. Integrin-βPS and Talin, picked as candidates in this screen, are known to play important role in the cell-cell interaction and myotendinous junction formation validating our screen. We have found candidates with enzymatic function, transcription activity, cell adhesion, protein folding and intracellular transport function. Tango1, an ER exit protein involved in collagen secretion was identified as a candidate molecule involved in the formation of myotendinous junction. Tango1 knockdown was found to affect development of muscle attachment sites and formation of myotendinous junction. Tango1 was also found to be involved in secretion of Viking (Collagen type IV and BM-40 from hemocytes and fat cells.

Interaction of monomeric Ebola VP40 protein with a plasma membrane: A coarse-grained molecular dynamics (CGMD) simulation study.

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Mohamad Yusoff, Mohamad Ariff; Abdul Hamid, Azzmer Azzar; Mohammad Bunori, Noraslinda; Abd Halim, Khairul Bariyyah

2018-06-01

Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP 2 ) and phosphatidylserine (PS) via its cationic patch. The hydrophobic loop at the C-terminal domain has also been shown to be important in the interaction between the VP40 and the membrane. However, details of the molecular mechanisms underpinning their interactions are not fully understood. This study aimed at investigating the effects of mutation in the cationic patch and hydrophobic loop on the interaction between the VP40 monomer and the plasma membrane using coarse-grained molecular dynamics simulation (CGMD). Our simulations revealed that the interaction between VP40 and the plasma membrane is mediated by the cationic patch residues. This led to the clustering of PIP 2 around the protein in the inner leaflet as a result of interactions between some cationic residues including R52, K127, K221, K224, K225, K256, K270, K274, K275 and K279 and PIP 2 lipids via electrostatic interactions. Mutation of the cationic patch or hydrophobic loop amino acids caused the protein to bind at the inner leaflet of the plasma membrane in a different orientation, where no significant clustering of PIP 2 was observed around the mutated protein. This study provides basic understanding of the interaction of the VP40 monomer and its mutants with the plasma membrane. Copyright © 2018 Elsevier Inc. All rights reserved.

Computational studies on the interactions of nanomaterials with proteins and their impacts

International Nuclear Information System (INIS)

An De-Yi; Li Jing-Yuan; Su Ji-Guo; Li Chun-Hua

2015-01-01

The intensive concern over the biosafety of nanomaterials demands the systematic study of the mechanisms underlying their biological effects. Many of the effects of nanomaterials can be attributed to their interactions with proteins and their impacts on protein function. On the other hand, nanomaterials show potential for a variety of biomedical applications, many of which also involve direct interactions with proteins. In this paper, we review some recent computational studies on this subject, especially those investigating the interactions of carbon and gold nanomaterials. Beside hydrophobic and π-stacking interactions, the mode of interaction of carbon nanomaterials can also be regulated by their functional groups. The coatings of gold nanomaterials similarly adjust their mode of interaction, in addition to coordination interactions with the sulfur groups of cysteine residues and the imidazole groups of histidine residues. Nanomaterials can interact with multiple proteins and their impacts on protein activity are attributed to a wide spectrum of mechanisms. These findings on the mechanisms of nanomaterial–protein interactions can further guide the design and development of nanomaterials to realize their application in disease diagnosis and treatment. (paper)

Spectroscopic study on the interaction of Bacillus subtilis {alpha}-amylase with cetyltrimethylammonium bromide

Energy Technology Data Exchange (ETDEWEB)

Omidyan, R., E-mail: r.omidyan@sci.ui.ac.i [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731 (Iran, Islamic Republic of); Kazemi, S.H. [Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731 (Iran, Islamic Republic of); Bordbar, A.K. [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Zaynalpour, S. [Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731 (Iran, Islamic Republic of)

2011-06-15

The interaction between {alpha}-amylase from Bacillus subtilis and cetyltrimethylammonium bromide (CTAB) has been investigated at various temperature conditions using fluorescence and circular dichroism (CD) spectroscopic methods. Fluorescence data revealed that the fluorescence quenching of {alpha}-amylase by CTAB is the result of complex formation between CTAB and {alpha}-amylase. The thermodynamic analysis on the binding interaction data shows that the interactions are strongly exothermic ({Delta}H{sup o}=-17.92 kJ mol{sup -1}) accompanied with increase in entropy ({Delta}S{sup o} between 109 to 135 J mol{sup -1} K{sup -1}). Thus the binding of CTAB to {alpha}-amylase is both enthalpic and entropic driven, which represent the predominate role of both electrostatic and hydrophobic interactions in complex formation process. The values of 2.17x10{sup -3} M{sup -1} and 1.30 have been obtained from associative binding constant (K{sub a}) and stoichiometry of binding number (n), from analysis of fluorescence data, respectively. Circular dichroism spectra showed the substantial conformational changes in secondary structure of {alpha}-amylase due to binding of CTAB, which represents the complete destruction of both secondary and tertiary structure of {alpha}-amylase by CTAB. - Research highlights: {yields} The Fluorescence quenching effect of {alpha}-amylase by CTAB is a consequence of formation {alpha}-amylase-CTAB complex. {yields} The {alpha}-helical analyzing from the CD spectra in the various concentration of CTAB shows strongly deformation of {alpha}-amylase. {yields} Thermodynamic analysis of quenching verify that the interactions are both enthalpy and entropic driven.

Thermodynamic study of the effects of ethanol on the interaction of ochratoxin A with human serum albumin

Energy Technology Data Exchange (ETDEWEB)

Li, Yin [Department of General and Physical Chemistry, University of Pécs, Ifjúság 6, H-7624 Pécs (Hungary); János Szentágothai Research Center, Ifjúság 20, H-7624 Pécs (Hungary); Czibulya, Zsuzsanna [Department of General and Physical Chemistry, University of Pécs, Ifjúság 6, H-7624 Pécs (Hungary); János Szentágothai Research Center, Ifjúság 20, H-7624 Pécs (Hungary); Chimie et Biologie des Membranes et Nanoobjets, CNRS-Université de Bordeaux, UMR 52478, ENITAB, Pessac (France); Poór, Miklós [Institute of Laboratory Medicine, University of Pécs, Ifjúság 13, H-7624, Pécs (Hungary); Lecomte, Sophie [Chimie et Biologie des Membranes et Nanoobjets, CNRS-Université de Bordeaux, UMR 52478, ENITAB, Pessac (France); Kiss, László [Department of General and Physical Chemistry, University of Pécs, Ifjúság 6, H-7624 Pécs (Hungary); János Szentágothai Research Center, Ifjúság 20, H-7624 Pécs (Hungary); and others

2014-04-15

Ethanol effect on the interaction of ochratoxin A (OTA) with human serum albumin (HSA) was investigated by using fluorescence spectroscopy and Raman spectroscopy. The Raman results showed that after the binding of OTA, the microenvironment of tryptophan residue on HSA became less hydrophobic. The fluorescence quenching observations revealed that the binding constant for the binding of OTA to HSA decreased as ethanol concentration increased. The thermodynamic studies showed that the binding process of OTA to HSA switched from being entropy-driven to enthalpy-driven in the presence of increasing concentrations (0.7–24.7%, vol/vol) of ethanol. Enthalpy–entropy compensation effect for the binding of OTA to HSA in the presence of different ethanol concentrations had been found. Based on the thermodynamic analyses, we concluded that the ethanol-induced variation of the shape of binding site of OTA on HSA and the solvent reorganization surrounding the OTA–HSA complex are the two dominant effects. -- Highlights: • The presence of ethanol can prohibit the binding of OTA to HSA. • Microenvironment of Trp214 on HSA becomes less hydrophobic after the binding of OTA. • Ethanol induces the interaction from being entropy-driven to enthalpy-driven. • Enthalpy–entropy compensation for the interaction was found.

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

Directory of Open Access Journals (Sweden)

Rui M. Almeida

2016-08-01

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

Constructing phylogenetic trees using interacting pathways.

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Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking.

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Tan, Xijuan; Wang, Zhuming; Chen, Donghua; Luo, Kai; Xiong, Xunyu; Song, Zhenghua

2014-08-01

The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI-CL model of lg[(I0-I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 10(3)-10(5) L mol(-1) and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT-pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT. Copyright © 2014 Elsevier Ltd. All rights reserved.

A QCM-D study of the concentration- and time-dependent interactions of human LL37 with model mammalian lipid bilayers.

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Lozeau, Lindsay D; Rolle, Marsha W; Camesano, Terri A

2018-07-01

The human antimicrobial peptide LL37 is promising as an alternative to antibiotics due to its biophysical interactions with charged bacterial lipids. However, its clinical potential is limited due to its interactions with zwitterionic mammalian lipids leading to cytotoxicity. Mechanistic insight into the LL37 interactions with mammalian lipids may enable rational design of less toxic LL37-based therapeutics. To this end, we studied concentration- and time-dependent interactions of LL37 with zwitterionic model phosphatidylcholine (PC) bilayers with quartz crystal microbalance with dissipation (QCM-D). LL37 mass adsorption and PC bilayer viscoelasticity changes were monitored by measuring changes in frequency (Δf) and dissipation (ΔD), respectively. The Voigt-Kelvin viscoelastic model was applied to Δf and ΔD to study changes in bilayer thickness and density with LL37 concentration. At low concentrations (0.10-1.00 μM), LL37 adsorbed onto bilayers in a concentration-dependent manner. Further analyses of Δf, ΔD and thickness revealed that peptide saturation on the bilayers was a threshold for interactions observed above 2.00 μM, interactions that were rapid, multi-step, and reached equilibrium in a concentration- and time-dependent manner. Based on these data, we proposed a model of stable transmembrane pore formation at 2.00-10.0 μM, or transition from a primarily lipid to a primarily protein film with a transmembrane pore formation intermediate state at concentrations of LL37 > 10 μM. The concentration-dependent interactions between LL37 and PC bilayers correlated with the observed concentration-dependent biological activities of LL37 (antimicrobial, immunomodulatory and non-cytotoxic at 0.1-1.0 μM, hemolytic and some cytotoxicity at 2.0-13 μM and cytotoxic at >13 μM). Copyright © 2018 Elsevier B.V. All rights reserved.

Comparative analysis of three drug-drug interaction screening systems against probable clinically relevant drug-drug interactions: a prospective cohort study.

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Muhič, Neža; Mrhar, Ales; Brvar, Miran

2017-07-01

Drug-drug interaction (DDI) screening systems report potential DDIs. This study aimed to find the prevalence of probable DDI-related adverse drug reactions (ADRs) and compare the clinical usefulness of different DDI screening systems to prevent or warn against these ADRs. A prospective cohort study was conducted in patients urgently admitted to medical departments. Potential DDIs were checked using Complete Drug Interaction®, Lexicomp® Online™, and Drug Interaction Checker®. The study team identified the patients with probable clinically relevant DDI-related ADRs on admission, the causality of which was assessed using the Drug Interaction Probability Scale (DIPS). Sensitivity, specificity, and positive and negative predictive values of screening systems to prevent or warn against probable DDI-related ADRs were evaluated. Overall, 50 probable clinically relevant DDI-related ADRs were found in 37 out of 795 included patients taking at least two drugs, most common of them were bleeding, hyperkalemia, digitalis toxicity, and hypotension. Complete Drug Interaction showed the best sensitivity (0.76) for actual DDI-related ADRs, followed by Lexicomp Online (0.50), and Drug Interaction Checker (0.40). Complete Drug Interaction and Drug Interaction Checker had positive predictive values of 0.07; Lexicomp Online had 0.04. We found no difference in specificity and negative predictive values among these systems. DDI screening systems differ significantly in their ability to detect probable clinically relevant DDI-related ADRs in terms of sensitivity and positive predictive value.

A little similarity goes a long way: the effects of peripheral but self-revealing similarities on improving and sustaining interracial relationships.

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West, Tessa V; Magee, Joe C; Gordon, Sarah H; Gullett, Lindy

2014-07-01

Integrating theory on close relationships and intergroup relations, we construct a manipulation of similarity that we demonstrate can improve interracial interactions across different settings. We find that manipulating perceptions of similarity on self-revealing attributes that are peripheral to the interaction improves interactions in cross-race dyads and racially diverse task groups. In a getting-acquainted context, we demonstrate that the belief that one's different-race partner is similar to oneself on self-revealing, peripheral attributes leads to less anticipatory anxiety than the belief that one's partner is similar on peripheral, nonself-revealing attributes. In another dyadic context, we explore the range of benefits that perceptions of peripheral, self-revealing similarity can bring to different-race interaction partners and find (a) less anxiety during interaction, (b) greater interest in sustained contact with one's partner, and (c) stronger accuracy in perceptions of one's partners' relationship intentions. By contrast, participants in same-race interactions were largely unaffected by these manipulations of perceived similarity. Our final experiment shows that among small task groups composed of racially diverse individuals, those whose members perceive peripheral, self-revealing similarity perform superior to those who perceive dissimilarity. Implications for using this approach to improve interracial interactions across different goal-driven contexts are discussed.

Study of weak interaction with p-p colliding beam

International Nuclear Information System (INIS)

Arafune, Jiro; Sugawara, Hirotaka

1975-01-01

Weak interaction in the energy range of TRISTAN project is discussed. The cross-section of production of weak boson in p-p reaction was calculated with the parton model. The observation of weak boson may be possible. The production rate of neutral weak boson was also estimated on the basis of the Weinberg model, and was almost same as that of weak boson. The method of observation of weak boson is suggested. The direct method is the observation of lepton pair due to the decay of neutral weak boson. It is expected that the spectrum of decay products (+ -) in the decay of weak boson shows a characteristic feature, and it shows the existence of weak boson. Weak interaction makes larger contribution in case of large momentum transfer than electromagnetic interaction. When the momentum transfer is larger than 60 GeV/c, the contribution of weak interaction is dominant over the others. Therefore, the experiments at high energy will give informations concerning the relations among the interactions of elementary particles. Possibility of study on the Higgs scalar meson is also discussed. (Kato, T.)

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution

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Koslen, Hannah R.; Chiel, Hillel J.; Mizutani, Claudia Mieko

2014-01-01

Morphogenetic gradients are essential to allocate cell fates in embryos of varying sizes within and across closely related species. We previously showed that the maternal NF-κB/Dorsal (Dl) gradient has acquired different shapes in Drosophila species, which result in unequally scaled germ layers along the dorso-ventral axis and the repositioning of the neuroectodermal borders. Here we combined experimentation and mathematical modeling to investigate which factors might have contributed to the fast evolutionary changes of this gradient. To this end, we modified a previously developed model that employs differential equations of the main biochemical interactions of the Toll (Tl) signaling pathway, which regulates Dl nuclear transport. The original model simulations fit well the D. melanogaster wild type, but not mutant conditions. To broaden the applicability of this model and probe evolutionary changes in gradient distributions, we adjusted a set of 19 independent parameters to reproduce three quantified experimental conditions (i.e. Dl levels lowered, nuclear size and density increased or decreased). We next searched for the most relevant parameters that reproduce the species-specific Dl gradients. We show that adjusting parameters relative to morphological traits (i.e. embryo diameter, nuclear size and density) alone is not sufficient to reproduce the species Dl gradients. Since components of the Tl pathway simulated by the model are fast-evolving, we next asked which parameters related to Tl would most effectively reproduce these gradients and identified a particular subset. A sensitivity analysis reveals the existence of nonlinear interactions between the two fast-evolving traits tested above, namely the embryonic morphological changes and Tl pathway components. Our modeling further suggests that distinct Dl gradient shapes observed in closely related melanogaster sub-group lineages may be caused by similar sequence modifications in Tl pathway components, which

Thermogravimetric studies of vapour-aerosol interactions

International Nuclear Information System (INIS)

Henshaw, J.; Newland, M.S.; Wood, S.J.

1991-01-01

Thermogravimetric analysis has been used to study the interaction of iodine vapour with cadmium, silver and manganese monoxide substrates. These studies have demonstrated the importance of time-dependence data on reaction rates. Iodine did not react with manganese monoxide (as expected from thermodynamic considerations); however, extensive reaction did occur with silver and cadmium. Two rate limiting mechanisms were observed: mass transfer of iodine molecules from the gas phase (leading to linear reaction rates) and parabolic kinetics (ie inversely proportional to the extent of reaction) when the rate was limited by a diffusion process through the reaction product. (author)

Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells

DEFF Research Database (Denmark)

Galli, Giorgio Giacomo; Carrara, Matteo; Francavilla, Chiara

2013-01-01

PRDM proteins belong to the SET- domain protein family involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we...... find that Prdm5 is highly expressed in mouse embryonic stem cells (mES) and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next generation sequencing technologies we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that......, despite Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, Cohesin and TFIIIC and co...

Entangled time in flocking: Multi-time-scale interaction reveals emergence of inherent noise.

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Niizato, Takayuki; Murakami, Hisashi

2018-01-01

Collective behaviors that seem highly ordered and result in collective alignment, such as schooling by fish and flocking by birds, arise from seamless shuffling (such as super-diffusion) and bustling inside groups (such as Lévy walks). However, such noisy behavior inside groups appears to preclude the collective behavior: intuitively, we expect that noisy behavior would lead to the group being destabilized and broken into small sub groups, and high alignment seems to preclude shuffling of neighbors. Although statistical modeling approaches with extrinsic noise, such as the maximum entropy approach, have provided some reasonable descriptions, they ignore the cognitive perspective of the individuals. In this paper, we try to explain how the group tendency, that is, high alignment, and highly noisy individual behavior can coexist in a single framework. The key aspect of our approach is multi-time-scale interaction emerging from the existence of an interaction radius that reflects short-term and long-term predictions. This multi-time-scale interaction is a natural extension of the attraction and alignment concept in many flocking models. When we apply this method in a two-dimensional model, various flocking behaviors, such as swarming, milling, and schooling, emerge. The approach also explains the appearance of super-diffusion, the Lévy walk in groups, and local equilibria. At the end of this paper, we discuss future developments, including extending our model to three dimensions.

Study on Human-structure Dynamic Interaction in Civil Engineering

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Gao, Feng; Cao, Li Lin; Li, Xing Hua

2018-06-01

The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

Interactions Dominate the Dynamics of Visual Cognition

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Stephen, Damian G.; Mirman, Daniel

2010-01-01

Many cognitive theories have described behavior as the summation of independent contributions from separate components. Contrasting views have emphasized the importance of multiplicative interactions and emergent structure. We describe a statistical approach to distinguishing additive and multiplicative processes and apply it to the dynamics of eye movements during classic visual cognitive tasks. The results reveal interaction-dominant dynamics in eye movements in each of the three tasks, and that fine-grained eye movements are modulated by task constraints. These findings reveal the interactive nature of cognitive processing and are consistent with theories that view cognition as an emergent property of processes that are broadly distributed over many scales of space and time rather than a componential assembly line. PMID:20070957

Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

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Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

2013-11-01

Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

An interactional ethnographic study of the construction of literate practices of science and writing in a university science classroom

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Sena, Nuno Afonso De Freitas Lopes De

An interactional ethnographic study informed by a sociocultural perspective was conducted to examine how a professor and students discursively and interactionally shaped the basis for engaging in the work of a community of geologists. Specifically, the study examined the role the Question of the Day, an interactive writing activity in the lecture, in affording students opportunities for learning the literate practices of science and how to incorporate them in thinking critically. A writing-intensive, introductory oceanography course given in the Geological Sciences Department was chosen because the professor designed it to emphasize writing in the discipline and science literacy within a science inquiry framework. The study was conducted in two phases: a pilot in 2002 and the current study in the Spring Quarter of 2003. Grounded in the view that members in a classroom construct a culture, this study explored the daily construction of the literate practices of science and writing. This view of classrooms was informed by four bodies of research: interactional ethnography, sociolinguistics sociology of science and Writing In the Disciplines. Through participant observation, data were collected in the lecture and laboratory settings in the form of field notes, video, interviews, and artifacts to explore issues of science literacy in discourse, social action, and writing. Examination of participation in the Question of the Day interactive writing activity revealed that it played a key role in initiating and supporting a view of science and inquiry. As the activity permitted collaboration, it encouraged students to engage in the social process to critically explore a discourse of science and key practices with and through their writing. In daily interaction, participants were shown to take up social positions as scientist and engage in science inquiry to explore theory, examine data, and articulately reformulate knowledge in making oral and written scientific arguments

TreePlus: interactive exploration of networks with enhanced tree layouts.

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Lee, Bongshin; Parr, Cynthia S; Plaisant, Catherine; Bederson, Benjamin B; Veksler, Vladislav D; Gray, Wayne D; Kotfila, Christopher

2006-01-01

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus.

Teacher-Student Interactions: Four Case Studies of Gender in Physical Education

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Davis, Kathryn; Nicaise, Virginia

2011-01-01

The aim of this study was to better understand gender interactions between teachers and students in high school physical education. Gender interactions were explored in relation to the theory of reflective practice. Interview data were examined as four case studies using individual and cross-case inductive analysis. Two common themes emerged: (a)…

Hi-Jack: a novel computational framework for pathway-based inference of host–pathogen interactions

KAUST Repository

Kleftogiannis, Dimitrios A.; Wong, Limsoon; Archer, John A.C.; Kalnis, Panos

2015-01-01

also describe host-pathogen interaction principles that can be used in the future for subsequent studies. Our case study on Mycobacterium tuberculosis (Mtb) revealed pathways in human-e.g. carbohydrate metabolism, lipids metabolism and pathways related

Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

Directory of Open Access Journals (Sweden)

Guo Hao

2011-05-01

Full Text Available Abstract Background High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance. Results Here we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes. Conclusions Our findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.

Correcting systematic inflation in genetic association tests that consider interaction effects: application to a genome-wide association study of posttraumatic stress disorder.

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Almli, Lynn M; Duncan, Richard; Feng, Hao; Ghosh, Debashis; Binder, Elisabeth B; Bradley, Bekh; Ressler, Kerry J; Conneely, Karen N; Epstein, Michael P

2014-12-01

Genetic association studies of psychiatric outcomes often consider interactions with environmental exposures and, in particular, apply tests that jointly consider gene and gene-environment interaction effects for analysis. Using a genome-wide association study (GWAS) of posttraumatic stress disorder (PTSD), we report that heteroscedasticity (defined as variability in outcome that differs by the value of the environmental exposure) can invalidate traditional joint tests of gene and gene-environment interaction. To identify the cause of bias in traditional joint tests of gene and gene-environment interaction in a PTSD GWAS and determine whether proposed robust joint tests are insensitive to this problem. The PTSD GWAS data set consisted of 3359 individuals (978 men and 2381 women) from the Grady Trauma Project (GTP), a cohort study from Atlanta, Georgia. The GTP performed genome-wide genotyping of participants and collected environmental exposures using the Childhood Trauma Questionnaire and Trauma Experiences Inventory. We performed joint interaction testing of the Beck Depression Inventory and modified PTSD Symptom Scale in the GTP GWAS. We assessed systematic bias in our interaction analyses using quantile-quantile plots and genome-wide inflation factors. Application of the traditional joint interaction test to the GTP GWAS yielded systematic inflation across different outcomes and environmental exposures (inflation-factor estimates ranging from 1.07 to 1.21), whereas application of the robust joint test to the same data set yielded no such inflation (inflation-factor estimates ranging from 1.01 to 1.02). Simulated data further revealed that the robust joint test is valid in different heteroscedasticity models, whereas the traditional joint test is invalid. The robust joint test also has power similar to the traditional joint test when heteroscedasticity is not an issue. We believe the robust joint test should be used in candidate-gene studies and GWASs of

A study of the interactions between glass-ionomer cement and S. sanguis biofilms

Science.gov (United States)

Hengtrakool, Chanotai

Glass-ionomer cements (GIC) have been used for dental procedures for many years and more recently in other medical applications such as bone cements, for bone reconstruction and also as drug release agents. The postulated caries-preventive activities of GIC are thought to result from their sealing ability, remineralization potential and antibacterial effects. Extensive 'in vitro' investigations have attempted to quantify these effects. In this study, an artificial mouth model, simulating 'in vivo' conditions at the tooth surface, was used to achieve a better understanding of the interaction of oral bacteria with the cements. This study investigated the interaction of Streptococcus sanguis, a common mouth commensal, with two glass-ionomer formulations (one containing fluoride and the other without fluoride ion) with particular reference to bacterial growth, changes in surface roughness and hardness of the glass-ionomer cement with respect to time. Restorative materials with rough surfaces will promote bacterial accumulation 'in vivo' and plaque formation is one factor in surface degradation. The constant depth film fermenter (CDFF) permits the examination of these phenomena and was used to investigate glass-ionomer/S. sanguis biofilm interaction over periods up to 14 days. In conjunction with these studies, surface roughness was measured using a 3-dimension laser profilometer and the surface hardness evaluated using a micro-indenter. Fluoride release from the cement was measured over 84 days. The results showed that autoclaving the CDFF prior to bacterial innoculate did not appear to affect the long-term fluoride release of the GIC. Laser profilometry revealed that the initial roughness and surface area of the GICs was significantly greater than the hydroxyapatite control. S. sanguis viable counts were significantly reduced for both glass-ionomer formulations in the shortterm, the greater reduction being with fluoride-GIC. S. sanguis biofilms produced similar

Studies on interfacial interactions of TiO2 nanoparticles with ...

Indian Academy of Sciences (India)

Administrator

Studies on interfacial interactions of TiO2 nanoparticles with bacterial cells under light and dark conditions by Swayamprava Dalai et al (pp 371–381). Graphical abstract. Sequence of events occurring in course of cell-NP interaction: Surface adsorption, internalization and bioaccumulation of NPs which leads to stress upon ...

Proteomic characterization of larval and adult developmental stages in Echinococcus granulosus reveals novel insight into host-parasite interactions.

Science.gov (United States)

Cui, Shu-Jian; Xu, Lei-Lei; Zhang, Ting; Xu, Ming; Yao, Jun; Fang, Cai-Yun; Feng, Zheng; Yang, Peng-Yuan; Hu, Wei; Liu, Feng

2013-06-12

Cystic hydatid disease is an important zoonosis caused by Echinococcus granulosus infection. The expression profiles of its parasitic life stages and host-Echinococcus interactions remain to be elucidated. Here, we identified 157 adult and 1588 protoscolex proteins (1610 in all), including 1290 novel identifications. Paramyosins and an antigen B (AgB) were the dominant adult proteins. Dog proteins (30) identified in adults indicated diminished local inflammation caused by adult infection. The protoscolex expresses proteins that have been reported to be antigens in other parasites, such as 6-phosphofructokinase and calcineurin B. Pathway analyses suggested that E. granulosus uses both aerobic and anaerobic carbohydrate metabolisms to generate ATP. E. granulosus expresses proteins involved in synthesis and metabolism of lipids or steroids. At least 339 of 390 sheep proteins identified in protoscolex were novel identifications not seen in previous analyses. IgGs and lambda light chains were the most abundant antibody species. Sheep proteins were enriched for detoxification pathways, implying that host detoxification effects play a central role during host-parasite interactions. Our study provides valuable data on E. granulosus expression characteristics, allowing novel insights into the molecular mechanisms involved in host-parasite interactions. In this study, the Echinococcus granulosus adult worm proteome was analyzed for the first time. The protein identification of E. granulosus protoscoleces was extended dramatically. We also identified the most abundant host proteins co-purified with Echinococcus. The results provide useful information pertaining to the molecular mechanisms behind host-Echinococcus interaction and Echinococcus biology. This data also increases the potential for identifying vaccine candidates and new therapeutic targets, and may aid in the development of protein probes for selective and sensitive diagnosis of echinococcosis infection. In

Time series analysis of embodied interaction: Movement variability and complexity matching as dyadic properties

Directory of Open Access Journals (Sweden)

Leonardo Zapata-Fonseca

2016-12-01

Full Text Available There is a growing consensus that a fuller understanding of social cognition depends on more systematic studies of real-time social interaction. Such studies require methods that can deal with the complex dynamics taking place at multiple interdependent temporal and spatial scales, spanning sub-personal, personal, and dyadic levels of analysis. We demonstrate the value of adopting an extended multi-scale approach by re-analyzing movement time series generated in a study of embodied dyadic interaction in a minimal virtual reality environment (a perceptual crossing experiment. Reduced movement variability revealed an interdependence between social awareness and social coordination that cannot be accounted for by either subjective or objective factors alone: it picks out interactions in which subjective and objective conditions are convergent (i.e. elevated coordination is perceived as clearly social, and impaired coordination is perceived as socially ambiguous. This finding is consistent with the claim that interpersonal interaction can be partially constitutive of direct social perception. Clustering statistics (Allan Factor of salient events revealed fractal scaling. Complexity matching defined as the similarity between these scaling laws was significantly more pronounced in pairs of participants as compared to surrogate dyads. This further highlights the multi-scale and distributed character of social interaction and extends previous complexity matching results from dyadic conversation to nonverbal social interaction dynamics. Trials with successful joint interaction were also associated with an increase in local coordination. Consequently, a local coordination pattern emerges on the background of complex dyadic interactions in the PCE task and makes joint successful performance possible.

Super-Coulombic atom-atom interactions in hyperbolic media

Science.gov (United States)

Cortes, Cristian L.; Jacob, Zubin

2017-01-01

Dipole-dipole interactions, which govern phenomena such as cooperative Lamb shifts, superradiant decay rates, Van der Waals forces and resonance energy transfer rates, are conventionally limited to the Coulombic near-field. Here we reveal a class of real-photon and virtual-photon long-range quantum electrodynamic interactions that have a singularity in media with hyperbolic dispersion. The singularity in the dipole-dipole coupling, referred to as a super-Coulombic interaction, is a result of an effective interaction distance that goes to zero in the ideal limit irrespective of the physical distance. We investigate the entire landscape of atom-atom interactions in hyperbolic media confirming the giant long-range enhancement. We also propose multiple experimental platforms to verify our predicted effect with phonon-polaritonic hexagonal boron nitride, plasmonic super-lattices and hyperbolic meta-surfaces as well. Our work paves the way for the control of cold atoms above hyperbolic meta-surfaces and the study of many-body physics with hyperbolic media.

Public-Key Encryption with Non-interactive Opening

DEFF Research Database (Denmark)

Damgård, Ivan Bjerre; Hofheinz, Dennis; Kiltz, Eike

2008-01-01

We formally define the primitive of public-key encryption with non-interactive opening (PKENO), where the receiver of a ciphertext C can, convincingly and without interaction, reveal what the result was of decrypting C, without compromising the scheme’s security. This has numerous applications...

Naphtha interaction with bitumen and clays : a preliminary study

Energy Technology Data Exchange (ETDEWEB)

Afara, M.; Munoz, V.; Mikula, R. [Natural Resources Canada, Devon, AB (Canada). CANMET Western Research Centre

2010-07-01

This PowerPoint presentation described a preliminary study conducted to characterize naphtha interactions with bitumen and clays. Coarse tailings, fluid-fine tailings, and froth treatment tailings are produced as a result of surface mine oil sands operations. Solvents are used to produce the bitumens, but the actual fraction of the solvent that evaporates and contributes to VOCs from tailing ponds is poorly understood. This study examined the interactions between the solvent, bitumen and mineral components in froth treatment tails. The study was conducted with aim of quantifying the VOC or solvent escaping from the froth treatment tailings. Samples containing bitumen, clay, a bitumen-clay mixture, or MFT were spiked with 3000 ppm of solvent. The amount of naphtha released was monitored by gas chromatography, mass spectrometry, and flame ionization detection of the evolved gases. The results were expressed as a percentage of the total hydrocarbon peak area of the sample versus a control. Results of the study showed that the naphtha interacted more strongly with the bitumen than with kaolinite and the clay minerals from the oil sands. Although initial solvent evaporation was reduced in the presence of bitumens and clays, long-term solvent releases will need to be quantified. tabs., figs.

Aryl-1H-imidazole[4,5f][1,10]phenanthroline Cu(II) complexes: Electrochemical and DNA interaction studies.

Science.gov (United States)

Rajebhosale, Bharati S; Dongre, Shivali N; Deshpande, Sameer S; Kate, Anup N; Kumbhar, Anupa A

2017-10-01

The reaction of aryl imidazo[4,5f] [1,10]phenanthrolines with Cu(NO 3 ) 2 lead to the formation of Cu(II) complexes of the type [Cu(L)(NO 3 ) 2 ] where L=PIP, 2-(phenyl) [4,5f] imidazo phenanthroline; HPIP=2-(2-hydroxyphenyl)imidazo [4,5f] phenanthroline and NIP=2-(naphthyl) [4,5f] imidazo phenanthroline. The interaction of these complexes with calf thymus DNA has been studied using viscosity measurements, UV-visible and fluorescence spectroscopy. Chemical nuclease activity of these complexes has also been investigated. All complexes cleave DNA via oxidative pathway involving singlet oxygen. Molecular docking studies revealed that these complexes bind to DNA through minor groove. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses1[OPEN

Science.gov (United States)

Waadt, Rainer; Manalansan, Bianca; Rauniyar, Navin; Munemasa, Shintaro; Booker, Matthew A.; Brandt, Benjamin; Waadt, Christian; Nusinow, Dmitri A.; Kay, Steve A.; Kunz, Hans-Henning; Schumacher, Karin; DeLong, Alison; Yates, John R.; Schroeder, Julian I.

2015-01-01

The plant hormone abscisic acid (ABA) controls growth and development and regulates plant water status through an established signaling pathway. In the presence of ABA, pyrabactin resistance/regulatory component of ABA receptor proteins inhibit type 2C protein phosphatases (PP2Cs). This, in turn, enables the activation of Sucrose Nonfermenting1-Related Protein Kinases2 (SnRK2). Open Stomata1 (OST1)/SnRK2.6/SRK2E is a major SnRK2-type protein kinase responsible for mediating ABA responses. Arabidopsis (Arabidopsis thaliana) expressing an epitope-tagged OST1 in the recessive ost1-3 mutant background was used for the copurification and identification of OST1-interacting proteins after osmotic stress and ABA treatments. These analyses, which were confirmed using bimolecular fluorescence complementation and coimmunoprecipitation, unexpectedly revealed homo- and heteromerization of OST1 with SnRK2.2, SnRK2.3, OST1, and SnRK2.8. Furthermore, several OST1-complexed proteins were identified as type 2A protein phosphatase (PP2A) subunits and as proteins involved in lipid and galactolipid metabolism. More detailed analyses suggested an interaction network between ABA-activated SnRK2-type protein kinases and several PP2A-type protein phosphatase regulatory subunits. pp2a double mutants exhibited a reduced sensitivity to ABA during seed germination and stomatal closure and an enhanced ABA sensitivity in root growth regulation. These analyses add PP2A-type protein phosphatases as another class of protein phosphatases to the interaction network of SnRK2-type protein kinases. PMID:26175513

Social Interaction and Collaboration among Oncology Nurses.

Science.gov (United States)

Moore, Jane; Prentice, Dawn; McQuestion, Maurene

2015-01-01

Collaboration is a complex process influenced by organizational, professional, interpersonal, and personal factors. Research has demonstrated that collaboration may also be influenced by social factors. Nurses spend much of their time working in collaborative teams, yet little is known about how they socially interact in practice. This qualitative case study explored nurse perceptions of social interaction in relation to collaboration. Data were collected using telephone interviews and documentary reviews from fourteen oncology nurses employed at one cancer center in Canada. Thematic analysis revealed two themes: knowing you is trusting you and formal and informal opportunities. Nurses reported that social interaction meant getting to know someone personally as well as professionally. Social interaction was enacted inside of work during breaks/meals and outside of work at planned events. Social interaction was facilitated by having a long-term current and/or previous professional and personal relationship. The barriers to social interaction included a lack of time to get to know each other, workload issues, and poor interpersonal skills. Findings suggest that social interaction is an important factor in the collaborative relationship among oncology nurses. Nurse leaders need to promote social interaction opportunities and facilitate educational sessions to improve social and interpersonal skills.

Infrared and x-ray photoelectron spectroscopic studies on sodium borosilicate glass interacted with thermally oxidized aluminides formed on alloy 690

International Nuclear Information System (INIS)

Yusufali, C.; Dutta, R.S.; Dey, G.K.; Kshirsagar, R.J.; Jagannath; Mishra, R.K.

2012-01-01

Thermally oxidized aluminides formed on Ni-Cr-Fe based superalloy 690 substrates were subjected to interaction with sodium borosilicate melt (used as matrices for immobilization of high-level radioactive liquid waste) at 1248 K for 192 hours. After the interaction, Fourier-transform infrared (FT-IR) spectroscopy analysis of glass samples indicated the incorporation of Al in the glass network. X-ray photoelectron spectroscopy (XPS) of glass specimens revealed modified glass structure. (author)

Exploring direct 3D interaction for full horizontal parallax light field displays using leap motion controller.

Science.gov (United States)

Adhikarla, Vamsi Kiran; Sodnik, Jaka; Szolgay, Peter; Jakus, Grega

2015-04-14

This paper reports on the design and evaluation of direct 3D gesture interaction with a full horizontal parallax light field display. A light field display defines a visual scene using directional light beams emitted from multiple light sources as if they are emitted from scene points. Each scene point is rendered individually resulting in more realistic and accurate 3D visualization compared to other 3D displaying technologies. We propose an interaction setup combining the visualization of objects within the Field Of View (FOV) of a light field display and their selection through freehand gesture tracked by the Leap Motion Controller. The accuracy and usefulness of the proposed interaction setup was also evaluated in a user study with test subjects. The results of the study revealed high user preference for free hand interaction with light field display as well as relatively low cognitive demand of this technique. Further, our results also revealed some limitations and adjustments of the proposed setup to be addressed in future work.

Pilot Study of Person Robot Interaction in a Public Transit Space

DEFF Research Database (Denmark)

Svenstrup, Mikael; Bak, Thomas; Maler, Ouri

2009-01-01

This paper describes a study of the effect of a human interactive robot placed in an urban transit space. The underlying hypothesis is that it is possible to create interesting new living spaces and induce value in terms of experiences, information or economics, by putting socially interactive...... showed harder than expected to start interaction with commuters due to their determination and speed towards their goal. Further it was demonstrated that it was possible to track and follow people, who were not beforehand informed about the experiment. The evaluation indicated that the distance...... to initiate interaction was shorter than would be expected for normal human to human interaction....

Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies.

Directory of Open Access Journals (Sweden)

Isha Bhutani

Full Text Available The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1 and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2 catalyze epimerization of decaprenylphosporyl ribose (DPR todecaprenylphosporyl arabinose (DPA and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269-330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB drug discovery and will facilitate drug development efforts against

Experimental and Numerical Studies of Atmosphere Water Interactions

KAUST Repository

Bou-Zeid, Elie

2011-07-04

Understanding and quantifying the interaction of the atmosphere with underlying water surfaces is of great importance for a wide range of scientific fields such as water resources management, climate studies of ocean-atmosphere exchange, and regional weat

The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Directory of Open Access Journals (Sweden)

Matthew D Dyer

2010-08-01

Full Text Available Bacillus anthracis, Francisella tularensis, and Yersinia pestis are bacterial pathogens that can cause anthrax, lethal acute pneumonic disease, and bubonic plague, respectively, and are listed as NIAID Category A priority pathogens for possible use as biological weapons. However, the interactions between human proteins and proteins in these bacteria remain poorly characterized leading to an incomplete understanding of their pathogenesis and mechanisms of immune evasion.In this study, we used a high-throughput yeast two-hybrid assay to identify physical interactions between human proteins and proteins from each of these three pathogens. From more than 250,000 screens performed, we identified 3,073 human-B. anthracis, 1,383 human-F. tularensis, and 4,059 human-Y. pestis protein-protein interactions including interactions involving 304 B. anthracis, 52 F. tularensis, and 330 Y. pestis proteins that are uncharacterized. Computational analysis revealed that pathogen proteins preferentially interact with human proteins that are hubs and bottlenecks in the human PPI network. In addition, we computed modules of human-pathogen PPIs that are conserved amongst the three networks. Functionally, such conserved modules reveal commonalities between how the different pathogens interact with crucial host pathways involved in inflammation and immunity.These data constitute the first extensive protein interaction networks constructed for bacterial pathogens and their human hosts. This study provides novel insights into host-pathogen interactions.

Gender differences in young children's interactions when learning fundamental motor skills.

Science.gov (United States)

Garcia, C

1994-09-01

The purpose of the study was to examine how young children interact in the context of learning fundamental motor skills. Twenty-nine preschool children were observed during a period of six consecutive months while they were participating in their daily motor skills program. Fieldwork research methodology was used and data were collected using participant observation techniques. During data analysis, emerging patterns were identified and cross-referenced against data collected from other sources (triangulation). Girls were found to interact in a cooperative, caring, and sharing manner. Boys were found to interact in a competitive, individualized, and egocentric manner. A cultural pattern of cooperative interaction among Asian children was found. In addition, both boys and girls tried to maintain their gender style of interaction when dealing with the opposite sex. This study reveals several aspects of the social environment that may need to be considered when teaching motor skills to young children.

Stapled Voltage-Gated Calcium Channel (CaV) α-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function.

Science.gov (United States)

Findeisen, Felix; Campiglio, Marta; Jo, Hyunil; Abderemane-Ali, Fayal; Rumpf, Christine H; Pope, Lianne; Rossen, Nathan D; Flucher, Bernhard E; DeGrado, William F; Minor, Daniel L

2017-06-21

For many voltage-gated ion channels (VGICs), creation of a properly functioning ion channel requires the formation of specific protein-protein interactions between the transmembrane pore-forming subunits and cystoplasmic accessory subunits. Despite the importance of such protein-protein interactions in VGIC function and assembly, their potential as sites for VGIC modulator development has been largely overlooked. Here, we develop meta-xylyl (m-xylyl) stapled peptides that target a prototypic VGIC high affinity protein-protein interaction, the interaction between the voltage-gated calcium channel (Ca V ) pore-forming subunit α-interaction domain (AID) and cytoplasmic β-subunit (Ca V β). We show using circular dichroism spectroscopy, X-ray crystallography, and isothermal titration calorimetry that the m-xylyl staples enhance AID helix formation are structurally compatible with native-like AID:Ca V β interactions and reduce the entropic penalty associated with AID binding to Ca V β. Importantly, electrophysiological studies reveal that stapled AID peptides act as effective inhibitors of the Ca V α 1 :Ca V β interaction that modulate Ca V function in an Ca V β isoform-selective manner. Together, our studies provide a proof-of-concept demonstration of the use of protein-protein interaction inhibitors to control VGIC function and point to strategies for improved AID-based Ca V modulator design.

Some significant but buried studies of embodiment and materiality in social interaction

DEFF Research Database (Denmark)

Nevile, Maurice Richard

When preparing a recent review on rising interest in ‘embodiment’ in EM CA research on social interaction (Nevile 2015) (e.g. gesture, body, mobility; cf. ‘multimodality’), considering over 500 studies, I was delighted to be reminded of, or often ‘discover’, some less-well-known-and-cited studies...... some to highlight from the prominent journal Research on Language and Social Interaction. The paper argues that active recognition of the contribution of the body-in-interaction might be relatively recent, but scholarly awareness of it is not (in EM CA and beyond). My aim is to resurrect some early...... discussion of doing CA and EM as a research community. Goodwin, C. (2000) Action and embodiment within situated human interaction. Journal of Pragmatics, 32, 1489–1522. Nevile, M. (2015) The embodied turn in research on language and social interaction. Research on Language and Social Interaction. 48,2: 121...