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Sample records for homology-dependent interactions determine

  1. Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA

    PubMed Central

    Liu, Chenli; Danilowicz, Claudia; Kleckner, Nancy; Prentiss, Mara

    2017-01-01

    Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro. Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA. We propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes. PMID:27580717

  2. Homology-Dependent Silencing by an Exogenous Sequence in the Drosophila Germline

    PubMed Central

    Pöyhönen, Maria; de Vanssay, Augustin; Delmarre, Valérie; Hermant, Catherine; Todeschini, Anne Laure; Teysset, Laure; Ronsseray, Stéphane

    2012-01-01

    The study of P transposable element repression in Drosophila melanogaster led to the discovery of the trans-silencing effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences) represses in trans, in the female germline, a homologous P-lacZ transgene inserted in euchromatin. TSE shows variegation in ovaries and displays a maternal effect as well as epigenetic transmission through meiosis. In addition, TSE is highly sensitive to mutations affecting heterochromatin components (including HP1) and the Piwi-interacting RNA silencing pathway (piRNA), a homology-dependent silencing mechanism that functions in the germline. TSE appears thus to involve the piRNA-based silencing proposed to play a major role in P repression. Under this hypothesis, TSE may also be established when homology between the telomeric and target loci involves sequences other than P elements, including sequences exogenous to the D. melanogaster genome. We have tested whether TSE can be induced via lacZ sequence homology. We generated a piggyBac-otu-lacZ transgene in which lacZ is under the control of the germline ovarian tumor promoter, resulting in strong expression in nurse cells and the oocyte. We show that all piggyBac-otu-lacZ transgene insertions are strongly repressed by maternally inherited telomeric P-lacZ transgenes. This repression shows variegation between egg chambers when it is incomplete and presents a maternal effect, two of the signatures of TSE. Finally, this repression is sensitive to mutations affecting aubergine, a key player of the piRNA pathway. These data show that TSE can occur when silencer and target loci share solely a sequence exogenous to the D. melanogaster genome. This functionally supports the hypothesis that TSE represents a general repression mechanism which can be co-opted by new transposable elements to regulate their activity after a transfer to the D. melanogaster

  3. Glycan Determinants of Heparin-Tau Interaction.

    PubMed

    Zhao, Jing; Huvent, Isabelle; Lippens, Guy; Eliezer, David; Zhang, Anqiang; Li, Quanhong; Tessier, Peter; Linhardt, Robert J; Zhang, Fuming; Wang, Chunyu

    2017-03-14

    Tau aggregates into paired helical filaments within neurons, a pathological hallmark of Alzheimer's disease. Heparin promotes tau aggregation and recently has been shown to be involved in the cellular uptake of tau aggregates. Although the tau-heparin interaction has been extensively studied, little is known about the glycan determinants of this interaction. Here, we used surface plasmon resonance (SPR) and NMR spectroscopy to characterize the interaction between two tau fragments, K18 and K19, and several polysaccharides, including heparin, heparin oligosaccharides, chemically modified heparin, and related glycans. Using a heparin-immobilized chip, SPR revealed that tau K18 and K19 bind heparin with a KD of 0.2 and 70 μM, respectively. In SPR competition experiments, N-desulfation and 2-O-desulfation had no effect on heparin binding to K18, whereas 6-O-desulfation severely reduced binding, suggesting a critical role for 6-O-sulfation in the tau-heparin interaction. The tau-heparin interaction became stronger with longer-chain heparin oligosaccharides. As expected for an electrostatics-driven interaction, a moderate amount of salt (0.3 M NaCl) abolished binding. NMR showed the largest chemical-shift perturbation (CSP) in R2 in tau K18, which was absent in K19, revealing differential binding sites in K18 and K19 to heparin. Dermatan sulfate binding produced minimal CSP, whereas dermatan disulfate, with the additional 6-O-sulfo group, induced much larger CSP. 2-O-desulfated heparin induced much larger CSP in K18 than 6-O-desulfated heparin. Our data demonstrate a crucial role for the 6-O-sulfo group in the tau-heparin interaction, which to our knowledge has not been reported before.

  4. Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants.

    PubMed

    Muchová, Veronika; Amiard, Simon; Mozgová, Iva; Dvořáčková, Martina; Gallego, Maria E; White, Charles; Fajkus, Jiří

    2015-01-01

    Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology-dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock-out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B-dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double-stranded breaks (measured as γ-H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S-phase, and is ATM-independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non-transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double-stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single-stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability.

  5. Selectivity of aggregation-determining interactions.

    PubMed

    Ganesan, Ashok; Debulpaep, Maja; Wilkinson, Hannah; Van Durme, Joost; De Baets, Greet; Jonckheere, Wim; Ramakers, Meine; Ivarsson, Ylva; Zimmermann, Pascale; Van Eldere, Johan; Schymkowitz, Joost; Rousseau, Frederic

    2015-01-30

    Protein aggregation is sequence specific, favoring self-assembly over cross-seeding with non-homologous sequences. Still, as the majority of proteins in a proteome are aggregation prone, the high level of homogeneity of protein inclusions in vivo both during recombinant overexpression and in disease remains surprising. To investigate the selectivity of protein aggregation in a proteomic context, we here compared the selectivity of aggregation-determined interactions with antibody binding. To that purpose, we synthesized biotin-labeled peptides, corresponding to aggregation-determining sequences of the bacterial protein β-galactosidase and two human disease biomarkers: C-reactive protein and prostate-specific antigen. We analyzed the selectivity of their interactions in Escherichia coli lysate, human serum and human seminal plasma, respectively, using a Western blot-like approach in which the aggregating peptides replace the conventional antibody. We observed specific peptide accumulation in the same bands detected by antibody staining. Combined spectroscopic and mutagenic studies confirmed accumulation resulted from binding of the peptide on the identical sequence of the immobilized target protein. Further, we analyzed the sequence redundancy of aggregating sequences and found that about 90% of them are unique within their proteome. As a result, the combined specificity and low sequence redundancy of aggregating sequences therefore contribute to the observed homogeneity of protein aggregation in vivo. This suggests that these intrinsic proteomic properties naturally compartmentalize aggregation events in sequence space. In the event of physiological stress, this might benefit the ability of cells to respond to proteostatic stress by allowing chaperones to focus on specific aggregation events rather than having to face systemic proteostatic failure.

  6. The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 Gene Codes for an S-Adenosyl-l-Homocysteine Hydrolase Required for DNA Methylation-Dependent Gene Silencing

    PubMed Central

    Rocha, Pedro S.C.F.; Sheikh, Mazhar; Melchiorre, Rosalba; Fagard, Mathilde; Boutet, Stéphanie; Loach, Rebecca; Moffatt, Barbara; Wagner, Conrad; Vaucheret, Hervé; Furner, Ian

    2005-01-01

    Genes introduced into higher plant genomes can become silent (gene silencing) and/or cause silencing of homologous genes at unlinked sites (homology-dependent gene silencing or HDG silencing). Mutations of the HOMOLOGY-DEPENDENT GENE SILENCING1 (HOG1) locus relieve transcriptional gene silencing and methylation-dependent HDG silencing and result in genome-wide demethylation. The hog1 mutant plants also grow slowly and have low fertility and reduced seed germination. Three independent mutants of HOG1 were each found to have point mutations at the 3′ end of a gene coding for S-adenosyl-l-homocysteine (SAH) hydrolase, and hog1-1 plants show reduced SAH hydrolase activity. A transposon (hog1-4) and a T-DNA tag (hog1-5) in the HOG1 gene each behaved as zygotic embryo lethal mutants and could not be made homozygous. The results suggest that the homozygous hog1 point mutants are leaky and result in genome demethylation and poor growth and that homozygous insertion mutations result in zygotic lethality. Complementation of the hog1-1 point mutation with a T-DNA containing the gene coding for SAH hydrolase restored gene silencing, HDG silencing, DNA methylation, fast growth, and normal seed viability. The same T-DNA also complemented the zygotic embryo lethal phenotype of the hog1-4 tagged mutant. A model relating the HOG1 gene, DNA methylation, and methylation-dependent HDG silencing is presented. PMID:15659630

  7. β-HPV 5 and 8 E6 Disrupt Homology Dependent Double Strand Break Repair by Attenuating BRCA1 and BRCA2 Expression and Foci Formation

    PubMed Central

    Wallace, Nicholas A.; Robinson, Kristin; Howie, Heather L.; Galloway, Denise A.

    2015-01-01

    Recent work has explored a putative role for the E6 protein from some β-human papillomavirus genus (β-HPVs) in the development of non-melanoma skin cancers, specifically β-HPV 5 and 8 E6. Because these viruses are not required for tumor maintenance, they are hypothesized to act as co-factors that enhance the mutagenic capacity of UV-exposure by disrupting the repair of the resulting DNA damage. Supporting this proposal, we have previously demonstrated that UV damage signaling is hindered by β-HPV 5 and 8 E6 resulting in an increase in both thymine dimers and UV-induced double strand breaks (DSBs). Here we show that β-HPV 5 and 8 E6 further disrupt the repair of these DSBs and provide a mechanism for this attenuation. By binding and destabilizing a histone acetyltransferase, p300, β-HPV 5 and 8 E6 reduce the enrichment of the transcription factor at the promoter of two genes critical to the homology dependent repair of DSBs (BRCA1 and BRCA2). The resulting diminished BRCA1/2 transcription not only leads to lower protein levels but also curtails the ability of these proteins to form repair foci at DSBs. Using a GFP-based reporter, we confirm that this reduced foci formation leads to significantly diminished homology dependent repair of DSBs. By deleting the p300 binding domain of β-HPV 8 E6, we demonstrate that the loss of robust repair is dependent on viral-mediated degradation of p300 and confirm this observation using a combination of p300 mutants that are β-HPV 8 E6 destabilization resistant and p300 knock-out cells. In conclusion, this work establishes an expanded ability of β-HPV 5 and 8 E6 to attenuate UV damage repair, thus adding further support to the hypothesis that β-HPV infections play a role in skin cancer development by increasing the oncogenic potential of UV exposure. PMID:25803638

  8. Biomaterial surface proteomic signature determines interaction with epithelial cells.

    PubMed

    Abdallah, Mohamed-Nur; Tran, Simon D; Abughanam, Ghada; Laurenti, Marco; Zuanazzi, David; Mezour, Mohamed A; Xiao, Yizhi; Cerruti, Marta; Siqueira, Walter L; Tamimi, Faleh

    2017-03-01

    Cells interact with biomaterials indirectly through extracellular matrix (ECM) proteins adsorbed onto their surface. Accordingly, it could be hypothesized that the surface proteomic signature of a biomaterial might determine its interaction with cells. Here, we present a surface proteomic approach to test this hypothesis in the specific case of biomaterial-epithelial cell interactions. In particular, we determined the surface proteomic signature of different biomaterials exposed to the ECM of epithelial cells (basal lamina). We revealed that the biomaterial surface chemistry determines the surface proteomic profile, and subsequently the interaction with epithelial cells. In addition, we found that biomaterials with surface chemistries closer to that of percutaneous tissues, such as aminated PMMA and aminated PDLLA, promoted higher selective adsorption of key basal lamina proteins (laminins, nidogen-1) and subsequently improved their interactions with epithelial cells. These findings suggest that mimicking the surface chemistry of natural percutaneous tissues can improve biomaterial-epithelial integration, and thus provide a rationale for the design of improved biomaterial surfaces for skin regeneration and percutaneous medical devices.

  9. Interspecies interactions are an integral determinant of microbial community dynamics

    PubMed Central

    Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  10. Consumer species richness and nutrients interact in determining producer diversity

    PubMed Central

    Groendahl, Sophie; Fink, Patrick

    2017-01-01

    While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration. PMID:28303953

  11. Nuclear matter radii determined by interaction cross sections

    SciTech Connect

    Ozawa, A.

    2005-10-19

    Experimental studies on nuclear matter radii determined by the interaction cross sections ({sigma}I) are reviewed. In particular, the procedure to determine the root-mean square matter radii from the measured {sigma}I by Galuber model analysis is described. Future {sigma}I measurements at the RI beam factory (RIBF) in RIKEN are introduced. As new calculations, the sensitivity of the skin is discussed in the case with a proton target based on Glauber-model calculations. In the energy region of RIBF, {sigma}I is sensitive for the skin; however, measurements with high accuracies are needed.

  12. Determination of protein-ligand interactions using differential scanning fluorimetry.

    PubMed

    Vivoli, Mirella; Novak, Halina R; Littlechild, Jennifer A; Harmer, Nicholas J

    2014-09-13

    A wide range of methods are currently available for determining the dissociation constant between a protein and interacting small molecules. However, most of these require access to specialist equipment, and often require a degree of expertise to effectively establish reliable experiments and analyze data. Differential scanning fluorimetry (DSF) is being increasingly used as a robust method for initial screening of proteins for interacting small molecules, either for identifying physiological partners or for hit discovery. This technique has the advantage that it requires only a PCR machine suitable for quantitative PCR, and so suitable instrumentation is available in most institutions; an excellent range of protocols are already available; and there are strong precedents in the literature for multiple uses of the method. Past work has proposed several means of calculating dissociation constants from DSF data, but these are mathematically demanding. Here, we demonstrate a method for estimating dissociation constants from a moderate amount of DSF experimental data. These data can typically be collected and analyzed within a single day. We demonstrate how different models can be used to fit data collected from simple binding events, and where cooperative binding or independent binding sites are present. Finally, we present an example of data analysis in a case where standard models do not apply. These methods are illustrated with data collected on commercially available control proteins, and two proteins from our research program. Overall, our method provides a straightforward way for researchers to rapidly gain further insight into protein-ligand interactions using DSF.

  13. Mood and personality interact to determine cognitive biases in pigs

    PubMed Central

    Asher, Lucy; Friel, Mary; Griffin, Kym

    2016-01-01

    Cognitive bias has become a popular way to access non-human animal mood, though inconsistent results have been found. In humans, mood and personality interact to determine cognitive bias, but to date, this has not been investigated in non-human animals. Here, we demonstrate for the first time, to the best of our knowledge, in a non-human animal, the domestic pig (Sus scrofa domesticus), that mood and personality interact, impacting on judgement. Pigs with a more proactive personality were more likely to respond optimistically to unrewarded ambiguous probes (spatially positioned between locations that were previously rewarded and unrewarded) independent of their housing (or enrichment) conditions. However, optimism/pessimism of reactive pigs in this task was affected by their housing conditions, which are likely to have influenced their mood state. Reactive pigs in the less enriched environment were more pessimistic and those in the more enriched environment, more optimistic. These results suggest that judgement in non-human animals is similar to humans, incorporating aspects of stable personality traits and more transient mood states. PMID:27852940

  14. Thunderstorm-environment interactions determined with three-dimensional trajectories

    NASA Technical Reports Server (NTRS)

    Wilson, G. S.

    1980-01-01

    Diagnostically determined three dimensional trajectories were used to reveal some of the scale interaction processes that occur between convective storms and their environment. Data from NASA's fourth Atmospheric Variability Experiment are analyzed. Two intense squall lines and numerous reports of severe weather occurred during the period. Convective storm systems with good temporal and spatial continuity are shown to be related to the development and movement of short wave circulation systems aloft that propagate eastward within a zonal mid tropospheric wind pattern. These short wave systems are found to produce the potential instability and dynamic triggering needed for thunderstorm formation. The environmental flow patterns, relative to convective storm systems, are shown to produce large upward air parcel movements in excess of 50 mb/3h in the immediate vicinity of the storms. The air undergoing strong lifting originates as potentially unstable low level air traveling into the storm environment from southern and southwestern directions. The thermo and hydrodynamical processes that lead to changes in atmospheric structure before, during, and after convective storm formation are described using total time derivatives of pressure or net vertical displacement, potential temperature, and vector wind calculated by following air parcels.

  15. Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures

    SciTech Connect

    McAdams, Harley; AlQuraishi, Mohammed

    2015-04-21

    Techniques for determining values for a metric of microscale interactions include determining a mesoscale metric for a plurality of mesoscale interaction types, wherein a value of the mesoscale metric for each mesoscale interaction type is based on a corresponding function of values of the microscale metric for the plurality of the microscale interaction types. A plurality of observations that indicate the values of the mesoscale metric are determined for the plurality of mesoscale interaction types. Values of the microscale metric are determined for the plurality of microscale interaction types based on the plurality of observations and the corresponding functions and compressed sensing.

  16. Determinants of Internet Use for Interactive Learning: An Exploratory Study

    ERIC Educational Resources Information Center

    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…

  17. Cracking the phosphatase code: docking interactions determine substrate specificity.

    PubMed

    Roy, Jagoree; Cyert, Martha S

    2009-12-08

    Phosphoserine- and phosphothreonine-directed phosphatases display remarkable substrate specificity, yet the sites that they dephosphorylate show little similarity in amino acid sequence. Studies reveal that docking interactions are key for the recognition of substrates and regulators by two conserved phosphatases, protein phosphatase 1 (PP1) and the Ca2+-calmodulin-dependent phosphatase calcineurin. In each case, a small degenerate sequence motif in the interacting protein directs low-affinity binding to a docking surface on the phosphatase that is distinct from the active site; several such interactions combine to confer overall binding specificity. Some docking surfaces are conserved, such as a hydrophobic groove on a face opposite the active site that serves as a major recognition surface for the "RVxF" motif of proteins that interact with PP1 and the "PxIxIT" motif of substrates of calcineurin. Secondary motifs combine with this primary targeting sequence to specify phosphatase binding. A comprehensive interactome for mammalian PP1 was described, analysis of which defines several PP1-binding motifs. Studies of "LxVP," a secondary calcineurin-binding sequence, establish that this motif is a conserved feature of calcineurin substrates and that the immunosuppressants FK506 and cyclosporin A inhibit the phosphatase by interfering with LxVP-mediated docking.

  18. STUDENT-TEACHER INTERACTION AS A DETERMINER OF EFFECTIVE TEACHING.

    ERIC Educational Resources Information Center

    LEWIS, EDWIN C.

    THIS STUDY TESTED THE HYPOTHESIS THAT THE EFFECTIVENESS OF A GIVEN TEACHER VARIES FROM ONE STUDENT TO ANOTHER AND THAT THIS DIFFERENCE IN EFFECTIVENESS IS A RESULT OF THE INTERACTION OF THE PERSONALITY PATTERNS OF THE STUDENT AND TEACHER. STUDENTS MAJORING IN MECHANICAL ENGINEERING, ANIMAL HUSBANDRY, AND HOME ECONOMICS WERE THE SUBJECTS. PERSONS…

  19. An ancient protein-DNA interaction underlying metazoan sex determination.

    PubMed

    Murphy, Mark W; Lee, John K; Rojo, Sandra; Gearhart, Micah D; Kurahashi, Kayo; Banerjee, Surajit; Loeuille, Guy-André; Bashamboo, Anu; McElreavey, Kenneth; Zarkower, David; Aihara, Hideki; Bardwell, Vivian J

    2015-06-01

    DMRT transcription factors are deeply conserved regulators of metazoan sexual development. They share the DM DNA-binding domain, a unique intertwined double zinc-binding module followed by a C-terminal recognition helix, which binds a pseudopalindromic target DNA. Here we show that DMRT proteins use a unique binding interaction, inserting two adjacent antiparallel recognition helices into a widened DNA major groove to make base-specific contacts. Versatility in how specific base contacts are made allows human DMRT1 to use multiple DNA binding modes (tetramer, trimer and dimer). Chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) indicates that multiple DNA binding modes also are used in vivo. We show that mutations affecting residues crucial for DNA recognition are associated with an intersex phenotype in flies and with male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction underlying much of metazoan sexual development.

  20. Interactions of nanoparticles with proteins: determination of equilibrium constants.

    PubMed

    Treuel, Lennart; Malissek, Marcelina

    2013-01-01

    The behavior of nanoparticles towards proteins is an important aspect across wide areas of nanotoxicology and nanomedicine. In this chapter, we describe a procedure to study the adsorption of proteins onto nanoparticle surfaces. Circular dichroism (CD) spectroscopy is utilized to quantify the amount of free protein in a solution, and the experimental information is evaluated to derive equilibrium constants for the protein adsorption/desorption equilibrium. These equilibrium constants are comparable parameters in describing the interactions between proteins and nanoparticles.

  1. Determining Interactions in PSA models: Application to a Space PSA

    SciTech Connect

    C. Smith; E. Borgonovo

    2010-06-01

    This paper addresses use of an importance measure interaction study of a probabilistic risk analysis (PSA) performed for a hypothetical aerospace lunar mission. The PSA methods used in this study follow the general guidance provided in the NASA Probabilistic Risk Assessment Procedures Guide for NASA Managers and Practitioners. For the PSA portion, we used phased-based event tree and fault tree logic structures are used to model a lunar mission, including multiple phases (from launch to return to the Earth surface) and multiple critical systems. Details of the analysis results are not provided in this paper – instead specific basic events are denoted by number (e.g., the first event is 1, the second is 2, and so on). However, in the model, we used approximately 150 fault trees and over 800 basic events. Following analysis and truncation of cut sets, we were left with about 400 basic events to evaluate. We used this model to explore interactions between different basic events and systems. These sensitivity studies provide high-level insights into features of the PSA for the hypothetical lunar mission.

  2. Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

    PubMed

    Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

    2016-05-12

    Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

  3. Determination of the CD148-Interacting Region in Thrombospondin-1

    PubMed Central

    Jiang, Rosie; Brantley-Sieders, Dana M.; Chen, Jin; Mernaugh, Raymond L.; Takahashi, Takamune

    2016-01-01

    CD148 is a transmembrane protein tyrosine phosphatase that is expressed in multiple cell types, including vascular endothelial cells and duct epithelial cells. Previous studies have shown a prominent role of CD148 to reduce growth factor signals and suppress cell proliferation and transformation. Further, we have recently shown that thrombospondin-1 (TSP1) serves as a functionally important ligand for CD148. TSP1 has multiple structural elements and interacts with various cell surface receptors that exhibit differing effects. In order to create the CD148-specific TSP1 fragment, here we investigated the CD148-interacting region in TSP1 using a series of TSP1 fragments and biochemical and biological assays. Our results demonstrate that: 1) CD148 binds to the 1st type 1 repeat in TSP1; 2) Trimeric TSP1 fragments that contain the 1st type repeat inhibit cell proliferation in A431D cells that stably express wild-type CD148 (A431D/CD148wt cells), while they show no effects in A431D cells that lack CD148 or express a catalytically inactive form of CD148. The anti-proliferative effect of the TSP1 fragment in A431D/CD148wt cells was largely abolished by CD148 knockdown and antagonized by the 1st, but not the 2nd and 3rd, type 1 repeat fragment. Furthermore, the trimeric TSP1 fragments containing the 1st type repeat increased the catalytic activity of CD148 and reduced phospho-tyrosine contents of EGFR and ERK1/2, defined CD148 substrates. These effects were not observed in the TSP1 fragments that lack the 1st type 1 repeat. Last, we demonstrate that the trimeric TSP1 fragment containing the 1st type 1 repeat inhibits endothelial cell proliferation in culture and angiogenesis in vivo. These effects were largely abolished by CD148 knockdown or deficiency. Collectively, these findings indicate that the 1st type 1 repeat interacts with CD148, reducing growth factor signals and inhibiting epithelial or endothelial cell proliferation and angiogenesis. PMID:27149518

  4. Multivalent Rab interactions determine tether-mediated membrane fusion

    PubMed Central

    Lürick, Anna; Gao, Jieqiong; Kuhlee, Anne; Yavavli, Erdal; Langemeyer, Lars; Perz, Angela; Raunser, Stefan; Ungermann, Christian

    2017-01-01

    Membrane fusion at endomembranes requires cross-talk between Rab GTPases and tethers to drive SNARE-mediated lipid bilayer mixing. Several tethers have multiple Rab-binding sites with largely untested function. Here we dissected the lysosomal HOPS complex as a tethering complex with just two binding sites for the Rab7-like Ypt7 protein to determine their relevance for fusion. Using tethering and fusion assays combined with HOPS mutants, we show that HOPS-dependent fusion requires both Rab-binding sites, with Vps39 being the stronger Ypt7 interactor than Vps41. The intrinsic amphipathic lipid packaging sensor (ALPS) motif within HOPS Vps41, a target of the vacuolar kinase Yck3, is dispensable for tethering and fusion but can affect tethering if phosphorylated. In combination, our data demonstrate that a multivalent tethering complex uses its two Rab bindings to determine the place of SNARE assembly and thus fusion at endomembranes. PMID:27852901

  5. Charged group surface accessibility determines micelleplexes formation and cellular interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Liu, Yang; Sen, Soumyo; Král, Petr; Gemeinhart, Richard A.

    2015-04-01

    Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The model micelle system was formed from methoxy-poly(ethylene glycol)-b-poly(lactide) (mPEG-PLA) mixed with methoxy-poly(ethylene glycol)-b-poly(lactide)-b-oligoarginine (mPEG-PLA-Rx, x = 8 or 15). Surface properties of the micelles were varied by controlling the oligoarginine block length and conjugation density. Micelles were observed to have a core-shell conformation in the aqueous environment where the PLA block constituted the hydrophobic core, mPEG and oligoarginine formed a hydrophilic corona. Significantly different thermodynamic behaviors were observed during the interaction of single stranded miRNA with micelles of different surface properties, and the resulting micelleplexes mediated substantial cellular association. Depending upon the oligoarginine length and density, micelles exhibited miRNA loading capacity directly related to the presentation of charged groups on the surface. The effect of charged group accessibility of cationic micelle on micelleplex properties provides guidance on future miRNA delivery system design.Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The

  6. Determining protein function and interaction from genome analysis

    DOEpatents

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

    2004-08-03

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

  7. Determining robot actions for tasks requiring sensor interaction

    NASA Technical Reports Server (NTRS)

    Budenske, John; Gini, Maria

    1989-01-01

    The performance of non-trivial tasks by a mobile robot has been a long term objective of robotic research. One of the major stumbling blocks to this goal is the conversion of the high-level planning goals and commands into the actuator and sensor processing controls. In order for a mobile robot to accomplish a non-trivial task, the task must be described in terms of primitive actions of the robot's actuators. Most non-trivial tasks require the robot to interact with its environment; thus necessitating coordination of sensor processing and actuator control to accomplish the task. The main contention is that the transformation from the high level description of the task to the primitive actions should be performed primarily at execution time, when knowledge about the environment can be obtained through sensors. It is proposed to produce the detailed plan of primitive actions by using a collection of low-level planning components that contain domain specific knowledge and knowledge about the available sensors, actuators, and sensor/actuator processing. This collection will perform signal and control processing as well as serve as a control interface between an actual mobile robot and a high-level planning system. Previous research has shown the usefulness of high-level planning systems to plan the coordination of activities such to achieve a goal, but none have been fully applied to actual mobile robots due to the complexity of interacting with sensors and actuators. This control interface is currently being implemented on a LABMATE mobile robot connected to a SUN workstation and will be developed such to enable the LABMATE to perform non-trivial, sensor-intensive tasks as specified by a planning system.

  8. Interaction of growth-determining systems with gravity

    NASA Astrophysics Data System (ADS)

    Merkys, A.; Laurinavičius, R.; Bendoraityté, D.; Švegždiené, D.; Rupainiené, O.

    The experiments have been carried out with lettuce shoots on board the Salyut-7 orbital station, the Kosmos-1667 biological satellite and under ground conditions at 180° plant inversion. By means of the centrifuge Biogravistat-1M the threshold value of gravitational sensitivity of lettuce shoots has been determined on board the Salyut-7 station. It was found to be equal to 2.9 × 10-3g for hypocotyls and 1.5 × 10-4g for roots. The following results have been received in the experiment performed on board the Kosmos-1667 satellite: a) under microgravity the proliferation of the meristem cells and the growth of roots did not differ from the control; b) the growth of hypocotyls in length was significantly enhanced in microgravity; c) under microgravity transverse growth of hypocotyls (increase in cross sectional area) was significantly increased due to enhancement of cortical parenchyma cell growth. At 180° inversion in Earth's gravity root extension growth and rate of cell division in the root apical meristem were decreased. The determination of DNA-fuchsin value in the nuclei of the cell root apexes showed that inversion affected processess of the cell cycle preceeding cytokinesis.

  9. Political dynamics determined by interactions between political leaders and voters.

    SciTech Connect

    Bernard, Michael Lewis; Bier, Asmeret; Backus, George A.; Hills, Richard Guy

    2010-03-01

    The political dynamics associated with an election are typically a function of the interplay between political leaders and voters, as well as endogenous and exogenous factors that impact the perceptions and goals of the electorate. This paper describes an effort by Sandia National Laboratories to model the attitudes and behaviors of various political groups along with that population's primary influencers, such as government leaders. To accomplish this, Sandia National Laboratories is creating a hybrid system dynamics-cognitive model to simulate systems- and individual-level political dynamics in a hypothetical society. The model is based on well-established psychological theory, applied to both individuals and groups within the modeled society. Confidence management processes are being incorporated into the model design process to increase the utility of the tool and assess its performance. This project will enhance understanding of how political dynamics are determined in democratic society.

  10. Attractive interactions among intermediate filaments determine network mechanics in vitro.

    PubMed

    Pawelzyk, Paul; Mücke, Norbert; Herrmann, Harald; Willenbacher, Norbert

    2014-01-01

    Mechanical and structural properties of K8/K18 and vimentin intermediate filament (IF) networks have been investigated using bulk mechanical rheometry and optical microrheology including diffusing wave spectroscopy and multiple particle tracking. A high elastic modulus G0 at low protein concentration c, a weak concentration dependency of G0 (G0 ∼ c(0.5 ± 0.1)) and pronounced strain stiffening are found for these systems even without external crossbridgers. Strong attractive interactions among filaments are required to maintain these characteristic mechanical features, which have also been reported for various other IF networks. Filament assembly, the persistence length of the filaments and the network mesh size remain essentially unaffected when a nonionic surfactant is added, but strain stiffening is completely suppressed, G0 drops by orders of magnitude and exhibits a scaling G0 ∼ c(1.9 ± 0.2) in agreement with microrheological measurements and as expected for entangled networks of semi-flexible polymers. Tailless K8Δ/K18ΔT and various other tailless filament networks do not exhibit strain stiffening, but still show high G0 values. Therefore, two binding sites are proposed to exist in IF networks. A weaker one mediated by hydrophobic amino acid clusters in the central rod prevents stretched filaments between adjacent cross-links from thermal equilibration and thus provides the high G0 values. Another strong one facilitating strain stiffening is located in the tail domain with its high fraction of hydrophobic amino acid sequences. Strain stiffening is less pronounced for vimentin than for K8/K18 due to electrostatic repulsion forces partly compensating the strong attraction at filament contact points.

  11. Reproductive interference determines persistence and exclusion in species interactions.

    PubMed

    Kishi, Shigeki; Nishida, Takayoshi; Tsubaki, Yoshitaka

    2009-09-01

    1. Reproductive interference is a negative interspecific sexual interaction that adversely affects the fitness of males and females during reproductive process. Theoretical studies suggest that because reproductive interference is characterized by positive frequency dependence it is far more likely to cause species exclusion than the density dependence of resource competition. However, the respective contributions of resource competition and reproductive interference to species exclusion, which have been frequently observed in many competition studies, remain unclear. 2. We show that reproductive interference is a far more critical cause of species exclusion than resource competition in the competition between Callosobruchus bean weevil species. In competition experiments over several generations, we manipulated the initial relative abundance of the adzuki bean beetle, Callosobruchus chinensis, and the southern cowpea beetle, Callosobruchus maculatus. When the initial adult ratio of C. chinensis : C. maculatus were 6 : 2 and 4 : 4, C. chinensis excluded C. maculatus. However, when C. maculatus was four times more abundant than C. chinensis at the start, we observed the opposite outcome. 3. A behavioural experiment using adults of the two species revealed asymmetric reproductive interference. The fecundity and longevity of C. maculatus females, but not those of C. chinensis females, decreased when the females were kept with heterospecific males. Fecundities of females of both species decreased as the number of heterospecific males increased. In contrast, resource competition at the larval stage resulted in higher survival of C. maculatus than of C. chinensis. 4. These results suggest that the positive frequency-dependent effect of reproductive interference resulted in species exclusion, depending on the initial population ratio of the two species, and the asymmetry of the interference resulted in C. chinensis being dominant in this study, as in previous studies

  12. Homology-dependent Gene Silencing in Paramecium

    PubMed Central

    Ruiz, Françoise; Vayssié, Laurence; Klotz, Catherine; Sperling, Linda; Madeddu, Luisa

    1998-01-01

    Microinjection at high copy number of plasmids containing only the coding region of a gene into the Paramecium somatic macronucleus led to a marked reduction in the expression of the corresponding endogenous gene(s). The silencing effect, which is stably maintained throughout vegetative growth, has been observed for all Paramecium genes examined so far: a single-copy gene (ND7), as well as members of multigene families (centrin genes and trichocyst matrix protein genes) in which all closely related paralogous genes appeared to be affected. This phenomenon may be related to posttranscriptional gene silencing in transgenic plants and quelling in Neurospora and allows the efficient creation of specific mutant phenotypes thus providing a potentially powerful tool to study gene function in Paramecium. For the two multigene families that encode proteins that coassemble to build up complex subcellular structures the analysis presented herein provides the first experimental evidence that the members of these gene families are not functionally redundant. PMID:9529389

  13. Steady-State and Kinetics-Based Affinity Determination in Effector-Effector Target Interactions.

    PubMed

    Reinhard, André; Nürnberger, Thorsten

    2017-01-01

    Dissecting the functional basis of pathogenicity and resistance in the context of plant innate immunity benefits greatly from detailed knowledge about biomolecular interactions, as both resistance and virulence depend on specific interactions between pathogen and host biomolecules. While in vivo systems provide biological context to host-pathogen interactions, these experiments typically cannot provide quantitative biochemical characterization of biomolecular interactions. However, in many cases, the biological function does not only depend on whether an interaction occurs at all, but rather on the "intensity" of the interaction, as quantified by affinity. Specifically, microbial effector proteins may bind more than one host target to exert virulence functions, and looking at these interactions more closely than would be possible in a purely black-and-white qualitative assay (as classically based on plant or yeast systems) can reveal new insights into the evolutionary arms race between host and pathogen. Recent advances in biomolecular interaction assays that can be performed in vitro allow quantification of binding events with ever greater fidelity and application range. Here, we describe assays based on microscale thermophoresis (MST) and surface plasmon resonance (SPR). Using these technologies allows affinity determination both in steady-state and in kinetic configurations, providing two conceptually independent pathways to arrive at quantitative affinity data describing the interactions of pathogen and host biomolecules.

  14. Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function.

    PubMed

    Droit, Arnaud; Poirier, Guy G; Hunter, Joanna M

    2005-04-01

    An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. One strategy to determine protein function is to identify the protein-protein interactions. The increasing use of high-throughput and large-scale bioinformatics-based studies has generated a massive amount of data stored in a number of different databases. A challenge for bioinformatics is to explore this disparate data and to uncover biologically relevant interactions and pathways. In parallel, there is clearly a need for the development of approaches that can predict novel protein-protein interaction networks in silico. Here, we present an overview of different experimental and bioinformatic methods to elucidate protein-protein interactions.

  15. The influence of bonding agents in improving interactions in composite propellants determined using image analysis.

    PubMed

    Dostanić, J; Husović, T V; Usćumlić, G; Heinemann, R J; Mijin, D

    2008-12-01

    Binder-oxidizer interactions in rocket composite propellants can be improved using adequate bonding agents. In the present work, the effectiveness of different 1,3,5-trisubstituted isocyanurates was determined by stereo and metallographic microscopy and using the software package Image-Pro Plus. The chemical analysis of samples was performed by a scanning electron microscope equipped for energy dispersive spectrometry.

  16. LEADERSHIP STATUS AS A MODULATOR OF THE DETERMINATION OF SOCIAL INTERACTION BY PRIOR REINFORCEMENT.

    DTIC Science & Technology

    determine degree of shift in judgment. Interaction effects on analysis of variance were significant for leader vs. non-leaders, positive vs. negative ... reinforcement . Thus, leaders are found to respond to cues in the outside world, non-leaders to ’internal’ mediating systems. (Author)

  17. Parental Interaction As A Determining Factor in Social Growth of the Individual in the Family.

    ERIC Educational Resources Information Center

    Markowitz, Max; Kadis, Asya L.

    Parental interaction is a prime determining factor in an individual's growth. Complementary relationships of the mother and father within the family: i.e., the bringing together of both the mothering attitude and the expectation of "growing up", contribute to the individual's maturation. Many analysts, realizing the importance of triadic…

  18. Historical contingency and ecological determinism interact to prime speciation in sticklebacks, Gasterosteus.

    PubMed

    Taylor, E B; McPhail, J D

    2000-12-07

    Historical contingency and determinism are often cast as opposing paradigms under which evolutionary diversification operates. It may be, however, that both factors act together to promote evolutionary divergence, although there are few examples of such interaction in nature. We tested phylogenetic predictions of an explicit historical model of divergence (double invasions of freshwater by marine ancestors) in sympatric species of three-spined sticklebacks (Gasterosteus aculeatus) where determinism has been implicated as an important factor driving evolutionary novelty. Microsatellite DNA variation at six loci revealed relatively low genetic variation in freshwater populations, supporting the hypothesis that they were derived by colonization of freshwater by more diverse marine ancestors. Phylogenetic and genetic distance analyses suggested that pairs of sympatric species have evolved multiple times, further implicating determinism as a factor in speciation. Our data also supported predictions based on the hypothesis that the evolution of sympatric species was contingent upon 'double invasions' of postglacial lakes by ancestral marine sticklebacks. Sympatric sticklebacks, therefore, provide an example of adaptive radiation by determinism contingent upon historical conditions promoting unique ecological interactions, and illustrate how contingency and determinism may interact to generate geographical variation in species diversity

  19. Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A; Mostofian, Barmak; Kucerka, Norbert; Drazba, Paul; Katsaras, John

    2012-01-01

    Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

  20. Determination of protein-ligand interactions using accelerator mass spectrometry: modified crosslinking assay.

    PubMed

    Hah, Sang Soo

    2009-05-01

    A highly sensitive detection method for the determination of protein-ligand interactions has been developed. Radiocarbon-labeled 17beta-estradiol was incubated with estrogen receptor-alpha; as a selective binding partner, and covalently attached using crosslinking agents, to form covalently linked protein-ligand complexes. After separation using a denaturing gel, the (14)C content in the sliced gels was identified by accelerator mass spectrometry. The obtained data demonstrated specific binding of the small molecule to its binding partner. In theory, this method can be applied to most protein-ligand interaction studies.

  1. Environmental responses, not species interactions, determine synchrony of dominant species in semiarid grasslands

    PubMed Central

    Tredennick, Andrew T.; de Mazancourt, Claire; Loreau, Michel; Adler, Peter B.

    2017-01-01

    Temporal asynchrony among species helps diversity to stabilize ecosystem functioning, but identifying the mechanisms that determine synchrony remains a challenge. Here, we refine and test theory showing that synchrony depends on three factors: species responses to environmental variation, interspecific interactions, and demographic stochasticity. We then conduct simulation experiments with empirical population models to quantify the relative influence of these factors on the synchrony of dominant species in five semiarid grasslands. We found that the average synchrony of per capita growth rates, which can range from 0 (perfect asynchrony) to 1 (perfect synchrony), was higher when environmental variation was present (0.62) rather than absent (0.43). Removing interspecific interactions and demographic stochasticity had small effects on synchrony. For the dominant species in these plant communities, where species interactions and demographic stochasticity have little influence, synchrony reflects the covariance in species’ responses to the environment. PMID:28144939

  2. Environmental responses, not species interactions, determine synchrony of dominant species in semiarid grasslands.

    PubMed

    Tredennick, Andrew T; de Mazancourt, Claire; Loreau, Michel; Adler, Peter B

    2017-02-01

    Temporal asynchrony among species helps diversity to stabilize ecosystem functioning, but identifying the mechanisms that determine synchrony remains a challenge. Here, we refine and test theory showing that synchrony depends on three factors: species responses to environmental variation, interspecific interactions, and demographic stochasticity. We then conduct simulation experiments with empirical population models to quantify the relative influence of these factors on the synchrony of dominant species in five semiarid grasslands. We found that the average synchrony of per capita growth rates, which can range from 0 (perfect asynchrony) to 1 (perfect synchrony), was higher when environmental variation was present (0.62) rather than absent (0.43). Removing interspecific interactions and demographic stochasticity had small effects on synchrony. For the dominant species in these plant communities, where species interactions and demographic stochasticity have little influence, synchrony reflects the covariance in species responses to the environment. This article is protected by copyright. All rights reserved.

  3. Interaction Behavior Between Niclosamide and Pepsin Determined by Spectroscopic and Docking Methods.

    PubMed

    Guo, Liuqi; Ma, Xiaoli; Yan, Jin; Xu, Kailin; Wang, Qing; Li, Hui

    2015-11-01

    The interaction between niclosamide (NIC) and pepsin was investigated using multispectroscopic and molecular docking methods. Binding constant, number of binding sites, and thermodynamic parameters at different temperatures were measured. Results of fluorescence quenching and synchronous fluorescence spectroscopy in combination with three-dimensional fluorescence spectroscopy showed that changes occurred in the microenvironment of tryptophan residues and the molecular conformation of pepsin. Molecular interaction distance and energy-transfer efficiency between pepsin and NIC were determined based on Förster nonradiative energy-transfer mechanism. Furthermore, the binding of NIC inhibited pepsin activity in vitro. All these results indicated that NIC bound to pepsin mainly through hydrophobic interactions and hydrogen bonds at a single binding site. In conclusion, this study provided substantial molecular-level evidence that NIC could induce changes in pepsin structure and conformation.

  4. Parameter-free determination of actual temperature at chemical freeze-out in nuclear interactions

    NASA Astrophysics Data System (ADS)

    Panagiotou, A. D.; Mavromanolakis, G.; Tzoulis, J.

    1995-07-01

    We propose a method to determine the actual temperature at chemical freeze-out in relativistic nucleus-nucleus collisions, using the experimental μq/T and μs/T values, obtained from strange particle ratios. We employ the Hadron Gas formalism, assuming only local thermal equilibration, to relate the quarkchemical potential and temperature. This relation constrains the allowed values of μq/T, μs/T and T, enabling the determination of the actual temperature. Comparison of the inverse slope parameter of the mT-distributions with the actual temperature determines the transverse flow velocity of the fireball matter. Knowledge of these quantities is essential in determining the EoS of nuclear matter and in evaluating interactions with regard to a possible phase transition to QGP.

  5. Life history determines genetic structure and evolutionary potential of host–parasite interactions

    PubMed Central

    Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

    2009-01-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

  6. Gastropod grazers and nutrients, but not light, interact in determining periphytic algal diversity.

    PubMed

    Liess, Antonia; Kahlert, Maria

    2007-05-01

    The potential interactions of grazing, nutrients and light in influencing autotroph species diversity have not previously been considered. Earlier studies have shown that grazing and nutrients interact in determining autotroph species diversity, since grazing decreases species diversity when nutrients (i.e. N or P) limit autotroph growth, but increases it when nutrients are replete. We hypothesized that increased light intensities would intensify the interactions between grazing and nutrients on algal species diversity, resulting in even stronger reductions in algal species diversity through grazing under nutrient-poor conditions, and to even stronger increases of algal species diversity through grazing under nutrient-rich conditions. We studied the effects of grazing (absent, present), nutrients (ambient, N + P enriched) and light (low light, high light) on benthic algal diversity and periphyton C:nutrient ratios (which can indicate algal nutrient limitation) in a factorial laboratory experiment, using the gastropod grazer Viviparus viviparus. Grazing decreased algal biomass and algal diversity, but increased C:P and N:P ratios of periphyton. Grazing also affected periphyton species composition, by decreasing the proportion of Spirogyra sp. and increasing the proportion of species in the Chaetophorales. Grazing effects on diversity as well as on periphyton N:P ratios were weakened when nutrients were added (interaction between grazing and nutrients). Chlorophyll a (Chl a) per area increased with nutrient addition and decreased with high light intensities. Light did not increase the strength of the interaction between grazing and nutrients on periphytic algal diversity. This study shows that nutrient addition substantially reduced the negative effects of grazing on periphytic algal diversity, whereas light did not interact with grazing or nutrient enrichment in determining periphytic algal diversity.

  7. Determination of 1-deoxynojirimycin in mulberry leaves using hydrophilic interaction chromatography with evaporative light scattering detection.

    PubMed

    Kimura, Toshiyuki; Nakagawa, Kiyotaka; Saito, Yuko; Yamagishi, Kenji; Suzuki, Masahiro; Yamaki, Kohji; Shinmoto, Hiroshi; Miyazawa, Teruo

    2004-03-24

    A simple and rapid method for determining 1-deoxynojirimycin (DNJ), a potent glucosidase inihibitor present in mulberry leaves (Morus alba and Morus bombysis), by high-performance liquid chromatography coupled to an evaporative light scattering detector (ELSD) has been developed. DNJ was separated from an extract of mulberry leaves on a TSKgel Amide-80 column, which is a representative column for hydrophilic interaction chromatography. During postcolumn detection, DNJ was detected by ELSD and concurrently identified by mass spectrometry. The detection limit was 100 ng. This method is sufficiently sensitive for determining DNJ in mulberry leaves and other related products.

  8. Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting.

    PubMed

    Han, Seungsu; Shin, Donghyuk; Choi, Hoon; Lee, Sangho

    2014-03-28

    Yeast Doa1/Ufd3 is an adaptor protein for Cdc48 (p97 in mammal), an AAA type ATPase associated with endoplasmic reticulum-associated protein degradation pathway and endosomal sorting into multivesicular bodies. Doa1 functions in the endosomal sorting by its association with Hse1, a component of endosomal sorting complex required for transport (ESCRT) system. The association of Doa1 with Hse1 was previously reported to be mediated between PFU domain of Doa1 and SH3 of Hse1. However, it remains unclear which residues are specifically involved in the interaction. Here we report that Doa1/PFU interacts with Hse1/SH3 with a moderate affinity of 5 μM. Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are found to be critical in the interaction while Phe-434, implicated in ubiquitin binding via a hydrophobic interaction, is not. Small-angle X-ray scattering measurements combined with molecular docking and biochemical analysis yield the solution structure of the Doa1/PFU:Hse1/SH3 complex. Taken together, our results suggest that hydrogen bonding is a major determinant in the interaction of Doa1/PFU with Hse1/SH3.

  9. Specific neosaxitoxin interactions with the Na+ channel outer vestibule determined by mutant cycle analysis.

    PubMed Central

    Penzotti, J L; Lipkind, G; Fozzard, H A; Dudley, S C

    2001-01-01

    The voltage-gated Na+ channel alpha-subunit consists of four homologous domains arranged circumferentially to form the pore. Several neurotoxins, including saxitoxin (STX), block the pore by binding to the outer vestibule of this permeation pathway, which is composed of four pore-forming loops (P-loops), one from each domain. Neosaxitoxin (neoSTX) is a variant of STX that differs only by having an additional hydroxyl group at the N1 position of the 1,2,3 guanidinium (N1-OH). We used this structural variant in mutant cycle experiments to determine interactions of the N1-OH and its guanidinium with the outer vestibule. NeoSTX had a higher affinity for the adult rat skeletal muscle Na+ channel (muI or Scn4a) than for STX (DeltaG approximately = 1.3 kcal/mol). Mutant cycle analysis identified groups that potentially interacted with each other. The N1 toxin site interacted most strongly with muI Asp-400 and Tyr-401. The interaction between the N1-OH of neoSTX and Tyr-401 was attractive (DeltaDeltaG = -1.3 +/- 0.1 kcal/mol), probably with formation of a hydrogen bond. A second possible attractive interaction to Asp-1532 was identified. There was repulsion between Asp-400 and the N1-OH (DeltaDeltaG = 1.4 +/- 0.1 kcal/mol), and kinetic analysis further suggested that the N1-OH was interacting negatively with Asp-400 at the transition state. Changes in pH altered the affinity of neoSTX, as would be expected if the N1-OH site were partially deprotonated. These interactions offer an explanation for most of the difference in blocking efficacy between neoSTX and STX and for the sensitivity of neoSTX to pH. Kinetic analysis suggested significant differences in coupling energies between the transition and the equilibrium, bound states. This is the first report to identify points of interaction between a channel and a non-peptide toxin. This interaction pattern was consistent with previous proposals describing the interactions of STX with the outer vestibule (Lipkind, G. M., and H

  10. Columnar interactions determine horizontal propagation of recurrent network activity in neocortex

    PubMed Central

    Wester, Jason C.; Contreras, Diego

    2012-01-01

    The cortex is organized in vertical and horizontal circuits that determine the spatiotemporal properties of distributed cortical activity. Despite detailed knowledge of synaptic interactions among individual cells in the neocortex, little is known about the rules governing interactions among local populations. Here we used self-sustained recurrent activity generated in cortex, also known as up-states, in rat thalamocortical slices in vitro to understand interactions among laminar and horizontal circuits. By means of intracellular recordings and fast optical imaging with voltage sensitive dyes, we show that single thalamic inputs activate the cortical column in a preferential L4→L2/3→L5 sequence, followed by horizontal propagation with a leading front in supra and infragranular layers. To understand the laminar and columnar interactions, we used focal injections of TTX to block activity in small local populations, while preserving functional connectivity in the rest of the network. We show that L2/3 alone, without underlying L5, does not generate self-sustained activity and is inefficient propagating activity horizontally. In contrast, L5 sustains activity in the absence of L2/3 and is necessary and sufficient to propagate activity horizontally. However, loss of L2/3 delays horizontal propagation via L5. Finally, L5 amplifies activity in L2/3. Our results show for the first time that columnar interactions between supra and infragranular layers are required for the normal propagation of activity in the neocortex. Our data suggest that supra and infragranular circuits with their specific and complex set of inputs and outputs, work in tandem to determine the patterns of cortical activation observed in vivo. PMID:22514308

  11. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

  12. Structural Determinants for the Interaction of Formyl Peptide Receptor 2 with Peptide Ligands*

    PubMed Central

    He, Hui-Qiong; Troksa, Erica L.; Caltabiano, Gianluigi; Pardo, Leonardo; Ye, Richard D.

    2014-01-01

    Unlike formyl peptide receptor 1 (FPR1), FPR2/ALX (FPR2) interacts with peptides of diverse sequences but has low affinity for the Escherichia coli-derived chemotactic peptide fMet-Leu-Phe (fMLF). Using computer modeling and site-directed mutagenesis, we investigated the structural requirements for FPR2 to interact with formyl peptides of different length and composition. In calcium flux assay, the N-formyl group of these peptides is necessary for activation of both FPR2 and FPR1, whereas the composition of the C-terminal amino acids appears more important for FPR2 than FPR1. FPR2 interacts better with pentapeptides (fMLFII, fMLFIK) than tetrapeptides (fMLFK, fMLFW) and tripeptide (fMLF) but only weakly with peptides carrying negative charges at the C terminus (e.g. fMLFE). In contrast, FPR1 is less sensitive to negative charges at the C terminus. A CXCR4-based homology model of FPR1 and FPR2 suggested that Asp-2817.32 is crucial for the interaction of FPR2 with certain formyl peptides as its negative charge may be repulsive with the terminal COO- group of fMLF and negatively charged Glu in fMLFE. Asp-2817.32 might also form a stable interaction with the positively charged Lys in fMLFK. Site-directed mutagenesis was performed to remove the negative charge at position 281 in FPR2. The D2817.32G mutant showed improved affinity for fMLFE and fMLF and reduced affinity for fMLFK compared with wild type FPR2. These results indicate that different structural determinants are used by FPR1 and FPR2 to interact with formyl peptides. PMID:24285541

  13. Interactions and diffusion in fine-stranded β-lactoglobulin gels determined via FRAP and binding.

    PubMed

    Schuster, Erich; Hermansson, Anne-Marie; Ohgren, Camilla; Rudemo, Mats; Lorén, Niklas

    2014-01-07

    The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of β-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the β-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na2-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and β-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na2-fluorescein is strongly influenced by electrostatic interactions in the positively charged β-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the β-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model.

  14. Comparison of signaling interactions determining annual and perennial plant growth in response to low temperature

    PubMed Central

    Wingler, Astrid

    2015-01-01

    Low temperature inhibits plant growth despite the fact that considerable rates of photosynthetic activity can be maintained. Instead of lower rates of photosynthesis, active inhibition of cell division and expansion is primarily responsible for reduced growth. This results in sink limitation and enables plants to accumulate carbohydrates that act as compatible solutes or are stored throughout the winter to enable re-growth in spring. Regulation of growth in response to temperature therefore requires coordination with carbon metabolism, e.g., via the signaling metabolite trehalose-6-phosphate. The phytohormones gibberellin (GA) and jasmonate (JA) play an important role in regulating growth in response to temperature. Growth restriction at low temperature is mainly mediated by DELLA proteins, whose degradation is promoted by GA. For annual plants, it has been shown that the GA/DELLA pathway interacts with JA signaling and C-repeat binding factor dependent cold acclimation, but these interactions have not been explored in detail for perennials. Growth regulation in response to seasonal factors is, however, particularly important in perennials, especially at high latitudes. In autumn, growth cessation in trees is caused by shortening of the daylength in interaction with phytohormone signaling. In perennial grasses seasonal differences in the sensitivity to GA may enable enhanced growth in spring. This review provides an overview of the signaling interactions that determine plant growth at low temperature and highlights gaps in our knowledge, especially concerning the seasonality of signaling responses in perennial plants. PMID:25628637

  15. Determination of the fermion pair size in a resonantly interacting superfluid.

    PubMed

    Schunck, Christian H; Shin, Yong-Il; Schirotzek, André; Ketterle, Wolfgang

    2008-08-07

    Fermionic superfluidity requires the formation of particle pairs, the size of which varies from the femtometre scale in neutron stars and nuclei to the micrometre scale in conventional superconductors. Many properties of the superfluid depend on the pair size relative to the interparticle spacing. This is expressed in 'BCS-BEC crossover' theories, describing the crossover from a Bardeen-Cooper-Schrieffer (BCS)-type superfluid of loosely bound, large Cooper pairs to Bose-Einstein condensates (BECs) of tightly bound molecules. Such a crossover superfluid has been realized in ultracold atomic gases where high-temperature superfluidity has been observed. The microscopic properties of the fermion pairs can be probed using radio-frequency spectroscopy. However, previous work was difficult to interpret owing to strong final-state interactions that were not well understood. Here we realize a superfluid spin mixture in which such interactions have negligible influence and present fermion pair dissociation spectra that reveal the underlying pairing correlations. This allows us to determine that the spectroscopic pair size in the resonantly interacting gas is 20 per cent smaller than the interparticle spacing. These are the smallest pairs so far observed in fermionic superfluids, highlighting the importance of small fermion pairs for superfluidity at high critical temperatures. We have also identified transitions from fermion pairs to bound molecular states and to many-body bound states in the case of strong final-state interactions.

  16. Determination of heat transfer coefficient for an interaction of sub-cooled gas and metal

    NASA Astrophysics Data System (ADS)

    Zaidi Sidek, Mohd; Syahidan Kamarudin, Muhammad

    2016-02-01

    Heat transfer coefficient (HTC) for a hot metal surface and their surrounding is one of the need be defined parameter in hot forming process. This study has been conducted to determine the HTC for an interaction between sub-cooled gas sprayed on a hot metal surface. Both experiments and finite element have been adopted in this work. Initially, the designated experiment was conducted to obtain temperature history of spray cooling process. Then, an inverse method was adopted to calculate the HTC value before we validate in a finite element simulation model. The result shows that the heat transfer coefficient for interaction of subcooled gas and hot metal surface is 1000 W/m2K.

  17. Determination of histamine in seafood by hydrophilic interaction chromatography/tandem mass spectrometry.

    PubMed

    Yoshida, Tatsuo; Hamada, Hirotoshi; Murakawa, Hiroshi; Yoshimoto, Hidekazu; Tobino, Toshiaki; Toda, Kei

    2012-01-01

    A simple method was developed to determine histamine, an important compound in chemical food poisoning, by extraction followed by hydrophilic interaction chromatography-tandem mass spectrometry using a hydrophilic column with sulfobetaine-type zwitterion groups. The quantitation range in seafood products was from 0.4 to 200 mg kg(-1) for 5 g food samples. Quantitative recoveries were obtained with four types of seafood product. These results agreed well with those from the more complex, conventional HPLC method, which requires sample derivatization with dansyl chloride.

  18. [Studies on the interaction between RNA with neutral red and determination of RNA by spectrophotometry].

    PubMed

    Si, Wen-Hui

    2007-06-01

    An analytical method for the determination of ribonucleic acid by spectrophotometry was established. At the maximum absorption wavelength for neutral red in B-R buffer solution, and under the best conditions, the decrease in the absorbance was linear with the amount of ribonucleic acid. The linearity range was 0.0-9.0 microg x mL(-1), the detection limit was 0.52 microg x mL(-1), and the correlation coeffient was 0.999 8. This method was simple, rapid, and selective. So its application to the determination of ribonucleic acid was satisfactory. The reaction mechanism was that the electrostatic interaction leads to molecular association of RNA with neutral red, resulting in anti-ion permutation and bonding reaction.

  19. Age, growth and size interact with stress to determine life span and mortality

    PubMed Central

    Roach, Deborah Ann

    2012-01-01

    Individuals in a large experimental field population, of the short-lived perennial species Plantago lanceolata, were followed to determine the sources of variation that influence mortality and life span. The design included multiple age groups with initially similar genetic structure, which made it possible to separate age effects from period effects and to identify the genetic component to variation in life span. During a period of stress, individuals of all ages showed parallel increases in mortality but different cohorts experienced this period of high mortality at different ages. This then influenced the distribution of life spans across cohorts. Age and size-age interactions influenced mortality during the period of stress. Smaller individuals died but only if they were old. Additionally, growth and age interacted with stress such that older individuals had negative growth and high mortality whereas younger individuals had positive growth and relatively lower mortality during stress. The results of this study show that it is not simply the environment that can have a major impact on demography in natural populations, rather, age, size and growth can interact with the environment to influence mortality and life span when the environment is stressful. PMID:22664575

  20. Macromolecular depletion as a determinant of RBC adhesive interactions: why blood is thicker than water.

    PubMed

    Neu, Björn; Meiselman, Herbert J

    2014-01-01

    If a surface is in contact with a solution containing macromolecules or proteins, and the loss of configurational entropy of these molecules at the surface is not balanced by adsorption energy, a polymer-poor layer will develop near the surface. If two such layers overlap, an attractive force develops due to the osmotic pressure difference between these depletion zones and the bulk phase. Recent studies have shown that depletion interaction plays a major role in red blood cell (RBC) aggregation and hence it is a major determinate of blood flow stability; depletion interaction also markedly affects RBC adhesion to vascular endothelial cells. Understanding and quantitating factors that regulate depletion in vivo are thus of importance, yet made difficult since only very small changes of the cell surface (e.g., glycocalyx thickness) such as seen during RBC aging can lead to massive changes of depletion interaction and hence cell-cell adhesion. It is suggested that insight into the in vivo relevance of depletion mechanisms may lead to an improved understanding of how and why blood flow is altered in many diseases, and may also provide new biomarkers (e.g., surface properties) that will aid in the development of novel or improved diagnostic and therapeutic tools.

  1. Effects of strong interactions in a half-metallic magnet: A determinant quantum Monte Carlo study

    SciTech Connect

    Jiang, M.; Pickett, W. E.; Scalettar, R. T.

    2013-04-03

    Understanding the effects of electron-electron interactions in half-metallic magnets (HMs), which have band structures with one gapped spin channel and one metallic channel, poses fundamental theoretical issues as well as having importance for their potential applications. Here we use determinant quantum Monte Carlo to study the impacts of an on-site Hubbard interaction U, finite temperature, and an external (Zeeman) magnetic field on a bilayer tight-binding model which is a half-metal in the absence of interactions, by calculating the spectral density, conductivity, spin polarization of carriers, and local magnetic properties. We quantify the effect of U on the degree of thermal depolarization, and follow relative band shifts and monitor when significant gap states appear, each of which can degrade the HM character. For this model, Zeeman coupling induces, at fixed particle number, two successive transitions: compensated half-metal with spin-down band gap → metallic ferromagnet → saturated ferromagnetic insulator. However, over much of the more relevant parameter regime, the half-metallic properties are rather robust to U.

  2. Effects of strong interactions in a half-metallic magnet: A determinant quantum Monte Carlo study

    DOE PAGES

    Jiang, M.; Pickett, W. E.; Scalettar, R. T.

    2013-04-03

    Understanding the effects of electron-electron interactions in half-metallic magnets (HMs), which have band structures with one gapped spin channel and one metallic channel, poses fundamental theoretical issues as well as having importance for their potential applications. Here we use determinant quantum Monte Carlo to study the impacts of an on-site Hubbard interaction U, finite temperature, and an external (Zeeman) magnetic field on a bilayer tight-binding model which is a half-metal in the absence of interactions, by calculating the spectral density, conductivity, spin polarization of carriers, and local magnetic properties. We quantify the effect of U on the degree of thermalmore » depolarization, and follow relative band shifts and monitor when significant gap states appear, each of which can degrade the HM character. For this model, Zeeman coupling induces, at fixed particle number, two successive transitions: compensated half-metal with spin-down band gap → metallic ferromagnet → saturated ferromagnetic insulator. However, over much of the more relevant parameter regime, the half-metallic properties are rather robust to U.« less

  3. Methods to determine the interactions of micro- and nanoparticles with mucus.

    PubMed

    Grießinger, Julia; Dünnhaupt, Sarah; Cattoz, Beatrice; Griffiths, Peter; Oh, Sejin; Borrós i Gómez, Salvador; Wilcox, Matthew; Pearson, Jeffrey; Gumbleton, Mark; Abdulkarim, Muthanna; Pereira de Sousa, Irene; Bernkop-Schnürch, Andreas

    2015-10-01

    The present review provides an overview of methods and techniques for studying interactions of micro- and nanoparticulate drug delivery system with mucus. Nanocarriers trapped by mucus are featuring a change in particle size and zeta potential that can be utilized to predict their mucus permeation behavior. Furthermore, interactions between nanoparticulate drug delivery systems and mucus layer modify the viscoelasticity of mucus which can be detected via rheological studies and quartz crystal microbalance with dissipation monitoring (QCM-D) analysis. Having a closer look at molecular interactions between drug carrier and mucus small-angle neutron scattering (SANS) is an appropriate analysis technique. Moreover, different methods to determine particle diffusion in mucus such as the newly established Transwell diffusion system, rotating silicone tube technique, multiple-particle tracking (MPT) and diffusion NMR are summarized within this review. The explanations and discussed pros and cons of collated methods and techniques should provide a good starting point for all those looking forward to move in this interesting field.

  4. Orbit Determination and Navigation of the Time History of Events and Macroscale Interactions during Substorms (THEMIS)

    NASA Technical Reports Server (NTRS)

    Morinelli, Patrick; Cosgrove, jennifer; Blizzard, Mike; Nicholson, Ann; Robertson, Mika

    2007-01-01

    This paper provides an overview of the launch and early orbit activities performed by the NASA Goddard Space Flight Center's (GSFC) Flight Dynamics Facility (FDF) in support of five probes comprising the Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft. The FDF was tasked to support THEMIS in a limited capacity providing backup orbit determination support for validation purposes for all five THEMIS probes during launch plus 30 days in coordination with University of California Berkeley Flight Dynamics Center (UCB/FDC). The FDF's orbit determination responsibilities were originally planned to be as a backup to the UCB/FDC for validation purposes only. However, various challenges early on in the mission and a Spacecraft Emergency declared thirty hours after launch placed the FDF team in the role of providing the orbit solutions that enabled contact with each of the probes and the eventual termination of the Spacecraft Emergency. This paper details the challenges and various techniques used by the GSFC FDF team to successfully perform orbit determination for all five THEMIS probes during the early mission. In addition, actual THEMIS orbit determination results are presented spanning the launch and early orbit mission phase. Lastly, this paper enumerates lessons learned from the THEMIS mission, as well as demonstrates the broad range of resources and capabilities within the FDF for supporting critical launch and early orbit navigation activities, especially challenging for constellation missions.

  5. Orbit Determination and Navigation of the Time History of Events and Macroscale Interactions during Substorms (THEMIS)

    NASA Technical Reports Server (NTRS)

    Morinelli, Patrick; Cosgrove, Jennifer; Blizzard, Mike; Robertson, Mike

    2007-01-01

    This paper provides an overview of the launch and early orbit activities performed by the NASA Goddard Space Flight Center's (GSFC) Flight Dynamics Facility (FDF) in support of five probes comprising the Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft. The FDF was tasked to support THEMIS in a limited capacity providing backup orbit determination support for validation purposes for all five THEMIS probes during launch plus 30 days in coordination with University of California Berkeley Flight Dynamics Center (UCB/FDC)2. The FDF's orbit determination responsibilities were originally planned to be as a backup to the UCB/FDC for validation purposes only. However, various challenges early on in the mission and a Spacecraft Emergency declared thirty hours after launch placed the FDF team in the role of providing the orbit solutions that enabled contact with each of the probes and the eventual termination of the Spacecraft Emergency. This paper details the challenges and various techniques used by the GSFC FDF team to successfully perform orbit determination for all five THEMIS probes during the early mission. In addition, actual THEMIS orbit determination results are presented spanning the launch and early orbit mission phase. Lastly, this paper enumerates lessons learned from the THEMIS mission, as well as demonstrates the broad range of resources and capabilities within the FDF for supporting critical launch and early orbit navigation activities, especially challenging for constellation missions.

  6. Micelle-enhanced and terbium-sensitized spectrofluorimetric determination of gatifloxacin and its interaction mechanism.

    PubMed

    Guo, Changchuan; Wang, Lei; Hou, Zhun; Jiang, Wei; Sang, Lihong

    2009-05-01

    A terbium-sensitized spectrofluorimetric method using an anionic surfactant, sodium dodecyl benzene sulfonate (SDBS), was developed for the determination of gatifloxacin (GFLX). A coordination complex system of GFLX-Tb(3+)-SDBS was studied. It was found that SDBS significantly enhanced the fluorescence intensity of the complex (about 11-fold). Optimal experimental conditions were determined as follows: excitation and emission wavelengths of 331 and 547nm, pH 7.0, 2.0x10(-4)moll(-1) terbium (III), and 2.0x10(-4)moll(-1) SDBS. The enhanced fluorescence intensity of the system (DeltaI(f)) showed a good linear relationship with the concentration of GFLX over the range of 5.0x10(-10) to 5.0x10(-8)moll(-1) with a correlation coefficient of 0.9996. The detection limit (3sigma) was determined as 6.0x10(-11)moll(-1). This method has been successfully applied to the determination of GFLX in pharmaceuticals and human urine/serum samples. Compared with most of other methods reported, the rapid and simple procedure proposed in the text offers higher sensitivity, wider linear range, and better stability. The interaction mechanism of the system is also studied by the research of ultraviolet absorption spectra, surface tension, solution polarity and fluorescence polarization.

  7. Protein-nanoparticle interactions evaluation by immunomethods: Surfactants can disturb quantitative determinations.

    PubMed

    Fornaguera, Cristina; Calderó, Gabriela; Solans, Conxita; Vauthier, Christine

    2015-08-01

    The adsorption of proteins on nanoparticle surface is one of the first events that occur when nanoparticles enter in the blood stream, which influences nanoparticles lifetime and further biodistribution. Albumin, which is the most abundant protein in serum and which has been deeply characterized, is an interesting model protein to investigate nanoparticle-protein interactions. Therefore, the interaction of nanoparticles with serum albumin has been widely studied. Immunomethods were suggested for the investigation of adsorption isotherms because of their ease to quantify the non-adsorbed bovine serum albumin without the need of applying separation methods that could modify the balance between the adsorbed and non-adsorbed proteins. The present work revealed that this method should be applied with caution. Artifacts in the determination of free protein can be generated by the presence of surfactants such as polysorbate 80, widely used in the pharmaceutical and biomedical field, that are needed to preserve the stability of nanoparticle dispersions. It was shown that the presence of traces of polysorbate 80 in the dispersion leads to an overestimation of the amount of bovine serum albumin remaining free in the dispersion medium when determined by both radial immunodiffusion and rocket immunoelectrophoresis. However, traces of poloxamer 188 did not result in clear perturbed migrations. These methods are not appropriate to perform adsorption isotherms of proteins on nanoparticle dispersions containing traces of remaining free surfactant. They should only be applied on dispersions that are free of surfactant that is not associated with nanoparticles.

  8. Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates.

    PubMed

    Bok, Jin Mo; Bae, Jong Ju; Choi, Han-Yong; Varma, Chandra M; Zhang, Wentao; He, Junfeng; Zhang, Yuxiao; Yu, Li; Zhou, X J

    2016-03-01

    A profound problem in modern condensed matter physics is discovering and understanding the nature of fluctuations and their coupling to fermions in cuprates, which lead to high-temperature superconductivity and the invariably associated strange metal state. We report the quantitative determination of normal and pairing self-energies, made possible by laser-based angle-resolved photoemission measurements of unprecedented accuracy and stability. Through a precise inversion procedure, both the effective interactions in the attractive d-wave symmetry and the repulsive part in the full symmetry are determined. The latter is nearly angle-independent. Near T c, both interactions are nearly independent of frequency and have almost the same magnitude over the complete energy range of up to about 0.4 eV, except for a low-energy feature at around 50 meV that is present only in the repulsive part, which has less than 10% of the total spectral weight. Well below T c, they both change similarly, with superconductivity-induced features at low energies. Besides finding the pairing self-energy and the attractive interactions for the first time, these results expose the central paradox of the problem of high T c: how the same frequency-independent fluctuations can dominantly scatter at angles ±π/2 in the attractive channel to give d-wave pairing and lead to angle-independent repulsive scattering. The experimental results are compared with available theoretical calculations based on antiferromagnetic fluctuations, the Hubbard model, and quantum-critical fluctuations of the loop-current order.

  9. Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates

    PubMed Central

    Bok, Jin Mo; Bae, Jong Ju; Choi, Han-Yong; Varma, Chandra M.; Zhang, Wentao; He, Junfeng; Zhang, Yuxiao; Yu, Li; Zhou, X. J.

    2016-01-01

    A profound problem in modern condensed matter physics is discovering and understanding the nature of fluctuations and their coupling to fermions in cuprates, which lead to high-temperature superconductivity and the invariably associated strange metal state. We report the quantitative determination of normal and pairing self-energies, made possible by laser-based angle-resolved photoemission measurements of unprecedented accuracy and stability. Through a precise inversion procedure, both the effective interactions in the attractive d-wave symmetry and the repulsive part in the full symmetry are determined. The latter is nearly angle-independent. Near Tc, both interactions are nearly independent of frequency and have almost the same magnitude over the complete energy range of up to about 0.4 eV, except for a low-energy feature at around 50 meV that is present only in the repulsive part, which has less than 10% of the total spectral weight. Well below Tc, they both change similarly, with superconductivity-induced features at low energies. Besides finding the pairing self-energy and the attractive interactions for the first time, these results expose the central paradox of the problem of high Tc: how the same frequency-independent fluctuations can dominantly scatter at angles ±π/2 in the attractive channel to give d-wave pairing and lead to angle-independent repulsive scattering. The experimental results are compared with available theoretical calculations based on antiferromagnetic fluctuations, the Hubbard model, and quantum-critical fluctuations of the loop-current order. PMID:26973872

  10. The interaction of intrinsic dynamics and network topology in determining network burst synchrony.

    PubMed

    Gaiteri, Chris; Rubin, Jonathan E

    2011-01-01

    The pre-Bötzinger complex (pre-BötC), within the mammalian respiratory brainstem, represents an ideal system for investigating the synchronization properties of complex neuronal circuits via the interaction of cell-type heterogeneity and network connectivity. In isolation, individual respiratory neurons from the pre-BötC may be tonically active, rhythmically bursting, or quiescent. Despite this intrinsic heterogeneity, coupled networks of pre-BötC neurons en bloc engage in synchronized bursting that can drive inspiratory motor neuron activation. The region's connection topology has been recently characterized and features dense clusters of cells with occasional connections between clusters. We investigate how the dynamics of individual neurons (quiescent/bursting/tonic) and the betweenness centrality of neurons' positions within the network connectivity graph interact to govern network burst synchrony, by simulating heterogeneous networks of computational model pre-BötC neurons. Furthermore, we compare the prevalence and synchrony of bursting across networks constructed with a variety of connection topologies, analyzing the same collection of heterogeneous neurons in small-world, scale-free, random, and regularly structured networks. We find that several measures of network burst synchronization are determined by interactions of network topology with the intrinsic dynamics of neurons at central network positions and by the strengths of synaptic connections between neurons. Surprisingly, despite the functional role of synchronized bursting within the pre-BötC, we find that synchronized network bursting is generally weakest when we use its specific connection topology, which leads to synchrony within clusters but poor coordination across clusters. Overall, our results highlight the relevance of interactions between topology and intrinsic dynamics in shaping the activity of networks and the concerted effects of connectivity patterns and dynamic heterogeneities.

  11. Climate warming and agricultural stressors interact to determine stream periphyton community composition.

    PubMed

    Piggott, Jeremy J; Salis, Romana K; Lear, Gavin; Townsend, Colin R; Matthaei, Christoph D

    2015-01-01

    Lack of knowledge about how the various drivers of global climate change will interact with multiple stressors already affecting ecosystems is the basis for great uncertainty in projections of future biological change. Despite concerns about the impacts of changes in land use, eutrophication and climate warming in running waters, the interactive effects of these stressors on stream periphyton are largely unknown. We manipulated nutrients (simulating agricultural runoff), deposited fine sediment (simulating agricultural erosion) (two levels each) and water temperature (eight levels, 0-6 °C above ambient) simultaneously in 128 streamside mesocosms. Our aim was to determine the individual and combined effects of the three stressors on the algal and bacterial constituents of the periphyton. All three stressors had pervasive individual effects, but in combination frequently produced synergisms at the population level and antagonisms at the community level. Depending on sediment and nutrient conditions, the effect of raised temperature frequently produced contrasting response patterns, with stronger or opposing effects when one or both stressors were augmented. Thus, warming tended to interact negatively with nutrients or sediment by weakening or reversing positive temperature effects or strengthening negative ones. Five classes of algal growth morphology were all affected in complex ways by raised temperature, suggesting that these measures may prove unreliable in biomonitoring programs in a warming climate. The evenness and diversity of the most abundant bacterial taxa increased with temperature at ambient but not with enriched nutrient levels, indicating that warming coupled with nutrient limitation may lead to a more evenly distributed bacterial community as temperatures rise. Freshwater management decisions that seek to avoid or mitigate the negative effects of agricultural land use on stream periphyton should be informed by knowledge of the interactive effects of

  12. Determination of dominant frequency of resting-state brain interaction within one functional system.

    PubMed

    Zhang, Yu-Jin; Duan, Lian; Zhang, Han; Biswal, Bharat B; Lu, Chun-Ming; Zhu, Chao-Zhe

    2012-01-01

    Accumulating evidence has revealed that the resting-state functional connectivity (RSFC) is frequency specific and functional system dependent. Determination of dominant frequency of RSFC (RSFC(df)) within a functional system, therefore, is of importance for further understanding the brain interaction and accurately assessing the RSFC within the system. Given the unique advantages over other imaging techniques, functional near-infrared spectroscopy (fNIRS) holds distinct merits for RSFC(df) determination. However, an obstacle that hinders fNIRS from potential RSFC(df) investigation is the interference of various global noises in fNIRS data which could bring spurious connectivity at the frequencies unrelated to spontaneous neural activity. In this study, we first quantitatively evaluated the interferences of multiple systemic physiological noises and the motion artifact by using simulated data. We then proposed a functional system dependent and frequency specific analysis method to solve the problem by introducing anatomical priori information on the functional system of interest. Both the simulated and real resting-state fNIRS experiments showed that the proposed method outperforms the traditional one by effectively eliminating the negative effects of the global noises and significantly improving the accuracy of the RSFC(df) estimation. The present study thus provides an effective approach to RSFC(df) determination for its further potential applications in basic and clinical neurosciences.

  13. Local electron-electron interaction strength in ferromagnetic nickel determined by spin-polarized positron annihilation.

    PubMed

    Ceeh, Hubert; Weber, Josef Andreas; Weber, Josef Andreass; Böni, Peter; Leitner, Michael; Benea, Diana; Chioncel, Liviu; Ebert, Hubert; Minár, Jan; Vollhardt, Dieter; Hugenschmidt, Christoph

    2016-02-16

    We employ a positron annihilation technique, the spin-polarized two-dimensional angular correlation of annihilation radiation (2D-ACAR), to measure the spin-difference spectra of ferromagnetic nickel. The experimental data are compared with the theoretical results obtained within a combination of the local spin density approximation (LSDA) and the many-body dynamical mean-field theory (DMFT). We find that the self-energy defining the electronic correlations in Ni leads to anisotropic contributions to the momentum distribution. By direct comparison of the theoretical and experimental results we determine the strength of the local electronic interaction U in ferromagnetic Ni as 2.0 ± 0.1 eV.

  14. Determination of major phlorotannins in Eisenia bicyclis using hydrophilic interaction chromatography: seasonal variation and extraction characteristics.

    PubMed

    Kim, Sang Min; Kang, Suk Woo; Jeon, Je-Seung; Jung, Yu-Jin; Kim, Woo-Ri; Kim, Chul Young; Um, Byung-Hun

    2013-06-15

    In this study, a hydrophilic interaction chromatography (HILIC) condition was developed for the simultaneous determination of five major phlorotannins from an extract of Eisenia bicyclis (Kjellman) Setchell with good linearity (r(2)>0.999). Based on this method, the seasonal variations and extraction characteristics, in terms of total extraction yield and the content of the phlorotannins, were investigated under various extraction conditions. In results, the yields and phlorotannins were increased two-to-four times in summer (June-October) and then, were decreased to normal levels in winter (November-March). In the extraction of E. bicyclis, ethanol percentage in water, extraction time and washing time significantly affected the yield of the extract and the phlorotannins, whereas the temperature and the sample/solvent ratio impacted the extraction to a lesser degree. These results will be useful information in the application of this macroalga in the commercial areas related to nutraceuticals, pharmaceuticals, and cosmeceuticals.

  15. Rigorous surface charge method for determining electrostatic interaction energies in biomolecular systems

    NASA Astrophysics Data System (ADS)

    Doerr, T. P.; Obolensky, O. I.; Ogurtsov, A. Y.; Yu, Yi-Kuo

    2014-03-01

    Classical electrostatics plays a crucial role in bimolecular systems, dominating the interactions that determine the formation and dissolution of complexes responsible for the operation of cells. For systems that can be modeled as a set of piecewise-constant dielectric bodies, surface charge methods are usually preferable in both analytical and numerical contexts. We present a numerical implementation of a surface charge method previously used in analytical contexts. The method is applied to a realistic model of trypsin, an important protein involved in digesting other proteins, and one of its inhibitors, benzamidine. The classical calculations are complemented by density function theory calculations at short separations for which the classical model is inappropriate. We find that the surface charge method correctly distinguishes between correct and incorrect docking sites. This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.

  16. Local electron-electron interaction strength in ferromagnetic nickel determined by spin-polarized positron annihilation

    PubMed Central

    Ceeh, Hubert; Weber, Josef Andreass; Böni, Peter; Leitner, Michael; Benea, Diana; Chioncel, Liviu; Ebert, Hubert; Minár, Jan; Vollhardt, Dieter; Hugenschmidt, Christoph

    2016-01-01

    We employ a positron annihilation technique, the spin-polarized two-dimensional angular correlation of annihilation radiation (2D-ACAR), to measure the spin-difference spectra of ferromagnetic nickel. The experimental data are compared with the theoretical results obtained within a combination of the local spin density approximation (LSDA) and the many-body dynamical mean-field theory (DMFT). We find that the self-energy defining the electronic correlations in Ni leads to anisotropic contributions to the momentum distribution. By direct comparison of the theoretical and experimental results we determine the strength of the local electronic interaction U in ferromagnetic Ni as 2.0 ± 0.1 eV. PMID:26879249

  17. Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

    PubMed Central

    Lázár, Viktória; Nagy, István; Spohn, Réka; Csörgő, Bálint; Györkei, Ádám; Nyerges, Ákos; Horváth, Balázs; Vörös, Andrea; Busa-Fekete, Róbert; Hrtyan, Mónika; Bogos, Balázs; Méhi, Orsolya; Fekete, Gergely; Szappanos, Balázs; Kégl, Balázs; Papp, Balázs; Pál, Csaba

    2014-01-01

    Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies. PMID:25000950

  18. General purpose computer program for interacting supersonic configurations. User's manual. [determining unsteady aerodynamic foreces

    NASA Technical Reports Server (NTRS)

    Crill, W.; Dale, B.

    1977-01-01

    The input data required to execute the computer program ISCON are described. The program generates a numerical procedure for the determination of unsteady aerodynamic forces on arbitrarily interacting wings and tails in supersonic flow. A velocity potential gradient method is used. Constant Mach number is assumed throughout the flow field. Lifting surfaces are represented by trapezoidal elements which can be generated automatically by the program. The wake field is represented by rectangular strip elements. The formulation is reviewed as well as input overview and input format. Instruction on how to use ISCON, a sample problem, and the restart feature are discussed. Program size limitations, computer program flow, and error messages are also included along with a description of the SS31 program used to compute the coefficients of surface spline.

  19. Diversification of the Structural Determinants of Fibroblast Growth Factor-Heparin Interactions

    PubMed Central

    Xu, Ruoyan; Ori, Alessandro; Rudd, Timothy R.; Uniewicz, Katarzyna A.; Ahmed, Yassir A.; Guimond, Scott E.; Skidmore, Mark A.; Siligardi, Giuliano; Yates, Edwin A.; Fernig, David G.

    2012-01-01

    The functions of a large number (>435) of extracellular regulatory proteins are controlled by their interactions with heparan sulfate (HS). In the case of fibroblast growth factors (FGFs), HS binding determines their transport between cells and is required for the assembly of high affinity signaling complexes with their cognate FGF receptor. However, the specificity of the interaction of FGFs with HS is still debated. Here, we use a panel of FGFs (FGF-1, FGF-2, FGF-7, FGF-9, FGF-18, and FGF-21) spanning five FGF subfamilies to probe their specificities for HS at different levels as follows: binding parameters, identification of heparin-binding sites (HBSs) in the FGFs, changes in their secondary structure caused by heparin binding and structures in the sugar required for binding. For interaction with heparin, the FGFs exhibit KD values varying between 38 nm (FGF-18) and 620 nm (FGF-9) and association rate constants spanning over 20-fold (FGF-1, 2,900,000 m−1 s−1 and FGF-9, 130,000 m−1 s−1). The canonical HBS in FGF-1, FGF-2, FGF-7, FGF-9, and FGF-18 differs in its size, and these FGFs have a different complement of secondary HBS, ranging from none (FGF-9) to two (FGF-1). Differential scanning fluorimetry identified clear preferences in these FGFs for distinct structural features in the polysaccharide. These data suggest that the differences in heparin-binding sites in both the protein and the sugar are greatest between subfamilies and may be more restricted within a FGF subfamily in accord with the known conservation of function within FGF subfamilies. PMID:23019343

  20. Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change.

    PubMed

    Gehring, Catherine; Flores-Rentería, Dulce; Sthultz, Christopher M; Leonard, Tierra M; Flores-Rentería, Lluvia; Whipple, Amy V; Whitham, Thomas G

    2014-03-01

    Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary.

  1. A practical method for depth of interaction determination in monolithic scintillator PET detectors.

    PubMed

    van Dam, Herman T; Seifert, Stefan; Vinke, Ruud; Dendooven, Peter; Löhner, Herbert; Beekman, Freek J; Schaart, Dennis R

    2011-07-07

    Several new methods for determining the depth of interaction (DOI) of annihilation photons in monolithic scintillator detectors with single-sided, multi-pixel readout are investigated. The aim is to develop a DOI decoding method that allows for practical implementation in a positron emission tomography system. Specifically, calibration data, obtained with perpendicularly incident gamma photons only, are being used. Furthermore, neither detector modifications nor a priori knowledge of the light transport and/or signal variances is required. For this purpose, a clustering approach is utilized in combination with different parameters correlated with the DOI, such as the degree of similarity to a set of reference light distributions, the measured intensity on the sensor pixel(s) closest to the interaction position and the peak intensity of the measured light distribution. The proposed methods were tested experimentally on a detector comprised of a 20 mm × 20 mm × 12 mm polished LYSO:Ce crystal coupled to a 4 × 4 multi-anode photomultiplier. The method based on the linearly interpolated measured intensities on the sensor pixels closest to the estimated (x, y)-coordinate outperformed the other methods, yielding DOI resolutions between ∼1 and ∼4.5 mm FWHM depending on the DOI, the (x, y) resolution and the amount of reference data used.

  2. A practical method for depth of interaction determination in monolithic scintillator PET detectors

    NASA Astrophysics Data System (ADS)

    van Dam, Herman T.; Seifert, Stefan; Vinke, Ruud; Dendooven, Peter; Löhner, Herbert; Beekman, Freek J.; Schaart, Dennis R.

    2011-07-01

    Several new methods for determining the depth of interaction (DOI) of annihilation photons in monolithic scintillator detectors with single-sided, multi-pixel readout are investigated. The aim is to develop a DOI decoding method that allows for practical implementation in a positron emission tomography system. Specifically, calibration data, obtained with perpendicularly incident gamma photons only, are being used. Furthermore, neither detector modifications nor a priori knowledge of the light transport and/or signal variances is required. For this purpose, a clustering approach is utilized in combination with different parameters correlated with the DOI, such as the degree of similarity to a set of reference light distributions, the measured intensity on the sensor pixel(s) closest to the interaction position and the peak intensity of the measured light distribution. The proposed methods were tested experimentally on a detector comprised of a 20 mm × 20 mm × 12 mm polished LYSO:Ce crystal coupled to a 4 × 4 multi-anode photomultiplier. The method based on the linearly interpolated measured intensities on the sensor pixels closest to the estimated (x, y)-coordinate outperformed the other methods, yielding DOI resolutions between ~1 and ~4.5 mm FWHM depending on the DOI, the (x, y) resolution and the amount of reference data used.

  3. Carbon Mineralizability Determines Interactive Effects on Mineralization of Pyrogenic Organic Matter and Soil Organic Carbon

    SciTech Connect

    Whitman, Thea L.; Zhu, Zihua; Lehmann, Johannes C.

    2014-10-31

    Soil organic carbon (SOC) is a critical and active pool in the global C cycle, and the addition of pyrogenic organic matter (PyOM) has been shown to change SOC cycling, increasing or decreasing mineralization rates (often referred to as priming). We adjusted the amount of easily mineralizable C in the soil, through 1-day and 6-month pre-incubations, and in PyOM made from maple wood at 350°C, through extraction. We investigated the impact of these adjustments on C mineralization interactions, excluding pH and nutrient effects and minimizing physical effects. We found short-term increases (+20-30%) in SOC mineralization with PyOM additions in the soil pre-incubated for 6 months. Over the longer term, both the 6-month and 1-day pre-incubated soils experienced net ~10% decreases in SOC mineralization with PyOM additions. This was possibly due to stabilization of SOC on PyOM surfaces, suggested by nanoscale secondary ion mass spectrometry. Additionally, the duration of pre-incubation affected priming interactions, indicating that there may be no optimal pre-incubation time for SOC mineralization studies. We show conclusively that relative mineralizability of SOC in relation to PyOM-24 C is an important determinant of the effect of PyOM additions on SOC mineralization.

  4. Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria

    PubMed Central

    Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.; Tennessen, Kristin; Woyke, Tanja; Kyrpides, Nikos C.; Ivanova, Natalia N.

    2015-01-01

    Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability. PMID:26584898

  5. Protein-protein interactions among components of the Drosophila primary sex determination signal.

    PubMed

    Liu, Y; Belote, J M

    1995-07-28

    Sex determination in Drosophila melanogaster is initiated in the early embryo by a signal provided by three types of genes: (1) X-linked numerator elements [e.g., sisterless-a (sis-a) and sisterless-b (sis-b)], (2) autosomally linked denominator elements [e.g., deadpan (dpn)], and (3) maternal factors [e.g., daughterless (da)]. This signal acts to stimulate transcription from an embryo-specific promoter of the master regulatory gene Sex-lethal (Sxl) in embryos that have two X chromosomes (females), while it fails to activate Sxl in those with only one X (males). It has been previously proposed that competitive dimerizations among the components of this signal might provide the molecular basis for this sex specificity. Here, we use the yeast two-hybrid system to demonstrate specific protein-protein interactions among the above-mentioned factors, and to delimit their interacting domains. These results support and extend the model of the molecular basis of the X/A ratio signal.

  6. Vortices determine the dynamics of biodiversity in cyclical interactions with protection spillovers

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2015-11-01

    If rock beats scissors and scissors beat paper, one might assume that rock beats paper too. But this is not the case for intransitive relationships that make up the famous rock-paper-scissors game. However, the sole presence of paper might prevent rock from beating scissors, simply because paper beats rock. This is the blueprint for the rock-paper-scissors game with protection spillovers, which has recently been introduced as a new paradigm for biodiversity in well-mixed microbial populations. Here we study the game in structured populations, demonstrating that protection spillovers give rise to spatial patterns that are impossible to observe in the classical rock-paper-scissors game. We show that the spatiotemporal dynamics of the system is determined by the density of stable vortices, which may ultimately transform to frozen states, to propagating waves, or to target waves with reversed propagation direction, depending further on the degree and type of randomness in the interactions among the species. If vortices are rare, the fixation to waves and complex oscillatory solutions is likelier. Moreover, annealed randomness in interactions favors the emergence of target waves, while quenched randomness favors collective synchronization. Our results demonstrate that protection spillovers may fundamentally change the dynamics of cyclic dominance in structured populations, and they outline the possibility of programming pattern formation in microbial populations.

  7. Stoichiometry determined exchange interactions in amorphous ternary transition metal oxides: Theory and experiment

    SciTech Connect

    Hu, Shu-jun; Yan, Shi-shen Zhang, Yun-peng; Zhao, Ming-wen; Kang, Shi-shou; Mei, Liang-mo

    2014-07-28

    Amorphous transition metal oxides exhibit exotic transport and magnetic properties, while the absence of periodic structure has long been a major obstacle for the understanding of their electronic structure and exchange interaction. In this paper, we have formulated a theoretical approach, which combines the melt-quench approach and the spin dynamic Monte-Carlo simulations, and based on it, we explored amorphous Co{sub 0.5}Zn{sub 0.5}O{sub 1−y} ternary transition metal oxides. Our theoretical results reveal that the microstructure, the magnetic properties, and the exchange interactions of Co{sub 0.5}Zn{sub 0.5}O{sub 1−y} are strongly determined by the oxygen stoichiometry. In the oxygen-deficient sample (y > 0), we have observed the long-range ferromagnetic spin ordering which is associated with the non-stoichiometric cobalt-rich region rather than metallic clusters. On the other hand, the microstructure of stoichiometric sample takes the form of continuous random networks, and no long-range ferromagnetism has been observed in it. Magnetization characterization of experimental synthesized Co{sub 0.61}Zn{sub 0.39}O{sub 1−y} films verifies the relation between the spin ordering and the oxygen stoichiometry. Furthermore, the temperature dependence of electrical transport shows a typical feature of semiconductors, in agreement with our theoretical results.

  8. Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria

    SciTech Connect

    Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.; Tennessen, Kristin; Woyke, Tanja; Kyrpides, Nikos C.; Ivanova, Natalia N.

    2015-11-20

    Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbioticand host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. Lastly, these analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.

  9. Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria

    DOE PAGES

    Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.; ...

    2015-11-20

    Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogeneticmore » distribution patterns and sequence signatures based on known precepts of symbioticand host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. Lastly, these analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.« less

  10. Non-invasive determination of external forces in vortex-pair-cylinder interactions

    NASA Astrophysics Data System (ADS)

    Hartmann, D.; Schröder, W.; Shashikanth, B. N.

    2012-06-01

    Expressions for the conserved linear and angular momenta of a dynamically coupled fluid + solid system are derived. Based on the knowledge of the flow velocity field, these expressions allow the determination of the external forces exerted on a body moving in the fluid such as, e.g., swimming fish. The verification of the derived conserved quantities is done numerically. The interaction of a vortex pair with a circular cylinder in various configurations of motions representing a generic test case for a dynamically coupled fluid + solid system is investigated in a weakly compressible Navier-Stokes setting using a Cartesian cut-cell method, i.e., the moving circular cylinder is represented by cut cells on a moving mesh. The objectives of this study are twofold. The first objective is to show the robustness of the derived expressions for the conserved linear and angular momenta with respect to bounded and discrete data sets. The second objective is to study the coupled dynamics of the vortex pair and a neutrally buoyant cylinder free to move in response to the fluid stresses exerted on its surface. A comparison of the vortex-body interaction with the case of a fixed circular cylinder evidences significant differences in the vortex dynamics. When the cylinder is fixed strong secondary vorticity is generated resulting in a repeating process between the primary vortex pair and the cylinder. In the neutrally buoyant cylinder case, a stable structure consisting of the primary vortex pair and secondary vorticity shear layers stays attached to the moving cylinder. In addition to these fundamental cases, the vortex-pair-cylinder interaction is studied for locomotion at constant speed and locomotion at constant thrust. It is shown that a similar vortex structure like in the neutrally buoyant cylinder case is obtained when the cylinder moves away from the approaching vortex pair at a constant speed smaller than the vortex pair translational velocity. Finally, the idealized

  11. Relative electron density determination using a physics based parameterization of photon interactions in medical DECT

    NASA Astrophysics Data System (ADS)

    van Abbema, Joanne K.; van Goethem, Marc-Jan; Greuter, Marcel J. W.; van der Schaaf, Arjen; Brandenburg, Sytze; van der Graaf, Emiel R.

    2015-05-01

    Radiotherapy and particle therapy treatment planning require accurate knowledge of the electron density and elemental composition of the tissues in the beam path to predict the local dose deposition. We describe a method for the analysis of dual energy computed tomography (DECT) images that provides the electron densities and effective atomic numbers of tissues. The CT measurement process is modelled by system weighting functions, which apply an energy dependent weighting to the parameterization of the total cross section for photon interactions with matter. This detailed parameterization is based on the theoretical analysis of Jackson and Hawkes and deviates, at most, 0.3% from the tabulated NIST values for the elements H to Zn. To account for beam hardening in the object as present in the CT image we implemented an iterative process employing a local weighting function, derived from the method proposed by Heismann and Balda. With this method effective atomic numbers between 1 and 30 can be determined. The method has been experimentally validated on a commercially available tissue characterization phantom with 16 inserts made of tissue substitutes and aluminium that has been scanned on a dual source CT system with tube potentials of 100 kV and 140 kV using a clinical scan protocol. Relative electron densities of all tissue substitutes have been determined with accuracy better than 1%. The presented DECT analysis method thus provides high accuracy electron densities and effective atomic numbers for radiotherapy and especially particle therapy treatment planning.

  12. Using SEM Analysis on Ion-Milled Shale Surface to Determine Shale-Fracturing Fluid Interaction

    NASA Astrophysics Data System (ADS)

    Lu, J.; Mickler, P. J.; Nicot, J. P.

    2014-12-01

    It is important to document and assess shale-fluid interaction during hydraulic fracturing (HF) in order to understand its impact on flowback water chemistry and rock property. A series of autoclave experiments were conducted to react shale samples from major oil and gas shales with synthetic HF containing various additives. To better determine mineral dissolution and precipitation at the rock-fluid interface, ion-milling technique was applied to create extremely flat rock surfaces that were examined before and after the autoclave experiments using a scanning electron microscope (SEM) coupled with energy dispersive spectroscopy (EDS) detectors. This method is able to reveal a level of detail not observable on broken surface or mechanically polished surface. It allows direct comparison of the same mineral and organic matter particles before and after the reaction experiments. Minerals undergone dissolution and newly precipitated materials are readily determined by comparing to the exact locations before reaction. The dissolution porosity and the thickness of precipitates can be quantified by tracing and measuring the geometry of the pores and precipitates. Changes in porosity and permeability were confirmed by mercury intrusion capillary tests.

  13. Sensitive determination of DNA based on the interaction between prulifloxacin-terbium(III) complex and DNA.

    PubMed

    Wu, Ting; Fang, Biyun; Chang, Lin; Liu, Min; Chen, Fang

    2013-01-01

    A simple spectrofluorimetric method is described for the determination of DNA, based on its enhancement of the fluorescence intensity of prulifloxacin (PUFX)-Tb(3+). The luminescence intensity of the PUFX-Tb(3+) complex increased up to 10-fold after adding DNA. The excitation and emission wavelengths were 345 and 545 nm, respectively. Under optimum conditions, variations in the fluorescence intensity showed a good linear relationship with the concentration of hsDNA in the range of 3.0 × 10(-9) to 1.0 × 10(-6) g/mL, with a correlation coefficient (R) of 0.997, and the detection limit was 2.1 × 10(-9) g/mL. The method was successfully applied to the determination of DNA in synthetic samples, and recoveries were in the range 97.3-102.0%. The mechanism of fluorescence enhancement of the PUFX-Tb(3+) complex by DNA is also discussed. The mechanism may involve formation of a ternary complex mainly by intercalation binding together with weak electrostatic interaction, which will increase the energy transition from ligand to Tb(3+), increasing the rigidity of the complex, and decreasing the radiationless energy loss through O-H vibration of the H2O molecule in the PUFX-Tb(3+) complex. Compared with the previous DNA probes, the proposed method is not only more robust and friendly to the environment, but also of relatively higher sensitivity.

  14. Determination of ankle external fixation stiffness by expedited interactive finite element analysis.

    PubMed

    Nielsen, Jonathan K; Saltzman, Charles L; Brown, Thomas D

    2005-11-01

    Interactive finite element analysis holds the potential to quickly and accurately determine the mechanical stiffness of alternative external fixator frame configurations. Using as an example Ilizarov distraction of the ankle, a finite element model and graphical user interface were developed that provided rapid, construct-specific information on fixation rigidity. After input of specific construct variables, the finite element software determined the resulting tibial displacement for a given configuration in typically 15s. The formulation was employed to investigate constructs used to treat end-stage arthritis, both in a parametric series and for five specific clinical distraction cases. Parametric testing of 15 individual variables revealed that tibial half-pins were much more effective than transfixion wires in limiting axial tibial displacement. Factors most strongly contributing to stiffening the construct included placing the tibia closer to the fixator rings, and mounting the pins to the rings at the nearest circumferential location to the bone. Benchtop mechanical validation results differed inappreciably from the finite element computations.

  15. Enhanced spectrophotometric determination of Losartan potassium based on its physicochemical interaction with cationic surfactant.

    PubMed

    Abdel-Fattah, Laila; Abdel-Aziz, Lobna; Gaied, Mariam

    2015-02-05

    In this study, a simple and sensitive spectrophotometric method was developed for determination of Losartan potassium (LST K), an angiotensin-II receptor (type AT1) antagonist, in presence of cationic surfactant cetyltrimethylammonium bromide (CTAB). The physicochemical interaction of LST K with CTAB was investigated. The effect of cationic micelles on the spectroscopic and acid-base properties of LST K was studied at pH 7.4. The binding constant (Kb) and the partition coefficient (Kx) of LST K-CTAB were 1.62×10(5) M(-1) and 1.38×10(5); respectively. The binding of LST K to CTAB micelles implied a shift in drug acidity constant (ΔpKa=0.422). The developed method is linear over the range 0.5-28 μg mL(-1). The accuracy was evaluated and was found to be 99.79±0.509% and the relative standard deviation for intraday and interday precision was 0.821 and 0.963; respectively. The method was successfully applied to determine LST K in pharmaceutical formulations.

  16. Relative electron density determination using a physics based parameterization of photon interactions in medical DECT.

    PubMed

    van Abbema, Joanne K; van Goethem, Marc-Jan; Greuter, Marcel J W; van der Schaaf, Arjen; Brandenburg, Sytze; van der Graaf, Emiel R

    2015-05-07

    Radiotherapy and particle therapy treatment planning require accurate knowledge of the electron density and elemental composition of the tissues in the beam path to predict the local dose deposition. We describe a method for the analysis of dual energy computed tomography (DECT) images that provides the electron densities and effective atomic numbers of tissues. The CT measurement process is modelled by system weighting functions, which apply an energy dependent weighting to the parameterization of the total cross section for photon interactions with matter. This detailed parameterization is based on the theoretical analysis of Jackson and Hawkes and deviates, at most, 0.3% from the tabulated NIST values for the elements H to Zn. To account for beam hardening in the object as present in the CT image we implemented an iterative process employing a local weighting function, derived from the method proposed by Heismann and Balda. With this method effective atomic numbers between 1 and 30 can be determined. The method has been experimentally validated on a commercially available tissue characterization phantom with 16 inserts made of tissue substitutes and aluminium that has been scanned on a dual source CT system with tube potentials of 100 kV and 140 kV using a clinical scan protocol. Relative electron densities of all tissue substitutes have been determined with accuracy better than 1%. The presented DECT analysis method thus provides high accuracy electron densities and effective atomic numbers for radiotherapy and especially particle therapy treatment planning.

  17. Enhanced spectrophotometric determination of Losartan potassium based on its physicochemical interaction with cationic surfactant

    NASA Astrophysics Data System (ADS)

    Abdel-Fattah, Laila; Abdel-Aziz, Lobna; Gaied, Mariam

    2015-02-01

    In this study, a simple and sensitive spectrophotometric method was developed for determination of Losartan potassium (LST K), an angiotensin-II receptor (type AT1) antagonist, in presence of cationic surfactant cetyltrimethylammonium bromide (CTAB). The physicochemical interaction of LST K with CTAB was investigated. The effect of cationic micelles on the spectroscopic and acid-base properties of LST K was studied at pH 7.4. The binding constant (Kb) and the partition coefficient (Kx) of LST K-CTAB were 1.62 × 105 M-1 and 1.38 × 105; respectively. The binding of LST K to CTAB micelles implied a shift in drug acidity constant (ΔpKa = 0.422). The developed method is linear over the range 0.5-28 μg mL-1. The accuracy was evaluated and was found to be 99.79 ± 0.509% and the relative standard deviation for intraday and interday precision was 0.821 and 0.963; respectively. The method was successfully applied to determine LST K in pharmaceutical formulations.

  18. [Determination of trigonelline in Trigonella foenum-graecum L. by hydrophilic interaction chromatography].

    PubMed

    Zhuo, Rongjie; Wang, Li; Wang, Longxing; Xiao, Hongbin; Cai, Shaoqing

    2010-04-01

    A method of hydrophilic interaction chromatography (HILIC) was established for the quantitative determination of trigonelline in Trigonella foenum-graecum L. HILIC analysis was performed on a Waters Atlantis HILIC Silica column (150 mm x 2.1 mm, 3 microm). The mobile phase consisted of acetonitrile-ammonium acetate (pH 4.4) (70:30, v/v), and the flow rate was 0. 4 mL/min. The detection wavelength was set at 265 nm. The method has good linearity in the range of 2.50-100 mg/L for trigonelline (r = 0.999 6). The recoveries were on an average of 102% by adding 29.2 mg/L and 43.8 mg/L with relative standard deviations (RSDs) of 4.17% and 2.28% (n = 3), respectively. The results indicate that the method is simple and rapid for the determination of strong polar trigonelline in Trigonella foenum-graecum L. Furthermore, it significantly reduces the equilibration time compared with ion-pair liquid chromatography (IPLC) recorded in the Pharmacopoeia of China. This new method can be used as a valid method for the quality control of Trigonella foenum-graecum L.

  19. Learning with Interactive Whiteboards: Determining the Factors on Promoting Interactive Whiteboards to Students by Technology Acceptance Model

    ERIC Educational Resources Information Center

    Kilic, Eylem; Güler, Çetin; Çelik, H. Eray; Tatli, Cemal

    2015-01-01

    Purpose: The purpose of this study is to investigate the factors which might affect the intention to use interactive whiteboards (IWBs) by university students, using Technology Acceptance Model by the structural equation modeling approach. The following hypothesis guided the current study: H1. There is a positive relationship between IWB…

  20. An Interactive network of long non-coding RNAs facilitates the Drosophila sex determination decision

    PubMed Central

    Mulvey, Brett B.; Olcese, Ursula; Cabrera, Janel R.; Horabin, Jamila I.

    2014-01-01

    Genome analysis in several eukaryotes shows a surprising number of transcripts which do not encode conventional messenger RNAs. Once considered noise, these non-coding RNAs (ncRNAs) appear capable of controlling gene expression by various means. We find Drosophila sex determination, specifically the master-switch gene Sex-lethal (Sxl), is regulated by long ncRNAs (>200 nt). The lncRNAs influence the dose sensitive establishment promoter of Sxl, SxlPe, which must be activated to specify female sex. They are primarily from two regions, R1 and R2, upstream of SxlPeand show a dynamic developmental profile. Of the four lncRNA strands only one, R2 antisense, has its peak coincident with SxlPe transcription, suggesting it may promote activation. Indeed, its expression is regulated by the X chromosome counting genes, whose dose determines whether SxlPe is transcribed. Transgenic lines which ectopically express each of the lncRNAs show they can act in trans, impacting the process of sex determination but also altering the levels of the other lncRNAs. Generally, expression of R1 is negative whereas R2 is positive to females. This ectopic expression also results in a change in the local chromatin marks, affecting the timing and strength of SxlPe transcription. The chromatin marks are those deposited by the Polycomb and Trithorax groups of chromatin modifying proteins, which we find bind to the lncRNAs. We suggest the increasing numbers of non-coding transcripts being identified are a harbinger of interacting networks similar to the one we describe. PMID:24954180

  1. An Evolving Genetic Architecture Interacts with Hill-Robertson Interference to Determine the Benefit of Sex.

    PubMed

    Whitlock, Alexander O B; Peck, Kayla M; Azevedo, Ricardo B R; Burch, Christina L

    2016-06-01

    Sex is ubiquitous in the natural world, but the nature of its benefits remains controversial. Previous studies have suggested that a major advantage of sex is its ability to eliminate interference between selection on linked mutations, a phenomenon known as Hill-Robertson interference. However, those studies may have missed both important advantages and important disadvantages of sexual reproduction because they did not allow the distributions of mutational effects and interactions (i.e., the genetic architecture) to evolve. Here we investigate how Hill-Robertson interference interacts with an evolving genetic architecture to affect the evolutionary origin and maintenance of sex by simulating evolution in populations of artificial gene networks. We observed a long-term advantage of sex-equilibrium mean fitness of sexual populations exceeded that of asexual populations-that did not depend on population size. We also observed a short-term advantage of sex-sexual modifier mutations readily invaded asexual populations-that increased with population size, as was observed in previous studies. We show that the long- and short-term advantages of sex were both determined by differences between sexual and asexual populations in the evolutionary dynamics of two properties of the genetic architecture: the deleterious mutation rate ([Formula: see text]) and recombination load ([Formula: see text]). These differences resulted from a combination of selection to minimize [Formula: see text] which is experienced only by sexuals, and Hill-Robertson interference experienced primarily by asexuals. In contrast to the previous studies, in which Hill-Robertson interference had only a direct impact on the fitness advantages of sex, the impact of Hill-Robertson interference in our simulations was mediated additionally by an indirect impact on the efficiency with which selection acted to reduce [Formula: see text].

  2. Climate warming and agricultural stressors interact to determine stream macroinvertebrate community dynamics.

    PubMed

    Piggott, Jeremy J; Townsend, Colin R; Matthaei, Christoph D

    2015-05-01

    Global climate change is likely to modify the ecological consequences of currently acting stressors, but potentially important interactions between climate warming and land-use related stressors remain largely unknown. Agriculture affects streams and rivers worldwide, including via nutrient enrichment and increased fine sediment input. We manipulated nutrients (simulating agricultural run-off) and deposited fine sediment (simulating agricultural erosion) (two levels each) and water temperature (eight levels, 0-6°C above ambient) simultaneously in 128 streamside mesocosms to determine the individual and combined effects of the three stressors on macroinvertebrate community dynamics (community composition and body size structure of benthic, drift and insect emergence assemblages). All three stressors had pervasive individual effects, but in combination often produced additive or antagonistic outcomes. Changes in benthic community composition showed a complex interplay among habitat quality (with or without sediment), resource availability (with or without nutrient enrichment) and the behavioural/physiological tendency to drift or emerge as temperature rose. The presence of sediment and raised temperature both resulted in a community of smaller organisms. Deposited fine sediment strongly increased the propensity to drift. Stressor effects were most prominent in the benthic assemblage, frequently reflected by opposite patterns in individuals quitting the benthos (in terms of their propensity to drift or emerge). Of particular importance is that community measures of stream health routinely used around the world (taxon richness, EPT richness and diversity) all showed complex three-way interactions, with either a consistently stronger temperature response or a reversal of its direction when one or both agricultural stressors were also in operation. The negative effects of added fine sediment, which were often stronger at raised temperatures, suggest that streams already

  3. Multiple interaction types determine the impact of ant predation of caterpillars in a forest community.

    PubMed

    Clark, Robert E; Farkas, Timothy E; Lichter-Marck, Isaac; Johnson, Emily R; Singer, Michael S

    2016-12-01

    Direct and indirect effects of predators are highly variable in complex communities, and understanding the sources of this variation is a research priority in community ecology. Recent evidence indicates that herbivore community structure is a primary determinant of predation strength and its cascading impacts on plants. In this study, we use variation in herbivore community structure among plant species to experimentally test two hypotheses in a temperate forest food web. First, variation in the strength of predator effects, such as ant predation of caterpillars, is predicted to be density dependent, exhibiting stronger effects when prey abundance is high (density-dependent predation hypothesis). Second, mutualistic interactions between ants and sap-feeding herbivores are expected to increase the abundance of predatory ants, strengthening predation effects on herbivores with cascading effects on host plants (keystone mutualism hypothesis). Using a large-scale predator exclusion experiment across eight dominant tree species, we tracked changes in insect density on 862 plants across two years, recording 2,322 ants, 1,062 sap-feeders, 5,322 caterpillars, and quantifying herbivory on 199, 338 leaves. In this experiment, density-dependent predation did not explain variation in the direct or indirect effects of ants on caterpillars and herbivory. In partial support of the keystone mutualism hypothesis, sap-feeders strengthened top-down effects of ants on caterpillars under some conditions. However, stronger ant predation of caterpillars did not lead to measurable trophic cascades on trees occupied by sap-feeders. Instead, the presence of sap-feeders was associated with increased per capita feeding damage by caterpillars, and this bottom-up effect attenuated the indirect effects of ants on host plants. These findings demonstrate that examining the multi-trophic impacts of mutualisms and predation in the context of the broader community can reveal patterns otherwise

  4. Determination of inorganic pharmaceutical counterions using hydrophilic interaction chromatography coupled with a Corona CAD detector.

    PubMed

    Huang, Z; Richards, M A; Zha, Y; Francis, R; Lozano, R; Ruan, J

    2009-12-05

    A simple generic approach was investigated for the determination of inorganic pharmaceutical counterions in drug substances using conventional high performance liquid chromatographic (HPLC) instruments. An intuitive approach combined Corona charged aerosol detection (CAD) with a polymer-based zwitterionic stationary phase in the hydrophilic interaction chromatography (HILIC) mode. Two generic methods based on this HILIC/CAD technique were developed to quantitate counterions such as Cl-, Br-, SO(4)(2-), K+, Ca2+ and Mg2+ in different pharmaceutical compounds. The development and capability of this HILIC/CAD technique analysis were examined. HILIC/CAD was compared to ion chromatography (IC), the most commonly used methodology for pharmaceutical counterion analysis. HILIC/CAD was found to have significant advantages in terms of: (1) being able to quantitate both anions and cations simultaneously without a need to change column/eluent or detection mode; (2) imposing much less restriction on the allowable organic percentage of the eluents than IC, and therefore being more appropriate for analysis of counterions of poorly water-soluble drugs; (3) requiring minimal training of the operating analysts. The precision and accuracy of counterion analysis using HILIC/CAD was not compromised. A typical precision of <2.0% was observed for all tested inorganic counterions; the determinations were within 2.0% relative to the theoretical counterion amount in the drug substance. Additionally, better accuracy was shown for Cl- in several drug substances as compared to IC. The main drawback of HILIC/CAD is its unsuitability for many of the current silica-based HILIC columns, because slight dissolution of silica leads to high baseline noise in the CAD detector. As a result of the universal detection characteristics of Corona CAD and the unique separation capabilities of a zwitterionic stationary phase, an intuitive and robust HPLC method was developed for the generic determination of

  5. Determining an Effective Shear Modulus in Tubular Organs for Fluid-Structure Interaction

    NASA Astrophysics Data System (ADS)

    Chisena, Robert; Brasseur, James; Costanzo, Francesco; Gregersen, Hans; Zhao, Jingbo

    2014-11-01

    Fluid-structure interaction (FSI) is central to the mechanics of fluid-filled tubular organs such as the intestine and esophagus. The motions of fluid chyme are driven by a muscularis wall layer of circular and longitudinal muscle fibers. The coupled motions of the fluid and elastic solid phases result from a local balance between active and passive muscle stress components, fluid pressure, and fluid viscous stresses. Model predictions depend on the passive elastic response of the muscularis layer, which is typically parameterized with an average isotropic elastic modulus (EM), currently measured in vivo and in vitro with estimates for total hoop stress within a distension experiment. We have shown that this approach contains serious error due to the overwhelming influence of incompressibility on the hydrostatic component. We present a new approach in which an effective shear modulus, containing only deviatoric contributions, is measured to overcome this serious error. Using in vitro measurements from pig intestines, we compare our new approach to the current method, showing vastly different predictions. We will also report on our current analysis which aims to determine the influence of residual stress on the EM measurements and comment on it use in FSI simulations.

  6. The compact conformation of fibronectin is determined by intramolecular ionic interactions.

    PubMed

    Johnson, K J; Sage, H; Briscoe, G; Erickson, H P

    1999-05-28

    Fibronectin exists in a compact or extended conformation, depending upon environmental pH and salt concentration. Using recombinant fragments expressed in bacteria and baculovirus, we determined the domains responsible for producing fibronectin's compact conformation. Our velocity and equilibrium sedimentation data show that FN2-14 (a protein containing FN-III domains 2 through 14) forms dimers in low salt. Experiments with smaller fragments indicates that the compact conformation is produced by binding of FN12-14 of one subunit to FN2-3 of the other subunit in the dimer. The binding is weakened at higher salt concentrations, implying an electrostatic interaction. Furthermore, segment FN7-14+A, which contains the alternatively spliced A domain between FN11 and 12, forms dimers, whereas FN7-14 without A does not. Segment FN12-14+A also forms dimers, but the isolated A domain does not. These data imply an association of domain A with FN12-14, and the presence of A may favor an open conformation by competing with FN2-3 for binding to FN12-14.

  7. Aerosol-cloud interaction determined by satellite data over the Baltic Sea countries

    NASA Astrophysics Data System (ADS)

    Saponaro, Giulia; Kolmonen, Pekka; Sogacheva, Larisa; de Leeuw, Gerrit

    2015-04-01

    The present study investigates the use of long-term satellite data to assess the influence of aerosols upon cloud parameters over the Baltic Sea region. This particular area offers the contrast of a very clean environment (Fennoscandia) against a more polluted one (Germany, Poland). The datasets consists of Collection 6 Level 3 daily observations from 2002 to 2014 collected by the NASA's Moderate-Resolution Imaging Spectrometer (MODIS) instrument on-board the Aqua platform. The MODIS aerosol optical depth (AOD) product is used as a proxy for the number concentration of aerosol particles while the cloud effective radius (CER) and cloud optical thickness (COT) describe cloud microphysical and optical properties respectively. Satellite data have certain limitations, such as the restriction to summer season due to solar zenith angle restrictions and the known problem of the ambiguity of the aerosol-cloud interface, for instance. Through the analysis of a 12-years dataset, distribution maps provide information on a regional scale about the first aerosol indirect effect (AIE) by determining the aerosol-cloud interaction (ACI). The ACI is defined as the change in cloud optical depth or effective radius as a function of aerosol load for a fixed liquid water path (LWP). The focusing point of the current study is the evaluation of regional trends of ACI over the observed area of the Baltic Sea.

  8. Self-interaction chromatography in pre-packed columns: a critical evaluation of self-interaction chromatography methodology to determine the second virial coefficient.

    PubMed

    Rakel, Natalie; Schleining, Kristina; Dismer, Florian; Hubbuch, Juergen

    2013-06-07

    The characterization of protein-protein interactions is commonly conducted via self-interaction chromatography to describe magnitude and direction of the interactions with the resulting osmotic second virial coefficient (B22). However, the method is invasive and protein immobilization on the adsorber surface can influence the results obtained. In order to replace batch immobilization procedures followed by a column packing, direct on-column preparation was optimized in terms of protein immobilization under a continuous flow. Surface load was measured applying a novel method based on partial least squares analysis of spectral scans to reduce analytical error when determining the amount of immobilized protein. Subsequently influencing parameters such as the effects of absolute surface load, injected protein concentration and distribution of protein orientation were analyzed and system performance evaluated. The results disprove the consistency of the SIC method regarding the non-random orientation of proteins on adsorber particles. Thus the determined B22-values differ quantitatively from those determined with static light scattering. Furthermore, variations in immobilization conditions influence the results obtained. These results make clear that SIC does not fulfill the theoretical framework of B22-analysis. It is rather a qualitative measure of protein-protein interactions in the respective system used for experimentation.

  9. Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

    PubMed Central

    Maghuly, Fatemeh; Ramkat, Rose C.; Laimer, Margit

    2014-01-01

    Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants. PMID

  10. Characterization of membrane and protein interaction determinants of the Agrobacterium tumefaciens VirB11 ATPase.

    PubMed Central

    Rashkova, S; Spudich, G M; Christie, P J

    1997-01-01

    The VirB11 ATPase is a putative component of the transport machinery responsible for directing the export of nucleoprotein particles (T complexes) across the Agrobacterium tumefaciens envelope to susceptible plant cells. Fractionation and membrane treatment studies showed that approximately 30% of VirB11 partitioned as soluble protein, whereas the remaining protein was only partially solubilized with urea from cytoplasmic membranes of wild-type strain A348 as well as a Ti-plasmidless strain expressing virB11 from an IncP replicon. Mutations in virB11 affecting protein function were mapped near the amino terminus (Q6L, P13L, and E25G), just upstream of a region encoding a Walker A nucleotide-binding site (F154H;L155M), and within the Walker A motif (P170L, K175Q, and delta GKT174-176). The K175Q and delta GKT174-176 mutant proteins partitioned almost exclusively with the cytoplasmic membrane, suggesting that an activity associated with nucleotide binding could modulate the affinity of VirB11 for the cytoplasmic membrane. The virB11F154H;L155M allele was transdominant over wild-type virB11 in a merodiploid assay, providing strong evidence that at least one form of VirB11 functions as a homo- or heteromultimer. An allele with a deletion of the first half of the gene, virB11 delta1-156, was transdominant in a merodiploid assay, indicating that the C-terminal half of VirB11 contains a protein interaction domain. Products of both virB11 delta1-156 and virB11 delta158-343, which synthesizes the N-terminal half of VirB11, associated tightly with the A. tumefaciens membrane, suggesting that both halves of VirB11 contain membrane interaction determinants. PMID:9006008

  11. Double-bottom chaotic map particle swarm optimization based on chi-square test to determine gene-gene interactions.

    PubMed

    Yang, Cheng-Hong; Lin, Yu-Da; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2014-01-01

    Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs) of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO) was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05). Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer.

  12. Double-Bottom Chaotic Map Particle Swarm Optimization Based on Chi-Square Test to Determine Gene-Gene Interactions

    PubMed Central

    Yang, Cheng-Hong; Chang, Hsueh-Wei

    2014-01-01

    Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs) of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO) was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05). Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer. PMID:24895547

  13. [Determination of melamine and ammeline in eggs and meat using hydrophilic interaction liquid chromatography].

    PubMed

    Li, Yanzhao; Hao, Weiqiang; Wang, Yubo; Chen, Qiang; Li, Jinchun; Sun, Xiaoli

    2012-07-01

    A hydrophilic interaction liquid chromatographic (HILIC) method for the determination of melamine and its degradation product ammeline in eggs and meat has been developed. The separation was carried out on a ZIC-HILIC column with 3 mmol/L NH4H2PO4 (pH 6.9)-acetonitrile (20: 80, v/v) as mobile phase at the flow rate of 0.8 mL/min, and detected at 220 nm. Compared with the reversed-phase liquid chromatography, this method can avoid the use of ion pair reagents and thus simplify the composition of mobile phase. Under the above chromatographic conditions, melamine and ammeline had good peak shapes and moderate retention times. Good separation between these compounds and the substances that were naturally contained in the samples can be achieved. For the sample preparation, the analytes were first extracted with 0.1% phosphoric acid due to the basicity of melamine and ammeline. Then, metaphosphoric acid and acetonitrile were used to remove proteins and saccharides by precipitation. After the filtration and removal of acetonitrile by rotary evaporation under vacuum, the filtrate was cleaned-up by solid-phase extraction (SPE) technique in which a cation exchange column was used. The SPE column was activated by using methanol and 0.1% phosphoric acid. A solution of 5% ammonia methanol was chosen as eluent. The residues obtained from the eluant by evaporating the solvent were resolved in the mobile phase. It was found that there was a good linear relationship between concentration and detector response within the range of 0.4-40 mg/L. The limits of detection were 2 mg/kg for both melamine and ammeline. The average recoveries were between 80% and 105% in the spiked range of 2-10 mg/kg. The relative standard deviations were not more than 10%. The solutions of melamine and ammeline were stable in a month. The established method can be used in practice to determine melamine and ammeline simultaneously in egg and meat samples.

  14. Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method.

    PubMed

    Nouretdinov, Ilia; Gammerman, Alex; Qi, Yanjun; Klein-Seetharaman, Judith

    2012-01-01

    Identifying protein-protein interactions (PPI's) is critical for understanding virtually all cellular molecular mechanisms. Previously, predicting PPI's was treated as a binary classification task and has commonly been solved in a supervised setting which requires a positive labeled set of known PPI's and a negative labeled set of non-interacting protein pairs. In those methods, the learner provides the likelihood of the predicted interaction, but without a confidence level associated with each prediction. Here, we apply a conformal prediction framework to make predictions and estimate confidence of the predictions. The conformal predictor uses a function measuring relative 'strangeness' interacting pairs to check whether prediction of a new example added to the sequence of already known PPI's would conform to the 'exchangeability' assumption: distribution of interacting pairs is invariant with any permutations of the pairs. In fact, this is the only assumption we make about the data. Another advantage is that the user can control a number of errors by providing a desirable confidence level. This feature of CP is very useful for a ranking list of possible interactive pairs. In this paper, the conformal method has been developed to deal with just one class - class interactive proteins - while there is not clearly defined of 'non-interactive'pairs. The confidence level helps the biologist in the interpretation of the results, and better assists the choices of pairs for experimental validation. We apply the proposed conformal framework to improve the identification of interacting pairs between HIV-1 and human proteins.

  15. [Morphogenesis and differentiation of the female genital tract. Genetic determinism and epithelium-stromal interactions].

    PubMed

    Amălinei, Cornelia

    2007-01-01

    The epithelium-stromal interaction is important in the process of morphogenesis, differentiation, and hormone response, in female genital tract. This review is organized in four sections: i) female genital tract morphogenesis, based on genetic determinism; ii) hormonal control of endometrial proliferation; iii) TGF-beta key-role in epithelium-stromal communication; iv) endometrial apoptosis. Female genital tract derives from the Müllerian ducts, a number of genes being involved in its regulation, like Lim1, Lhx9, Emx, Pax-2, Hox-A9, Hox-A10, Hox-A11, Hox-A13, Wnt-4, Wnt-7, WT1, SF-1, and GATA-4. TGF-beta, whose expression is modulated by ovarian steroids, regulates cell growth, differentiation, apoptosis, inflammatory and immune responses, extracellular matrix deposition, adhesion molecules, proteases, and protease inhibitor expression. In the endometrium, TGF-beta regulates its own expression, and that of extracellular matrix, adhesion molecules and proteases implicated in trophoblast invasion, angiogenesis, and tumor metastasis during embryo implantation, endometriosis, irregular bleeding, and endometrial cancer. Cellular response elicited by TGF-beta, mediated through a serine/threonine kinase receptor, induces the recruitment of multiple intracellular signals, specifically Smads, whose activation and subsequent translocation into the nucleus results in gene expression. Ubiquitin is involved in the degradation of short lived, regulatory or misfolded proteins, by tagging them to be taken to the proteasome. In the endometrium, ubiquitin may allow cells of stromal origin to grow, survive and evade T-cell mediated disposal, showing a functional duality. A complete understanding of the complex regulatory endometrial epithelium-stromal mechanism, concertating genes, hormones, and cytokines, may provide new therapeutic targets in female reproductive tract pathology.

  16. Interactions between local climate and grazing determine the population dynamics of the small herb Viola biflora.

    PubMed

    Evju, Marianne; Halvorsen, Rune; Rydgren, Knut; Austrheim, Gunnar; Mysterud, Atle

    2010-08-01

    Plants of low stature may benefit from the presence of large herbivores through removal of tall competitive neighbours and increased light availability. Accordingly, removal of grazers has been predicted to disfavour small species. In addition to this indirect beneficial effect, the population dynamics of plants is strongly influenced by variation in external conditions such as temperature and precipitation. However, few studies have examined the interaction between large herbivores and inter-annual variation in climate for the population dynamics of small plant species not preferred by herbivores. We studied three populations of the perennial herb Viola biflora exposed to different sheep densities (high, low and zero) for 6 years in a field experiment. Plants were also impacted by invertebrate and small vertebrate herbivores (rodents). Rates of growth were marginally higher at high sheep densities, and during warm summers both survival and growth were higher when sheep were present. Thus, while the height of tall herbs was positively related to July temperature, it was less so in the treatments with sheep, suggesting that sheep reduce the negative effects of interspecific competition for this small herb. Life table response experiment analyses revealed that the population growth rate (lambda) was slightly lower in the absence of sheep, but between-year variation in lambda was larger than variation among sheep density treatments. lambda was negatively related to July temperature, with an additional negative effect of vertebrate grazing frequency (sheep or rodent grazing). The evidence from this 6-year study suggests that the population dynamics of Viola biflora is determined by a complex interplay between climate and grazing by both large and small herbivores.

  17. Interaction of exposure concentration and duration in determining acute toxic effects of sarin vapor in rats.

    PubMed

    Mioduszewski, R; Manthei, J; Way, R; Burnett, D; Gaviola, B; Muse, W; Thomson, S; Sommerville, D; Crosier, R

    2002-04-01

    Sarin (GB) vapor exposure is associated with both systemic and local toxic effects occurring primarily via the inhalation and ocular routes. The objective of these studies was to develop models for predicting dose-response effects of GB vapor concentrations as a function of exposure duration. Thus, the probability of GB vapor-induced lethality was estimated in rats exposed to various combinations of exposure concentration and duration. Groups of male and female Sprague-Dawley rats were exposed to one of a series of GB vapor concentrations for a single duration (5-360 min) in a whole-body dynamic chamber. The onset of clinical signs and changes in blood cholinesterase activity were measured with each exposure. Separate effective concentrations for lethality in 50% of the exposed population (LC50) and corresponding dose-response slopes were determined for each exposure duration by the Bliss probit method. Contrary to that predicted by Haber's rule, the interaction of LC50 x time (LCT50) values increased with exposure duration (i.e., the CT for 50% lethality in the exposed population and corresponding dose-response slope was not constant over time). A plot of log (LCT50) versus log (exposure time) showed significant curvature. Predictive models derived from multifactor probit analysis of results describing the relationship between exposure conditions and probability of lethality in the rat are discussed. Overall, female rats were more sensitive to GB vapor toxicity than male rats over the range of exposure concentration and duration studied. Miosis was the initial clinical sign noted after the start of GB vapor exposure. Although blood cholinesterase activity was significantly inhibited by GB vapor exposure, poor correlation between cholinesterase inhibition and exposure conditions or cholinesterase inhibition and severity of clinical signs was noted.

  18. Structural determinants for NF-Y/DNA interaction at the CCAAT box.

    PubMed

    Nardone, Valentina; Chaves-Sanjuan, Antonio; Nardini, Marco

    2016-09-25

    The recently determined crystal structures of the sequence-specific transcription factor NF-Y have illuminated the structural mechanism underlying transcription at the CCAAT box. NF-Y is a trimeric protein complex composed by the NF-YA, NF-YB, and NF-YC subunits. NF-YB and NF-YC contain a histone-like domain and assemble on a head-to-tail fashion to form a dimer, which provides the structural scaffold for the DNA sugar-phosphate backbone binding (mimicking the nucleosome H2A/H2B-DNA assembly) and for the interaction with NF-YA. The NF-YA subunit hosts two structurally extended α-helices; one is involved in NF-YB/NF-YC binding and the other inserts deeply into the DNA minor groove, providing exquisite sequence-specificity for recognition and binding of the CCAAT box. The analysis of these structural data is expected to serve as a powerful guide for future experiments aimed at understanding the role of post-translational modification at NF-Y regulation sites and to unravel the three-dimensional architecture of higher order complexes formed between NF-Y and other transcription factors that act synergistically for transcription activation. Moreover, these structures represent an excellent starting point to challenge the formation of a stable hybrid nucleosome between NF-Y and core histone proteins, and to rationalize the fine molecular details associated with the wide combinatorial association of plant NF-Y subunits. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

  19. Attributions about, and Instructions on How To Treat, Their Neonates as Determinants of Mothers' Interaction Behavior.

    ERIC Educational Resources Information Center

    Hollenbeck, Albert R.; Gewirtz, Jacob L.

    Two experiments explored the influence of neonate characteristics on maternal behavior. Experiment 1 investigated the influence of maternal attribution to the neonate of certain behavioral characteristics on maternal behavior in interaction. After videotaped mother-neonate pair interaction, neonates were removed for a nominal examination. Mothers…

  20. Moving forward: dispersal and species interactions determine biotic responses to climate change.

    PubMed

    Urban, Mark C; Zarnetske, Phoebe L; Skelly, David K

    2013-09-01

    We need accurate predictions about how climate change will alter species distributions and abundances around the world. Most predictions assume simplistic dispersal scenarios and ignore biotic interactions. We argue for incorporating the complexities of dispersal and species interactions. Range expansions depend not just on mean dispersal, but also on the shape of the dispersal kernel and the population's growth rate. We show how models using species-specific dispersal can produce more accurate predictions than models applying all-or-nothing dispersal scenarios. Models that additionally include species interactions can generate distinct outcomes. For example, species interactions can slow climate tracking and produce more extinctions than models assuming no interactions. We conclude that (1) just knowing mean dispersal is insufficient to predict biotic responses to climate change, and (2) considering interspecific dispersal variation and species interactions jointly will be necessary to anticipate future changes to biological diversity. We advocate for collecting key information on interspecific dispersal differences and strong biotic interactions so that we can build the more robust predictive models that will be necessary to inform conservation efforts as climates continue to change.

  1. Development and validation of a hydrophilic interaction liquid chromatographic method for determination of aromatic amines in environmental water

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A simple, precise, and accurate hydrophilic interaction liquid chromatographic (HILIC) method has been developed for the determination of 5 aromatic amines in environmental water samples. Chromatography was carried out on a bare silica column, using a mixture of acetonitrile: phosphate buffer (10 mM...

  2. The masculinity paradox: facial masculinity and beardedness interact to determine women's ratings of men's facial attractiveness.

    PubMed

    Dixson, B J W; Sulikowski, D; Gouda-Vossos, A; Rantala, M J; Brooks, R C

    2016-11-01

    In many species, male secondary sexual traits have evolved via female choice as they confer indirect (i.e. genetic) benefits or direct benefits such as enhanced fertility or survival. In humans, the role of men's characteristically masculine androgen-dependent facial traits in determining men's attractiveness has presented an enduring paradox in studies of human mate preferences. Male-typical facial features such as a pronounced brow ridge and a more robust jawline may signal underlying health, whereas beards may signal men's age and masculine social dominance. However, masculine faces are judged as more attractive for short-term relationships over less masculine faces, whereas beards are judged as more attractive than clean-shaven faces for long-term relationships. Why such divergent effects occur between preferences for two sexually dimorphic traits remains unresolved. In this study, we used computer graphic manipulation to morph male faces varying in facial hair from clean-shaven, light stubble, heavy stubble and full beards to appear more (+25% and +50%) or less (-25% and -50%) masculine. Women (N = 8520) were assigned to treatments wherein they rated these stimuli for physical attractiveness in general, for a short-term liaison or a long-term relationship. Results showed a significant interaction between beardedness and masculinity on attractiveness ratings. Masculinized and, to an even greater extent, feminized faces were less attractive than unmanipulated faces when all were clean-shaven, and stubble and beards dampened the polarizing effects of extreme masculinity and femininity. Relationship context also had effects on ratings, with facial hair enhancing long-term, and not short-term, attractiveness. Effects of facial masculinization appear to have been due to small differences in the relative attractiveness of each masculinity level under the three treatment conditions and not to any change in the order of their attractiveness. Our findings suggest that

  3. Determination of distributions of the quadrupole interaction in amorphous solids by 27Al satellite transition spectroscopy.

    PubMed

    Jäger, C; Kunath, G; Losso, P; Scheler, G

    1993-04-01

    27Al Satellite transition spectroscopy (SATRAS) has been used to extract both the quadrupole interaction and its distribution width from MAS spectra of glasses. Using this method a measurement at a single magnetic field strength allows one to obtain the true chemical shifts and the quadrupole interaction (and its distributions) with high accuracy, including quantification of the results. In contrast to earlier investigations the central transition MAS lineshapes can be described without assumptions and give correct relative proportions of differently coordinated Al species in glasses. The distribution model for the quadrupole interaction and the resulting MAS lineshapes are discussed in detail including a description of the experimental requirements. Experimental results of 27Al SATRAS spectra of a ternary Al2O3-B2O3-P2O5 glass exhibiting 4-, 5-, and 6-coordinated aluminum species clearly prove different mean values and distribution widths for the quadrupole interaction in the various AlOx polyhedra.

  4. Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones.

    PubMed

    Engler, J O; Rödder, D; Elle, O; Hochkirch, A; Secondi, J

    2013-11-01

    Climate is a major factor delimiting species' distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species' interactions in hybrid zones and their responses to future climate change. We investigated the moving hybrid zone between the breeding ranges of two parapatric passerines in Europe. We conducted SDMs representing the climatic conditions during the breeding season. Our results show a large mismatch between the realized and potential distributions of the two species, suggesting that interspecific interactions, not climate, account for the present location of the contact zone. The SDM scenarios show that the southerly distributed species, Hippolais polyglotta, might lose large parts of its southern distribution under climate change, but a similar gain of novel habitat along the hybrid zone seems unlikely, because interactions with the other species (H. icterina) constrain its range expansion. Thus, whenever biotic interactions limit range expansion, species may become 'trapped' if range loss due to climate change is faster than the movement of the contact zone. An increasing number of moving hybrid zones are being reported, but the proximate causes of movement often remain unclear. In a global context of climate change, we call for more interest in their interactions with climate change.

  5. Determination of the interaction impedance of coupled cavity slow wave structures

    NASA Technical Reports Server (NTRS)

    Connolly, D. J.

    1976-01-01

    The interaction impedance of coupled cavity slow wave structures can be measured by perturbing the resonances of a shorted length of the structure using a dielectric rod. An analysis of this procedure is presented. The analysis retains radial as well as axial electric fields and all significant space harmonics. The results obtained are easily programmed formulas for calculating total interaction impedance or Pierce impedance using the experimental data.

  6. DETERMINING CONFIDENCE OF PREDICTED INTERACTIONS BETWEEN HIV-1 AND HUMAN PROTEINS USING CONFORMAL METHOD

    PubMed Central

    Nouretdinov, Ilia; Gammerman, Alex; Qi, Yanjun; Klein-Seetharaman, Judith

    2011-01-01

    Identifying protein-protein interactions (PPI’s) is critical for understanding virtually all cellular molecular mechanisms. Previously, predicting PPI’s was treated as a binary classification task and has commonly been solved in a supervised setting which requires a positive labeled set of known PPI’s and a negative labeled set of non-interacting protein pairs. In those methods, the learner provides the likelihood of the predicted interaction, but without a confidence level associated with each prediction. Here, we apply a conformal prediction framework to make predictions and estimate confidence of the predictions. The conformal predictor uses a function measuring relative ’strangeness’ interacting pairs to check whether prediction of a new example added to the sequence of already known PPI’s would conform to the ’exchangeability’ assumption: distribution of interacting pairs is invariant with any permutations of the pairs. In fact, this is the only assumption we make about the data. Another advantage is that the user can control a number of errors by providing a desirable confidence level. This feature of CP is very useful for a ranking list of possible interactive pairs. In this paper, the conformal method has been developed to deal with just one class - class interactive proteins - while there is not clearly defined of ’non-interactive’ pairs. The confidence level helps the biologist in the interpretation of the results, and better assists the choices of pairs for experimental validation. We apply the proposed conformal framework to improve the identification of interacting pairs between HIV-1 and human proteins. PMID:22174286

  7. Application of the Stoner-Wohlfarth model with interaction for the determination of the saturation magnetisation, anisotropy field, and mean field interaction in bulk amorphous ferromagnets

    NASA Astrophysics Data System (ADS)

    Collocott, S. J.

    2011-08-01

    Magnetic hysteresis curves of bulk amorphous ferromagnet alloys of composition Nd 60Fe 30Al 10, Nd 60Fe 20Co 10Al 10 and Pr 58Fe 24Al 18 have been measured in applied magnetic fields up to 9 T at temperatures in the range 10-350 K. The behaviour of the demagnetisation curve in the first quadrant is interpreted using a mean field interaction model as proposed by Callen et al. [Phys. Rev. B 16 (1977) 263], which extends the Stoner-Wohlfarth model [Philos. Trans. Roy. Soc. A 240 (1948) 599] for a random distribution of non-interacting uniaxial grains. Application of the mean field interaction model enables the determination of the saturation magnetisation Ms, anisotropy field Ha, and interaction parameter d, and from these other magnetic parameters, such as the anisotropy constant, K, are deduced. For the three alloys, the temperature dependent behaviour of Ms, Ha, d and K over the range 20-350 K are found to be qualitatively similar, though there are quantitative differences. In all cases Ms increases with decreasing temperature, both Ha and K increase with decreasing temperature, reaching a peak in the range 75-120 K, and then decreasing, and d decreases approximately linearly as the temperature decreases. The physical mechanisms responsible for coercivity in these materials are discussed in the context of random anisotropy and a strong pinning model of domain walls.

  8. Aggrecan nanoscale solid-fluid interactions are a primary determinant of cartilage dynamic mechanical properties.

    PubMed

    Nia, Hadi Tavakoli; Han, Lin; Bozchalooi, Iman Soltani; Roughley, Peter; Youcef-Toumi, Kamal; Grodzinsky, Alan J; Ortiz, Christine

    2015-03-24

    Poroelastic interactions between interstitial fluid and the extracellular matrix of connective tissues are critical to biological and pathophysiological functions involving solute transport, energy dissipation, self-stiffening and lubrication. However, the molecular origins of poroelasticity at the nanoscale are largely unknown. Here, the broad-spectrum dynamic nanomechanical behavior of cartilage aggrecan monolayer is revealed for the first time, including the equilibrium and instantaneous moduli and the peak in the phase angle of the complex modulus. By performing a length scale study and comparing the experimental results to theoretical predictions, we confirm that the mechanism underlying the observed dynamic nanomechanics is due to solid-fluid interactions (poroelasticity) at the molecular scale. Utilizing finite element modeling, the molecular-scale hydraulic permeability of the aggrecan assembly was quantified (kaggrecan = (4.8 ± 2.8) × 10(-15) m(4)/N·s) and found to be similar to the nanoscale hydraulic permeability of intact normal cartilage tissue but much lower than that of early diseased tissue. The mechanisms underlying aggrecan poroelasticity were further investigated by altering electrostatic interactions between the molecule's constituent glycosaminoglycan chains: electrostatic interactions dominated steric interactions in governing molecular behavior. While the hydraulic permeability of aggrecan layers does not change across species and age, aggrecan from adult human cartilage is stiffer than the aggrecan from newborn human tissue.

  9. Reconsidering risk: adapting public policies to intergenerational determinants and biosocial interactions in health-related needs.

    PubMed

    Strully, Kate W; Conley, Dalton

    2004-12-01

    According to recent research, interactions between infant health and environment can play crucial roles in clustering health and economic disadvantage among certain families. Researchers have provided a clear example of such intergenerational biosocial cycles when they document that interactions between parental low birth weight status and prenatal environment are associated with the risk of a low birth weight, and that interactions between a child's birth weight status and early childhood environment are associated with adult socioeconomic outcomes. In this article, we consider how existing policies may be revised to more effectively address such interactions between social and biological risk categories. We are particularly concerned in this discussion with revising risk categories so they can encompass biological risk, social risk, and developmental frameworks. A framework of biosocial risk is quite flexible and may be applied to a variety of issues and programs; however, in this article we focus on the single case of low birth weight to illustrate our argument. In considering specific applications, we further explore how attention to biosocial interactions may reshape Medicaid, special education, the Earned Income Tax Credit, and Temporary Assistance for Needy Families.

  10. The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome

    PubMed Central

    Asaro, Alexandra; Ziegler, Gregory; Ziyomo, Cathrine; Hoekenga, Owen A.; Dilkes, Brian P.; Baxter, Ivan

    2016-01-01

    Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment. PMID:27770027

  11. Chromosomal Replication Dynamics and Interaction with the β Sliding Clamp Determine Orientation of Bacterial Transposable Elements

    PubMed Central

    Gómez, Manuel J.; Díaz-Maldonado, Héctor; González-Tortuero, Enrique; López de Saro, Francisco J.

    2014-01-01

    Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact with the host. Here, we report a survey of the orientation patterns of ISs in bacterial chromosomes with the objective of gaining insight into the interplay between ISs and host chromosomal functions. We find that a significant fraction of IS families present a consistent and family-specific orientation bias with respect to chromosomal DNA replication, especially in Firmicutes. Additionally, we find that the transposases of up to nine different IS families with different transposition pathways interact with the β sliding clamp, an essential replication factor, suggesting that this is a widespread mechanism of interaction with the host. Although we find evidence that the interaction with the β sliding clamp is common to all bacterial phyla, it also could explain the observed strong orientation bias found in Firmicutes, because in this group β is asymmetrically distributed during synthesis of the leading or lagging strands. Besides the interaction with the β sliding clamp, other asymmetries also play a role in the biased orientation of some IS families. The utilization of the highly conserved replication sliding clamps suggests a mechanism for host regulation of IS proliferation and also a universal platform for IS dispersal and transmission within bacterial populations and among phylogenetically distant species. PMID:24614824

  12. Interfacial and intermolecular interactions determining the rotational orientation of C60 adsorbed on Au(111)

    NASA Astrophysics Data System (ADS)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

    Close-packed monolayers of fullerenes on metallic substrates are very rich systems with respect to their rotational degrees of freedom and possible interactions with different adsorption sites or next neighbours. In this connection, we report in detail on the (2√3 × 2√3)R30°-superstructure of C60 with respect to the Au(111)-surface. We use molecular orbital imaging in systematic UHV-STM studies to reveal the delicate balance of interfacial and intermolecular interactions in this system. Thus, bright C60-molecules in 5:6-top and 6:6-top geometries are observed depending on the respective next neighbours. Moreover, tiny changes in the appearance of the unoccupied molecular orbitals of dim C60-molecules in hex-vac positions are identified which are caused by the respective interaction with the facets surrounding the Au-vacancy.

  13. Mass-Sensitive Biosensor Systems to Determine the Membrane Interaction of Analytes.

    PubMed

    Hoß, Sebastian G; Bendas, Gerd

    2017-01-01

    Biosensors are devices that transform a biological interaction into a readout signal, which is evaluable for analytical purposes. The general strength of biosensor approaches is the avoidance of time-consuming and cost-intensive labeling procedures of the analytes. In this chapter, we give insight into a mass-sensitive surface-acoustic wave (SAW) biosensor, which represents an elegant and highly sensitive method to investigate binding events at a molecular level. The principle of SAW technology is based on the piezoelectric properties of the sensors, so as to binding events and their accompanied mass increase at the sensor surface are detectable by a change in the oscillation of the surface acoustic wave. In combination with model membranes, transferred to the sensor surface, the analytical value of SAW biosensors has strongly been increased and extended to different topics of biomedical investigations, including antibiotic research. The interaction with the bacterial membrane or certain target structures therein is the essential mode of action for various antibacterial compounds. Beside targeted interaction, an unspecific membrane binding or membrane insertion of drugs can contribute to the antibacterial activity by changing the lateral order of membrane constituents or by interfering with the membrane barrier function. Those pleiotropic effects are hardly to illustrate in the bacterial systems and need a detailed view at the in vitro level. Here, we illustrate the usefulness of a SAW biosensor in combination with model membranes to investigate the mode of membrane interaction of antibiotic active peptides. Using two different peptides we exemplary describe the interaction analysis in a two-step gain of information: (1) a binding intensity or affinity by analyzing the phase changes of oscillation, and (2) mode of membrane interaction, i.e., surface binding or internalization of the peptide by following the amplitude of oscillation.

  14. An Interactive Classroom Activity Demonstrating Reaction Mechanisms and Rate-Determining Steps

    ERIC Educational Resources Information Center

    Jennings, Laura D.; Keller, Steven W.

    2005-01-01

    An interactive classroom activity that includes two-step reaction of unwrapping and eating chocolate candies is described which brings not only the reaction intermediate, but also the reactants and products into macroscopic view. The qualitative activation barriers of both steps can be adjusted independently.

  15. Species interactions determine the spatial mortality patterns emerging in plant communities after extreme events

    PubMed Central

    Liao, Jinbao; Bogaert, Jan; Nijs, Ivan

    2015-01-01

    Gap disturbance is assumed to maintain species diversity by creating environmental heterogeneity. However, little is known about how interactions with neighbours, such as competition and facilitation, alter the emerging gap patterns after extreme events. Using a spatially explicit community model we demonstrate that negative interactions, especially intraspecific competition, greatly promote both average gap size and gap-size diversity relative to positive interspecific interaction. This suggests that competition would promote diversity maintenance but also increase community invasibility, as large gaps with a wide size variety provide more diverse niches for both local and exotic species. Under interspecific competition, both gap metrics interestingly increased with species richness, while they were reduced under intraspecific competition. Having a wider range of species interaction strengths led to a smaller average gap size only under intraspecific competition. Increasing conspecific clumping induced larger gaps with more variable sizes under intraspecific competition, in contrast to interspecific competition. Given the range of intraspecific clumping in real communities, models or experiments based on randomly synthesized communities may yield biased estimates of the opportunities for potential colonizers to fill gaps. Overall, our “static” model on gap formation offers perspectives to better predict recolonization opportunity and thus community secondary succession under extreme event regimes. PMID:26054061

  16. Second virial coefficient determination of a therapeutic peptide by self-interaction chromatography.

    PubMed

    Payne, Robert W; Nayar, Rajiv; Tarantino, Ralph; Del Terzo, Sam; Moschera, John; Di, Jie; Heilman, David; Bray, Brian; Manning, Mark Cornell; Henry, Charles S

    2006-01-01

    Self-interaction of macromolecules has been shown to play an important role in a number of physical processes, including crystallization, solubility, viscosity, and aggregation. Peptide self-interaction is not as well studied as for larger proteins, but should play an equally important role. The osmotic second virial coefficient, B, can be used to quantify peptide and protein self-interaction. B values are typically measured using static light scattering (SLS). Peptides, however, do not scatter enough light to allow such measurements. This study describes the first use of self-interaction chromatography (SIC) for the measurement of peptide B values because SIC does not have the molecular size limitations of SLS. In the present work, SIC was used to measure B for enfuvirtide, a 36-amino acid therapeutic peptide, as a function of salt concentration, salt type, and pH. B was found to correlate strongly with solubility and apparent molecular weight. In general, the solubility of enfuvirtide increases with pH from 6 to 10 and decreases as the salt concentration increases from 0 to 0.5M for three different salts. The effect of peptide concentration on B was also investigated and shown to have a significant effect, but only at high concentrations (>80 mg/mL).

  17. Species interactions determine the spatial mortality patterns emerging in plant communities after extreme events.

    PubMed

    Liao, Jinbao; Bogaert, Jan; Nijs, Ivan

    2015-06-08

    Gap disturbance is assumed to maintain species diversity by creating environmental heterogeneity. However, little is known about how interactions with neighbours, such as competition and facilitation, alter the emerging gap patterns after extreme events. Using a spatially explicit community model we demonstrate that negative interactions, especially intraspecific competition, greatly promote both average gap size and gap-size diversity relative to positive interspecific interaction. This suggests that competition would promote diversity maintenance but also increase community invasibility, as large gaps with a wide size variety provide more diverse niches for both local and exotic species. Under interspecific competition, both gap metrics interestingly increased with species richness, while they were reduced under intraspecific competition. Having a wider range of species interaction strengths led to a smaller average gap size only under intraspecific competition. Increasing conspecific clumping induced larger gaps with more variable sizes under intraspecific competition, in contrast to interspecific competition. Given the range of intraspecific clumping in real communities, models or experiments based on randomly synthesized communities may yield biased estimates of the opportunities for potential colonizers to fill gaps. Overall, our "static" model on gap formation offers perspectives to better predict recolonization opportunity and thus community secondary succession under extreme event regimes.

  18. π–π Interaction Energies as Determinants of the Photodimerization of Mono-, Di-, and Triazastilbenes

    PubMed Central

    2015-01-01

    We describe the quantitative [2 + 2] photocycloaddition of crystalline trans-2,4-dichloro-6-styrylpyrimidine to produce the corresponding htt r-ctt cyclobutane dimer, and we present 1H NMR analysis of the photolysis of this and six other mono-, di-, and triazastilbenes in solid and solution states. Density functional (M06-2X) and correlated ab initio (MP2) calculations were used to obtain interaction energies between two monomers of each azastilbene. These energies mirror the relative polarization of the stilbene moieties and can be quantitatively correlated with the rate of reaction and selective formation of the htt r-ctt dimers. In the solid state, poor correlation is observed between interaction energy and reactivity/selectivity. This lack of correlation is explained through X-ray analysis of the azastilbene monomers and is shown to be in accordance with the principles of Schmidt’s topochemical postulate. Conversely, in solution there is a strong positive correlation (R2 = 0.96) between interaction energies and formation of the htt r-ctt dimer. These results are the first to show this correlation and to demonstrate the utility of calculated interaction energies as a tool for the prediction of stereo- and regioselectivity in solution-state stilbene-type photocycloadditions. PMID:24837276

  19. Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

    PubMed Central

    Moller, Abraham G.

    2017-01-01

    Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum. PMID:28097058

  20. Use of Factorial Analysis to Determine the Interaction Between Parameters of a Land Surface Model

    NASA Astrophysics Data System (ADS)

    Varejão, C. G.; Varejão, E. V.; Costa, M. H.

    2007-05-01

    Land surface models use several parameters to represent biophysical processes. These parameters frequently are unknown, reproducing with uncertainty the characteristics of the ecosystem in study. Model calibration techniques find values for each parameter that reduce uncertainty. However, the calibration process is computationally expensive, since is necessary a lot of model runs to have their parameters adjusted. The more parameters are considered, more difficult the process is, particularly when there are interactions among them, and a modification in a parameter value implies in the change of the optimum value of the other parameters. The use of a factorial experiment allows the identification of possible inert parameters, whose values do not influence the final result of the experiment and, therefore, could be excluded from the calibration process. In this work we used factorial analysis to verify the existence of interaction among 5 parameters of the land surface IBIS model - Beta2 (distribution of fine roots), Vmax (maximum Rubisco enzyme capacity), m (coefficient related to the stomatal conductance), CHS (heat capacity of stems) and CHU (heat capacity of leaves) - evaluated against the output fluxes Rn (net radiation), H (sensible heat flux), LE (latent heat flux) and NEE (net ecosystem CO2 exchange). Data was collected at the Amazon tropical rainforest site known as K83, near Santarem, Brazil. The knowledge of the existing interactions between the parameters can considerably reduce the computational cost of further optimization processes, since each parameter that does not interact with others should be optimized independently.

  1. Determinants of Mobile Wireless Technology for Promoting Interactivity in Lecture Sessions: An Empirical Analysis

    ERIC Educational Resources Information Center

    Gan, Chin Lay; Balakrishnan, Vimala

    2014-01-01

    The aim of this paper is to identify adoption factors of mobile wireless technology to increase interactivity between lecturers and students during lectures. A theoretical framework to ascertain lecturers' intentions to use mobile wireless technology during lectures (dependent variable) is proposed with seven independent variables. The…

  2. The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions

    PubMed Central

    Senes, Alessandro; Ubarretxena-Belandia, Iban; Engelman, Donald M.

    2001-01-01

    The Cα—H⋅⋅⋅O hydrogen bond has been given little attention as a determinant of transmembrane helix association. Stimulated by recent calculations suggesting that such bonds can be much stronger than has been supposed, we have analyzed 11 known membrane protein structures and found that apparent carbon α hydrogen bonds cluster frequently at glycine-, serine-, and threonine-rich packing interfaces between transmembrane helices. Parallel right-handed helix–helix interactions appear to favor Cα—H⋅⋅⋅O bond formation. In particular, Cα—H⋅⋅⋅O interactions are frequent between helices having the structural motif of the glycophorin A dimer and the GxxxG pair. We suggest that Cα—H⋅⋅⋅O hydrogen bonds are important determinants of stability and, depending on packing, specificity in membrane protein folding. PMID:11481472

  3. Phase equilibrium calculations of ternary liquid mixtures with binary interaction parameters and molecular size parameters determined from molecular dynamics.

    PubMed

    Oh, Suk Yung; Bae, Young Chan

    2010-07-15

    The method presented in this paper was developed to predict liquid-liquid equilibria in ternary liquid mixtures by using a combination of a thermodynamic model and molecular dynamics simulations. In general, common classical thermodynamic models have many parameters which are determined by fitting a model with experimental data. This proposed method, however, provides a simple procedure for calculating liquid-liquid equilibria utilizing binary interaction parameters and molecular size parameters determined from molecular dynamics simulations. This method was applied to mixtures containing water, hydrocarbons, alcohols, chlorides, ketones, acids, and other organic liquids over various temperature ranges. The predicted results agree well with the experimental data without the use of adjustable parameters.

  4. Determining the elastic properties of aptamer-ricin single molecule multiple pathway interactions

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Park, Bosoon; Kwon, Yongkuk; Xu, Bingqian

    2014-05-01

    We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed three stable binding conformations, each of which has its special elastic properties. These different unbinding pathways were investigated by the dynamic force spectroscopy. A series-spring model combining the worm-like-chain model and Hook's law was used to estimate the apparent spring constants of the aptamer and linker molecule polyethylene glycol. The aptamer in its three different unbinding pathways showed different apparent spring constants. The two reaction barriers in the unbinding pathways also influence the apparent spring constant of the aptamer. This special elastic behavior of aptamer was used to distinguish its three unbinding pathways under different loading rates. This method also offered a way to distinguish and discard the non-specific interactions in single molecule experiments.

  5. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

    PubMed

    Zhang, Yong; Moqtaderi, Zarmik; Rattner, Barbara P; Euskirchen, Ghia; Snyder, Michael; Kadonaga, James T; Liu, X Shirley; Struhl, Kevin

    2009-08-01

    We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.

  6. Label-Free Determination of the Dissociation Constant of Small Molecule-Aptamer Interaction by Isothermal Titration Calorimetry.

    PubMed

    Vogel, Marc; Suess, Beatrix

    2016-01-01

    Isothermal titration calorimetry (ITC) is a powerful label-free technique to determine the binding constant as well as thermodynamic parameters of a binding reaction and is therefore well suited for the analysis of small molecule-RNA aptamer interaction. We will introduce you to the method and present a protocol for sample preparation and the calorimetric measurement. A detailed note section will point out useful tips and pitfalls.

  7. Antigen availability determines CD8+ T cell-dendritic cell interaction kinetics and memory fate decisions

    PubMed Central

    Henrickson, Sarah E.; Stutte, Susanne; Quigley, Michael; Alexe, Gabriela; Iannacone, Matteo; Flynn, Michael P.; Omid, Shaida; Jesneck, Jonathan L.; Imam, Sabrina; Mempel, Thorsten R.; Mazo, Irina B.; Haining, William N.; von Andrian, Ulrich H.

    2014-01-01

    Summary T cells are activated by antigen (Ag) bearing dendritic cells (DCs) in lymph nodes in 3 phases. The duration of the initial phase of transient, serial DC-T cell interactions is inversely correlated with Ag dose. The second phase, characterized by stable DC-T cell contacts, is believed to be necessary for full-fledged T cell activation. Here we have shown that this is not the case. CD8+ T cells interacting with DCs presenting low-dose, short-lived Ag did not transition to phase 2, while higher Ag dose yielded phase 2 transition. Both antigenic constellations promoted T cell proliferation and effector differentiation, but yielded different transcriptome signatures at 12h and 24h. T cells that experienced phase 2 developed long-lived memory, whereas conditions without stable contacts yielded immunological amnesia. Thus, T cells make fate decisions within hours after Ag exposure resulting in long-term memory or abortive effector responses, correlating with T cell-DCs interaction kinetics. PMID:24054328

  8. A selective determination of azide by ion-interaction reversed-phase HPLC

    SciTech Connect

    Gennaro, M.C.; Abrigo, C.; Marengo, E.; Liberatori, A.

    1993-01-01

    A method is presented for the analysis of sodium azide, based on the use of ion-interaction reversed-phase HPLC chromatography. A C-18 reversed-phase is the stationary phase and octylammonium ortho-phosphate at different pH values is the interaction reagent. Spectrophotometric detection at 230 nm is employed. The analysis is free from interference by acetate, carbonate, chloride, fluoride, sulfite, hydrazine, hydroxylamine, nitrate, bromide, iodide, sulfide, thiocyanate and nitrite. A good correlation (r[sup 2] = 0.9782) is obtained between peak area and concentration in the range between 1 and 250 ppb. Samples of tap water spiked with sodium azide (in the range within 25 and 250 ppb) gave per cent average recovery of 98%. The method sensitivity, expressed as signal-to-noise ratio equal to 3, is 50 ppb when the pH of the interaction reagent is equal to 3.0, 30 ppb for pH 6.4 and 10 ppb at pH 8.0.

  9. Determination of the interaction parameter and topological scaling features of symmetric star polymers in dilute solution.

    PubMed

    Rai, Durgesh K; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2015-07-01

    Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(d(f)=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene.

  10. Determination of Lipid-Protein Interactions in Lung Surfactants Using Computer Simulations and Structural Bioinformatics.

    NASA Astrophysics Data System (ADS)

    Kaznessis, Yiannis

    2001-06-01

    Proteins are the primary components of the networks that conduct the flows of mass, energy and information in living organisms. The discovery of the principles of protein structure and function allows the development of design rules for biological activities. The microscopic nature of the operating mechanisms of protein activity, and the vast complexity of the networks of interaction call for the employment of powerful computational methodologies that can decipher the physicochemical and evolutionary principles underlying protein structure and function. An example will be presented that reflects the strength of computational approaches. Atomistic molecular dynamics simulations and structural bioinformatics tools are employed to investigate the interactions between the first 25 N-terminal residues of surfactant protein B (SP-B 1-25) and the lipid components of the lung surfactant (LS). An understanding of the molecular level interactions between the LS components is essential for the establishment of design rules for the development of synthetic LS and the treatment of the neonatal respiratory distress syndrome, which results from deficiency or inactivation of LS.

  11. Molecular determinants of α–synuclein mutants’ oligomerization and membrane interactions

    PubMed Central

    Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolf; Overk, Cassia; Gonzalez, Tania; Trejo, Margarita; Spencer, Brian; Kosberg, Kori; Masliah, Eliezer

    2016-01-01

    Parkinson’s disease (PD) is associated with the formation of toxic α-synuclein oligomers and their penetration the cell membrane. Familial forms of PD are caused by the point mutations A53T, A30P, E46K, and H50Q. Artificial point mutations E35K and E57K also increase oligomerization and pore formation. We generated structural conformations of α-synuclein and the abovementioned mutants using molecular dynamics. We elucidated four main regions in these conformers contacting the membrane and found that the region including residues 37–45 (Zone2) may have maximum membrane penetration. E57K mutant had the highest rate of interaction with the membrane by Zone2, followed by A53T, E46K, E35K mutants, and wt α-synuclein. The mutant A30P had the smallest percentage of conformers that contact the membrane than all other mutants and wt α-synuclein. These results were confirmed by experiments. We identified the key amino acids that can interact with the membrane (Y38, E62, and N65 (1st hydrophilic layer); E104, E105, and D115 (2nd hydrophilic layer), and V15 and V26 (central hydrophobic layer)) and the residues that are involved in the interprotein contacts (L38, V48, V49, Q62, and T64). Understanding the molecular interactions of α-synuclein mutants is important for the design of compounds blocking the formation of toxic oligomers. PMID:25561023

  12. A methodology for determining interactions in probabilistic safety assessment models by varying one parameter at a time.

    PubMed

    Borgonovo, Emanuele

    2010-03-01

    In risk analysis problems, the decision-making process is supported by the utilization of quantitative models. Assessing the relevance of interactions is an essential information in the interpretation of model results. By such knowledge, analysts and decisionmakers are able to understand whether risk is apportioned by individual factor contributions or by their joint action. However, models are oftentimes large, requiring a high number of input parameters, and complex, with individual model runs being time consuming. Computational complexity leads analysts to utilize one-parameter-at-a-time sensitivity methods, which prevent one from assessing interactions. In this work, we illustrate a methodology to quantify interactions in probabilistic safety assessment (PSA) models by varying one parameter at a time. The method is based on a property of the functional ANOVA decomposition of a finite change that allows to exactly determine the relevance of factors when considered individually or together with their interactions with all other factors. A set of test cases illustrates the technique. We apply the methodology to the analysis of the core damage frequency of the large loss of coolant accident of a nuclear reactor. Numerical results reveal the nonadditive model structure, allow to quantify the relevance of interactions, and to identify the direction of change (increase or decrease in risk) implied by individual factor variations and by their cooperation.

  13. Potentiometric Determination of Phytic Acid and Investigations of Phytate Interactions with Some Metal Ions.

    PubMed

    Marolt, Gregor; Pihlar, Boris

    2015-01-01

    Determination of correct amount (concentration) of phytic acid is of vital importance when dealing with protonation and/or metal complexation equilibria. A novel approach for precise and reliable assay of phytic acid, based on the difference between end points by potentiometric titration, has been presented. Twelve phytic acid protons are classified into three groups of acidity, which enables detection of 2 to 3 distinct equivalent points (EPs) depending on experimental conditions, e.g. counter-ion concentration. Using the differences between individual EPs enables correct phytate determination as well as identification of potential contamination and/or determination of initial protonation degree. Impact of uncertainty of phytate amount on the calculation of protonation constants has been evaluated using computer simulation program (Hyperquad2013). With the analysis of titration curves different binding sites on phytate ligand have been proposed for complexation of Ca2+ and Fe3+ ions.

  14. Trophic interactions determine the effects of drought on an aquatic ecosystem.

    PubMed

    Amundrud, Sarah L; Srivastava, Diane S

    2016-06-01

    Species interactions can be important mediators of community and ecosystem responses to environmental stressors. However, we still lack a mechanistic understanding of the indirect ecological effects of stress that arise via altered species interactions. To understand how species interactions will be altered by environmental stressors, we need to know if the species that are vulnerable to such stressors also have large impacts on the ecosystem. As predators often exhibit certain traits that are linked to a high vulnerability to stress (e.g., large body size, long generation time), as well as having large effects on communities (e.g., top-down trophic effects), predators may be particularly likely to mediate ecological effects of environmental stress. Other functional groups, like facilitators, are known to have large impacts on communities, but their vulnerability to perturbations remains undocumented. Here, we use aquatic insect communities in bromeliads to examine the indirect effects of an important stressor (drought) on community and ecosystem responses. In a microcosm experiment, we manipulated predatory and facilitative taxa under a range of experimental droughts, and quantified effects on community structure and ecosystem function. Drought, by adversely affecting the top predator, had indirect cascading effects on the entire food web, altering community composition and decomposition. We identified the likely pathway of how drought cascaded through the food web from the top-down as drought -->predator --> shredder --> decomposition. This stress-induced cascade depended on predators exhibiting both a strong vulnerability to drought and large impacts on prey (especially shredders), as well as shredders exhibiting high functional importance as decomposers.

  15. Heparin stability by determining unsubstituted amino groups using hydrophilic interaction chromatography mass spectrometry.

    PubMed

    Fu, Li; Li, Lingyun; Cai, Chao; Li, Guoyun; Zhang, Fuming; Linhardt, Robert J

    2014-09-15

    The thermal instability of the anticoagulant heparin is associated, in part, with the solvolytic loss of N-sulfo groups. This study describes a new method to assess the increased content of unsubstituted amino groups present in thermally stressed and autoclave-sterilized heparin formulations. N-Acetylation of heparin samples with acetic anhydride-d6 is followed by exhaustive heparinase treatment and disaccharide analysis by hydrophilic interaction chromatography mass spectrometry (HILIC-MS). The introduction of a stable isotopic label provides a sensitive probe for the detection and localization of the lost N-sulfo groups, potentially providing valuable insights into the degradation mechanism and the reasons for anticoagulant potency loss.

  16. Using isothermal titration calorimetry to determine thermodynamic parameters of protein-glycosaminoglycan interactions.

    PubMed

    Dutta, Amit K; Rösgen, Jörg; Rajarathnam, Krishna

    2015-01-01

    It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein-glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide various thermodynamic parameters-enthalpy, entropy, free energy (binding constant), and stoichiometry-from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein-GAG interactions.

  17. The Determinants of Negative Maternal Parenting Behaviours: Maternal, Child, and Paternal Characteristics and Their Interaction

    ERIC Educational Resources Information Center

    Kopala-Sibley, Daniel C.; Zuroff, David C.; Koestner, Richard

    2012-01-01

    This study tested Belsky's determinants of parenting, namely maternal characteristics, child characteristics, and contextual issues, namely the mother's perception of the husband as a father, husband, and person. Three hundred and seventy-nine mothers first investigated by Sears, Maccoby, and Levin completed a standardised interview to assess…

  18. Physiological responses in a Concealed Information Test are determined interactively by encoding procedure and questioning format.

    PubMed

    Ambach, Wolfgang; Dummel, Sebastian; Lüer, Theresa; Vaitl, Dieter

    2011-09-01

    Physiological responses in the Concealed Information Test (CIT) are known to depend on the depth of encoding critical items; CIT questions commonly refer to knowledge about critical items. It is unclear to what extent (1) different modes of item handling in a mock-crime, and (2) alternative questioning formats, e.g. asking about participants' particular actions with the critical items, influence the physiological responses. In the presented mock-crime study with fifty-three participants, two questioning formats, i.e. "Did you see …?" (viewing questioning) and "Did you steal …?" (stealing questioning), were compared between subjects. The mode of encoding, stealing vs. merely viewing the critical objects, was varied within subject. Skin conductance, electrocardiogram, respiration, and finger pulse were recorded. For both questioning formats and each physiological measure, physiological responses to stolen as well as merely viewed objects differed from those to irrelevant objects. Considering viewing questioning, responses to stolen and merely viewed objects did not differ, with the exception of greater phasic decreases of heart rate for stolen objects. Considering stealing questioning, responses to stolen objects exceeded those to merely viewed objects with each physiological measure. The statistically proven interaction between mode of encoding a particular object and questioning format sheds light on the factors influencing the physiological responses in a CIT. The level of subjective significance of a particular item might emerge interactively from the mode of item handling and the questioning format.

  19. Host Fate is Rapidly Determined by Innate Effector-Microbial Interactions During Acinetobacter baumannii Bacteremia

    PubMed Central

    Bruhn, Kevin W.; Pantapalangkoor, Paul; Nielsen, Travis; Tan, Brandon; Junus, Justin; Hujer, Kristine M.; Wright, Meredith S.; Bonomo, Robert A.; Adams, Mark D.; Chen, Wangxue; Spellberg, Brad

    2015-01-01

    Background. Acinetobacter baumannii is one of the most antibiotic-resistant pathogens. Defining mechanisms driving pathogenesis is critical to enable new therapeutic approaches. Methods. We studied virulence differences across a diverse panel of A. baumannii clinical isolates during murine bacteremia to elucidate host-microbe interactions that drive outcome. Results. We identified hypervirulent strains that were lethal at low intravenous inocula and achieved very high early, and persistent, blood bacterial densities. Virulent strains were nonlethal at low inocula but lethal at 2.5-fold higher inocula. Finally, relatively avirulent (hypovirulent) strains were nonlethal at 20-fold higher inocula and were efficiently cleared by early time points. In vivo virulence correlated with in vitro resistance to complement and macrophage uptake. Depletion of complement, macrophages, and neutrophils each independently increased bacterial density of the hypovirulent strain but insufficiently to change lethality. However, disruption of all 3 effector mechanisms enabled early bacterial densities similar to hypervirulent strains, rendering infection 100% fatal. Conclusions. The lethality of A. baumannii strains depends on distinct stages. Strains resistant to early innate effectors are able to establish very high early bacterial blood density, and subsequent sustained bacteremia leads to Toll-like receptor 4–mediated hyperinflammation and lethality. These results have important implications for translational efforts to develop therapies that modulate host-microbe interactions. PMID:25378635

  20. How van der Waals interactions determine the unique properties of water.

    PubMed

    Morawietz, Tobias; Singraber, Andreas; Dellago, Christoph; Behler, Jörg

    2016-07-26

    Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.

  1. Interaction between hypothalamic dorsomedial nucleus and the suprachiasmatic nucleus determines intensity of food anticipatory behavior

    PubMed Central

    Acosta-Galvan, Guadalupe; Yi, Chun-Xia; van der Vliet, Jan; Jhamandas, Jack H.; Panula, Pertti; Angeles-Castellanos, Manuel; del Carmen Basualdo, María; Escobar, Carolina; Buijs, Ruud M.

    2011-01-01

    Food anticipatory behavior (FAA) is induced by limiting access to food for a few hours daily. Animals anticipate this scheduled meal event even without the suprachiasmatic nucleus (SCN), the biological clock. Consequently, a food-entrained oscillator has been proposed to be responsible for meal time estimation. Recent studies suggested the dorsomedial hypothalamus (DMH) as the site for this food-entrained oscillator, which has led to considerable controversy in the literature. Herein we demonstrate by means of c-Fos immunohistochemistry that the neuronal activity of the suprachiasmatic nucleus (SCN), which signals the rest phase in nocturnal animals, is reduced when animals anticipate the scheduled food and, simultaneously, neuronal activity within the DMH increases. Using retrograde tracing and confocal analysis, we show that inhibition of SCN neuronal activity is the consequence of activation of GABA-containing neurons in the DMH that project to the SCN. Next, we show that DMH lesions result in a loss or diminution of FAA, simultaneous with increased activity in the SCN. A subsequent lesion of the SCN restored FAA. We conclude that in intact animals, FAA may only occur when the DMH inhibits the activity of the SCN, thus permitting locomotor activity. As a result, FAA originates from a neuronal network comprising an interaction between the DMH and SCN. Moreover, this study shows that the DMH–SCN interaction may serve as an intrahypothalamic system to gate activity instead of rest overriding circadian predetermined temporal patterns. PMID:21402951

  2. Determination of the exchange interaction energy from the polarization expansion of the wave function

    NASA Astrophysics Data System (ADS)

    Gniewek, Piotr; Jeziorski, Bogumił

    2016-10-01

    The exchange contribution to the energy of the hydrogen atom interacting with a proton is calculated from the polarization expansion of the wave function using the conventional surface-integral formula and two formulas involving volume integrals: the formula of the symmetry-adapted perturbation theory (SAPT) and the variational formula recommended by us. At large internuclear distances R , all three formulas yield the correct expression -(2 /e ) R e-R , but they approximate it with very different convergence rates. In the case of the SAPT formula, the convergence is geometric with the error falling as 3-K, where K is the order of the applied polarization expansion. The error of the surface-integral formula decreases exponentially as aK/(K +1 ) , where a =ln2 - 1/2. The variational formula performs best, its error decays as K1 /2[aK/(K+1 ) ] 2 . These convergence rates are much faster than those resulting from approximating the wave function through the multipole expansion. This shows the efficiency of the partial resummation of the multipole series effected by the polarization expansion. Our results demonstrate also the benefits of incorporating the variational principle into the perturbation theory of molecular interactions.

  3. How van der Waals interactions determine the unique properties of water

    PubMed Central

    Morawietz, Tobias; Singraber, Andreas; Dellago, Christoph; Behler, Jörg

    2016-01-01

    Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water’s density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum. PMID:27402761

  4. Determinants of geographic patterns of diseases: interaction of lactose/lactase status and sunshine exposure.

    PubMed

    Szilagyi, Andrew

    2010-11-01

    Geographic patterns of diseases depend on multilayered causes. However, the division of the world's population into two phenotypes regarding lactose digestion and sunshine exposure to fixed areas of the globe are two relatively slow changing variables. It is hypothesized that it is a vectorial interaction between these two variables that provide a backbone to risk modification of many diseases. Lactase non persistence status tends to follow sunshine exposure particularly in Europe but Lactase persistence status is also been shown to be related to pastoral life styles in spotty regions of Africa, Middle East and China. Current emphasis of research favours the modifying role of vitamin D and sunshine. Nevertheless it was demonstrated that national digester/nondigester status has mathematical relationships to geographic distribution of some diseases. These relationships are also similar to that described for the effects of latitude through sunshine and vitamin D. This observation raises a question as to how each one affects disease outcome. In this paper lactose/lactase interactions are first reviewed for eight exemplary diseases. Based on population findings and corroborative meta-analyses gleaned from the literature 6 types of interactions may be classified. Then in a preliminary fashion lactose digester and maldigester status are related to relative annual sunshine exposure. Further the relative national annual sunshine exposure is evaluated to outcomes of the same exemplary diseases. The patterns related to sunshine reflect that obtained with national lactase status proportions and also corroborate a literature review. However, correlations are weak to moderate and only ovarian cancer reached conventional statistical significance. Because these comparisons are based on modest number of national data firm conclusions cannot be made. However, it is argued that evolutionary pressures exerted by regional sunshine exposure may have had influence on a number of relevant

  5. Identification of novel interaction sites that determine specificity between fibroblast growth factor homologous factors and voltage-gated sodium channels.

    PubMed

    Wang, Chaojian; Wang, Chuan; Hoch, Ethan G; Pitt, Geoffrey S

    2011-07-08

    Fibroblast growth factor homologous factors (FHFs, FGF11-14) bind to the C termini (CTs) of specific voltage-gated sodium channels (VGSC) and thereby regulate their function. The effect of an individual FHF on a specific VGSC varies greatly depending upon the individual FHF isoform. How individual FHFs impart distinctive effects on specific VGSCs is not known and the specificity of these pairwise interactions is not understood. Using several biochemical approaches combined with functional analysis, we mapped the interaction site for FGF12B on the Na(V)1.5 C terminus and discovered previously unknown determinants necessary for FGF12 interaction. Also, we demonstrated that FGF12B binds to some, but not all Na(V)1 CTs, suggesting specificity of interaction. Exploiting a human single nucleotide polymorphism in the core domain of FGF12 (P149Q), we identified a surface proline that contributes a part of this pairwise specificity. This proline is conserved among all FHFs, and mutation of the homologous residue in FGF13 also leads to loss of interaction with a specific VGSC CT (Na(V)1.1) and loss of modulation of the resultant Na(+) channel function. We hypothesized that some of the specificity mediated by this proline may result from differences in the affinity of the binding partners. Consistent with this hypothesis, surface plasmon resonance data showed that the P149Q mutation decreased the binding affinity between FHFs and VGSC CTs. Moreover, immunocytochemistry revealed that the mutation prevented proper subcellular targeting of FGF12 to the axon initial segment in neurons. Together, these results give new insights into details of the interactions between FHFs and Na(V)1.x CTs, and the consequent regulation of Na(+) channels.

  6. Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms.

    PubMed

    Nadell, Carey D; Ricaurte, Deirdre; Yan, Jing; Drescher, Knut; Bassler, Bonnie L

    2017-01-13

    Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics in Pseudomonas aeruginosa biofilms. Irrespective of initial frequency, in competition with matrix mutants, wild-type cells always increase in relative abundance in planar microfluidic devices under simple flow regimes. By contrast, in microenvironments with complex, irregular flow profiles - which are common in natural environments - wild-type matrix-producing and isogenic non-producing strains can coexist. This result stems from local obstruction of flow by wild-type matrix producers, which generates regions of near-zero shear that allow matrix mutants to locally accumulate. Our findings connect the evolutionary stability of matrix production with the hydrodynamics and spatial structure of the surrounding environment, providing a potential explanation for the variation in biofilm matrix secretion observed among bacteria in natural environments.

  7. Interaction of Exposure Concentration and Duration in Determining Acute Toxic Effects of Sarin Vapor in Rats

    DTIC Science & Technology

    2002-01-01

    effects occur in the rat and 2) develop models for predicting dose - response effects of low CW agent concentrations as a function of exposure duration. Sarin...effective concentrations for lethality (LC50) and miosis (EC50) in 50% of the exposed population and corresponding dose - response slopes were determined for...exposure duration (i.e., the CT for 50% lethality exposed population and corresponding dose - response slope was not constant over time). A plot of Log (LCt50

  8. Comparison of zonal elution and nonlinear chromatography in determination of the interaction between seven drugs and immobilised β(2)-adrenoceptor.

    PubMed

    Li, Qian; Wang, Jing; Zheng, Yuqing Yuan; Yang, Lingjian; Zhang, Yajun; Bian, Liujiao; Zheng, Jianbin; Li, Zijian; Zhao, Xinfeng; Zhang, Youyi

    2015-07-03

    Zonal elution and nonlinear chromatography are two mainstream models for the determination of drug-protein interaction in affinity chromatography. This work intended to compare the results by zonal elution with that by nonlinear chromatography when it comes to the analysis of the interaction between seven drugs and immobilised β2-adrenoceptor (β2-AR). The results of the zonal elution showed that clorprenaline, clenbuterol, methoxyphenamine, salbutamol, terbutaline, tulobuterol and bambuterol have only one type of binding site on immobilised β2-AR, while nonlinear chromatography confirmed the existence of at least two types of binding sites between β2-AR and clorprenaline, clenbuterol and bambuterol. On these sites, both zonal elution and nonlinear chromatography presented the same rank order for the association constants of the seven drugs. Compared with the data from zonal elution, the association constants calculated using nonlinear chromatography gave a good linear response to the corresponding values by radio-ligand binding assay. The sampling efficiencies of nonlinear chromatography were clearly higher than zonal elution. Nonlinear chromatography will probably become a powerful alternative for the high throughput determination of drug-protein interaction.

  9. Interactions between social structure, demography, and transmission determine disease persistence in primates.

    PubMed

    Ryan, Sadie J; Jones, James H; Dobson, Andrew P

    2013-01-01

    Catastrophic declines in African great ape populations due to disease outbreaks have been reported in recent years, yet we rarely hear of similar disease impacts for the more solitary Asian great apes, or for smaller primates. We used an age-structured model of different primate social systems to illustrate that interactions between social structure and demography create 'dynamic constraints' on the pathogens that can establish and persist in primate host species with different social systems. We showed that this varies by disease transmission mode. Sexually transmitted infections (STIs) require high rates of transmissibility to persist within a primate population. In particular, for a unimale social system, STIs require extremely high rates of transmissibility for persistence, and remain at extremely low prevalence in small primates, but this is less constrained in longer-lived, larger-bodied primates. In contrast, aerosol transmitted infections (ATIs) spread and persist at high prevalence in medium and large primates with moderate transmissibility;, establishment and persistence in small-bodied primates require higher relative rates of transmissibility. Intragroup contact structure - the social network - creates different constraints for different transmission modes, and our model underscores the importance of intragroup contacts on infection prior to intergroup movement in a structured population. When alpha males dominate sexual encounters, the resulting disease transmission dynamics differ from when social interactions are dominated by mother-infant grooming events, for example. This has important repercussions for pathogen spread across populations. Our framework reveals essential social and demographic characteristics of primates that predispose them to different disease risks that will be important for disease management and conservation planning for protected primate populations.

  10. Interspecies interactions determine the impact of the gut microbiota on nutrient allocation in Drosophila melanogaster.

    PubMed

    Newell, Peter D; Douglas, Angela E

    2014-01-01

    The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes.

  11. Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

    PubMed Central

    Douglas, Angela E.

    2014-01-01

    The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes. PMID:24242251

  12. Interaction of a potential vacuolar targeting receptor with amino- and carboxyl-terminal targeting determinants.

    PubMed

    Kirsch, T; Saalbach, G; Raikhel, N V; Beevers, L

    1996-06-01

    A protein of 80 kD from developing pea (Pisum sativum) cotyledons has previously been shown to exhibit characteristics of a vacuolar targeting receptor by means of its affinity for the amino-terminal vacuolar targeting sequence of proaleurain from barley (Hordeum vulgare). In this report we show that the same protein also binds to the amino-terminal targeting peptide of prosporamin from sweet potato (Ipomoea batatas) and to the carboxyl-terminal targeting determinant of pro-2S albumin from Brazil nut (Bertholletia excelsa). The receptor protein does not bind to the carboxyl-terminal propeptide (representing the targeting sequence) of barley lectin. The binding of the 80-kD protein to the sporamin determinant involves a motif (NPIR) that has been shown to be crucial for vacuolar targeting in vivo. The binding to the carboxyl-terminal targeting determinant of pro-2S albumin appears to involve the carboxyl-terminal propeptide and the adjacent five amino acids of the mature protein. The 80-kD protein does not bind to peptide sequences that have been shown to be incompetent in directing vacuolar targeting.

  13. Sigma and Pi Interactions of the Pyrrolic Ligand Sandwich-Like Lanthanide Phthalocyanines Determined from Magnetic Susceptibility and Ligand-Field Theory

    DTIC Science & Technology

    1990-06-25

    ACCESSION NO. 11, TITLE (include Security Classification) UNCLASSIFIED: Sigma and Pi Interactions of the Pyrro- lic Ligand Sandwich-Like Lanthanide ...4135007---05 TECHNICAL REPORT NO. 36 Sigma and Pi Interactions of the Pyrrolic Ligand Sandwich-Like Lanthanide Phthalocyanines Determined From Magnetic...Hill Chapel Hill, North Carolina 27599-3290 Sigma and Pi Interactions of the Pyrrolic Ligand Sandwich-Like Lanthanide Phthalocyanines Determined From

  14. Determination of the Polymer-Solvent Interaction Parameter for PEG Hydrogels in Water: Application of a Self Learning Algorithm

    PubMed Central

    Akalp, Umut; Chu, Stanley; Skaalure, Stacey C.; Bryant, Stephanie J.; Doostan, Alireza; Vernerey, Franck J.

    2015-01-01

    Concentrating on the case of poly(ethylene glycol) hydrogels, this paper introduces a methodology that enables a natural integration between the development of a so-called mechanistic model and experimental data relating material’s processing to response. In a nutshell, we develop a data-driven modeling component that is able to learn and indirectly infer its own parameters and structure by observing experimental data. Using this method, we investigate the relationship between processing conditions, microstructure and chemistry (cross-link density and polymer-solvent interactions) and response (swelling and elasticity) of non-degradable and degradable PEG hydrogels. We show that the method not only enables the determination of the polymer-solvent interaction parameter, but also it predicts that this parameter, among others, varies with processing conditions and degradation. The proposed methodology therefore offers a new approach that accounts for subtle changes in the hydrogel processing. PMID:25999615

  15. F-Chart/SLR: an interactive program for determining the performance of active and passive solar buildings

    SciTech Connect

    Sullivan, P.; Wright, W.

    1980-01-01

    Methods for determining the performance of active and passive buildings have been developed by the University of Wisconsin-Madison, Solar Energy Laboratory and the Los Alamos Scientific Laboratory, respectively. The University of Wisconsin work, FCHART, is documented in Solar Heating Design by the F-chart Method, and in an interactive computer program available from the University. Los Alamos' work, the Solar Load Ratio (SLR) method, is documented in a number of individual papers as well as in the Passive Design Handbook. The SLR method is at present primarily a hand calculational procedure although the main features of the program have previously been incorporated in a hand-held programmable calculator program, PASCALC. An overview of a Northeast Solar Energy Center/Total Environmental Action, Inc. computer program which combines the detailed calculational procedures of the SLR method with the interactive features of the FCHART program is presented.

  16. Determinants of male health: the interaction of biological and social factors

    PubMed Central

    de Kretser, David M.

    2010-01-01

    This review discusses the social and biological factors that may influence male development from conception to adulthood and also underlie the development of health disorders. It will provide assistance to those who may be considering the formulation of a male health policy. It aims to emphasize that social determinants function on a biological background that is profoundly influenced by a male's genome, inherited from his parents. The importance of the male-specific reproductive disorders is emphasized, but these also affect somatic structures through the secretion of androgens secreted from the testes. In turn, the function of the cardiovascular and nervous systems can significantly influence reproductive processes such as erectile dysfunction. PMID:20364153

  17. Individual and social determinants of obesity in strategic health messages: Interaction with political ideology.

    PubMed

    Young, Rachel; Hinnant, Amanda; Leshner, Glenn

    2016-07-01

    Antiobesity health communication campaigns often target individual behavior, but these ads might inflate the role of individual responsibility at the expense of other health determinants. In a 2 × 2 full-factorial, randomized, online experiment, 162 American adults viewed antiobesity advertisements that varied in emphasizing social or individual causation for obesity through text and images. Locus for attribution of responsibility for obesity causes and solutions was measured, as was how these responses were moderated by political ideology. Participants who viewed text emphasizing individual responsibility were less likely to agree that genetic factors caused obesity. Conservative participants who viewed images of overweight individuals were less likely than liberal participants to agree that social factors were responsible for causing obesity. In addition, among conservative participants who viewed images of fast food versus images of overweight individuals, agreement that the food industry bore some responsibility mediated support for policy solutions to obesity. These findings, among others, demonstrate that awareness of multilevel determinants of health outcomes can be a precursor of support for policy solutions to obesity among those not politically inclined to support antiobesity policy. In addition, stigmatizing images of overweight individuals in antiobesity campaigns might overemphasize the role of individual behavior in obesity at the expense of other factors.

  18. Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms

    PubMed Central

    Nadell, Carey D; Ricaurte, Deirdre; Yan, Jing; Drescher, Knut; Bassler, Bonnie L

    2017-01-01

    Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics in Pseudomonas aeruginosa biofilms. Irrespective of initial frequency, in competition with matrix mutants, wild-type cells always increase in relative abundance in planar microfluidic devices under simple flow regimes. By contrast, in microenvironments with complex, irregular flow profiles – which are common in natural environments – wild-type matrix-producing and isogenic non-producing strains can coexist. This result stems from local obstruction of flow by wild-type matrix producers, which generates regions of near-zero shear that allow matrix mutants to locally accumulate. Our findings connect the evolutionary stability of matrix production with the hydrodynamics and spatial structure of the surrounding environment, providing a potential explanation for the variation in biofilm matrix secretion observed among bacteria in natural environments. DOI: http://dx.doi.org/10.7554/eLife.21855.001 PMID:28084994

  19. Determinants of aggressive behavior: Interactive effects of emotional regulation and inhibitory control.

    PubMed

    Hsieh, I-Ju; Chen, Yung Y

    2017-01-01

    Aggressive behavior can be defined as any behavior intended to hurt another person, and it is associated with many individual and social factors. This study examined the relationship between emotional regulation and inhibitory control in predicting aggressive behavior. Seventy-eight participants (40 males) completed self-report measures (Negative Mood Regulation Scale and Buss-Perry Aggression Questionnaire), a stop signal task, and engaged in a modified version of Taylor Aggression Paradigm (TAP) exercise, in which the outcome was used as a measure of direct physical aggression. We used a hierarchical, mixed-model multiple regression analysis test to examine the effects of emotion regulation and inhibitory control on physical reactive aggression. Results indicated an interaction between emotion regulation and inhibitory control on aggression. For participants with low inhibitory control only, there was a significant difference between high and low emotion regulation on aggression, such that low emotion regulation participants registered higher aggression than high emotion regulation participants. This difference was not found among participants with high inhibitory control. These results have implications for refining and targeting training and rehabilitation programs aimed at reducing aggressive behavior.

  20. Determination of interfacial Dzyaloshinskii-Moriya exchange interaction from static domain size imaging

    NASA Astrophysics Data System (ADS)

    Agrawal, Parnika; Lemesh, Ivan; Schlotter, Sarah; Beach, Geoffrey

    Dzyaloshinskii-Moriya interaction (DMI) has been identified [1-2] as a necessary ingredient for the formation of chiral spin structures such as skyrmions and Néel domain walls in perpendicularly magnetized thin films. Various simulation and experimental studies have tried to quantify DMI from domain wall and skyrmion [3-4] motion with applied currents and magnetic fields. Here, a means to quantify DMI in multilayer films using only static magnetic characterizations is proposed. Static domain structure is observed using magnetic force microscopy (MFM) in multilayer stacks of [Pt(2.5-7.5nm)/CoFeB(0.8nm)/MgO(1.5nm)]15 where the thickness tpt of the Pt layer is systematically varied from 2.5 nm to 7.5 nm. A variation of domain size from ~300 nm to ~70 nm is seen in the labyrinthine demagnetized state as tpt is decreased. It is shown that the domain size as a function of tpt can be well-fitted analytically by a model in which the domain wall energy is the sole free parameter. Additional measurements of magnetic anisotropy of the film reveal the significant contribution of interfacial DMI (~1.4 mJ/m2) to the domain wall energy.

  1. A new method for depth of interaction determination in PET detectors

    NASA Astrophysics Data System (ADS)

    Pizzichemi, M.; Stringhini, G.; Niknejad, T.; Liu, Z.; Lecoq, P.; Tavernier, S.; Varela, J.; Paganoni, M.; Auffray, E.

    2016-06-01

    A new method for obtaining depth of interaction (DOI) information in PET detectors is presented in this study, based on sharing and redirection of scintillation light among multiple detectors, together with attenuation of light over the length of the crystals. The aim is to obtain continuous DOI encoding with single side readout, and at the same time without the need for one-to-one coupling between scintillators and detectors, allowing the development of a PET scanner with good spatial, energy and timing resolutions while keeping the complexity of the system low. A prototype module has been produced and characterized to test the proposed method, coupling a LYSO scintillator matrix to a commercial SiPMs array. Excellent crystal separation is obtained for all the scintillators in the array, light loss due to depolishing is found to be negligible, energy resolution is shown to be on average 12.7% FWHM. The mean DOI resolution achieved is 4.1 mm FWHM on a 15 mm long crystal and preliminary coincidence time resolution was estimated in 353 ps FWHM.

  2. Precise, fast, and flexible determination of protein interactions by affinity capillary electrophoresis: part 3: anions.

    PubMed

    Xu, Yuanhong; Redweik, Sabine; El-Hady, Deia Abd; Albishri, Hassan M; Preu, Lutz; Wätzig, Hermann

    2014-08-01

    The binding of physiologically anionic species or negatively charged drug molecules to proteins is of great importance in biochemistry and medicine. Since affinity capillary electrophoresis (ACE) has already proven to be a suitable analytical tool to study the influence of ions on proteins, this technique was applied here for comprehensively studying the influence of various anions on proteins of BSA, β-lactoglobulin, ovalbumin, myoglobin, and lysozyme. The analysis was performed using different selected anions of succinate, glutamate, phosphate, acetate, nitrate, iodide, thiocyanate, and pharmaceuticals (salicylic acid, aspirin, and ibuprofen) that exist in the anionic form at physiological pH 7.4. Due to the excellent repeatability and precision of the ACE measurements, not necessarily strong but significant influences of the anions on the proteins were found in many cases. Different influences in the observed bindings indicated change of charge, mass, or conformational changes of the proteins due to the binding with the studied anions. Combining the mobility-shift and pre-equilibrium ACE modes, rapidity and reversibility of the protein-anion bindings were discussed. Further, circular dichroism has been used as an orthogonal approach to characterize the interactions between the studied proteins and anions to confirm the ACE results. Since phosphate and various anions from amino acids and small organic acids such as succinate or acetate are present in very high concentrations in the cellular environment, even weak influences are certainly relevant as well.

  3. Determination of interaction forces between parallel dislocations by the evaluation of J integrals of plane elasticity

    NASA Astrophysics Data System (ADS)

    Lubarda, Vlado A.

    2016-03-01

    The Peach-Koehler expressions for the glide and climb components of the force exerted on a straight dislocation in an infinite isotropic medium by another straight dislocation are derived by evaluating the plane and antiplane strain versions of J integrals around the center of the dislocation. After expressing the elastic fields as the sums of elastic fields of each dislocation, the energy momentum tensor is decomposed into three parts. It is shown that only one part, involving mixed products from the two dislocation fields, makes a nonvanishing contribution to J integrals and the corresponding dislocation forces. Three examples are considered, with dislocations on parallel or intersecting slip planes. For two edge dislocations on orthogonal slip planes, there are two equilibrium configurations in which the glide and climb components of the dislocation force simultaneously vanish. The interactions between two different types of screw dislocations and a nearby circular void, as well as between parallel line forces in an infinite or semi-infinite medium, are then evaluated.

  4. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

    PubMed Central

    Kroschwald, Sonja; Maharana, Shovamayee; Mateju, Daniel; Malinovska, Liliana; Nüske, Elisabeth; Poser, Ina; Richter, Doris; Alberti, Simon

    2015-01-01

    RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine. DOI: http://dx.doi.org/10.7554/eLife.06807.001 PMID:26238190

  5. Performance of zwitterionic hydrophilic interaction LC for the determination of iodinated X-ray contrast agents.

    PubMed

    Echeverría, Silvia; Herrero, Pol; Borrull, Francesc; Fontanals, Núria; Pocurull, Eva

    2013-12-01

    This study compares the separation performance of a group of iodinated X-ray contrast media on four different columns. The first three were two stationary phases (SPs) modified with C18 and a polar-embedded SP (polar amide group bonded to an alkyl chain), all of which worked under RP-LC mode. The fourth was a zwitterionic sulphoalkylbetaine SP, working under the hydrophilic interaction LC (HILIC) mode. After the optimisation of the different parameters, the zwitterionic column displayed the best separation, which also overcomes the problems encountered when these analytes were separated under RP-LC. Moreover, when HILIC is coupled to MS/MS, sensitivity is enhanced. However, when sewage samples were analysed by SPE followed by the optimal HILIC-MS/MS, the sensitivity of the method was affected due to the high matrix effect, which had to be solved by dilution of the extract. Finally, the method was preliminarily validated with sewage and the figures of merit were comparable to those of the SPE-RP-LC-MS/MS.

  6. Lifetime Number of Mates Interacts with Female Age to Determine Reproductive Success in Female Guppies

    PubMed Central

    Evans, Jonathan P.

    2012-01-01

    In many species, mating with multiple males confers benefits to females, but these benefits may be offset by the direct and indirect costs associated with elevated mating frequency. Although mating frequency (number of mating events) is often positively associated with the degree of multiple mating (actual number of males mated), most studies have experimentally separated these effects when exploring their implications for female fitness. In this paper I describe an alternative approach using the guppy Poecilia reticulata, a livebearing freshwater fish in which females benefit directly and indirectly from mating with multiple males via consensual matings but incur direct and indirect costs of mating as a consequence of male sexual harassment. In the present study, females were experimentally assigned different numbers of mates throughout their lives in order to explore how elevated mating frequency and multiple mating combine to influence lifetime reproductive success (LRS) and survival (i.e. direct components of female fitness). Under this mating design, survival and LRS were not significantly affected by mating treatment, but there was a significant interaction between brood size and reproductive cycle (a correlate of female age) because females assigned to the high mating treatment produced significantly fewer offspring later in life compared to their low-mating counterparts. This negative effect of mating treatment later in life may be important in these relatively long-lived fishes, and this effect may be further exacerbated by the known cross-generational fitness costs of sexual harassment in guppies. PMID:23071816

  7. Determination of ethyl glucuronide in human hair by hydrophilic interaction liquid chromatography-tandem mass spectrometry.

    PubMed

    Yaldiz, Fadile; Daglioglu, Nebile; Hilal, Ahmet; Keten, Alper; Gülmen, Mete Korkut

    2013-10-01

    Ethyl glucuronide (EtG) is a direct metabolite of ethanol and has been utilized as a marker for alcohol intake. This study presents development, validation and application of a new hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method for the analysis of EtG in human hair samples. The linearity was assessed in the range of 5-2000 pg/mg hair, with a correlation coefficient of >0.99. The method was selective and sensitive, with a limit of detection (LOD) and limit of quantitation (LOQ) of 0.05 pg/mg and 0.18 pg/mg in hair, respectively. Differently from the extraction procedures in the literature, a fast and simple liquid-liquid method was used and highest recoveries and cleanest extracts were obtained. The method was successfully applied to 30 human hair samples which were taken from those who state they consume alcohol. EtG concentrations in the hair samples of alcohol users participated in this study, ranged between 1.34 and 82.73 pg/mg. From the concentration of EtG in hair strands 20 of the 30 subjects can be considered regular moderate drinkers.

  8. Biotic interactions as determinants of ecosystem structure in prairie wetlands: An example using fish

    USGS Publications Warehouse

    Hanson, M.A.; Zimmer, K.D.; Butler, Malcolm G.; Tangen, B.A.; Herwig, B.R.; Euliss, N.H.

    2005-01-01

    Wetlands are abundant throughout the prairie pothole region (PPR), an area comprising over 700,000 km2 in central North America. Prairie wetland communities are strongly influenced by regional physiography and climate, resulting in extreme spatial and temporal variability relative to other aquatic ecosystems. Given the strong influence of abiotic factors, PPR wetland communities have been viewed traditionally in the context of their responses to chemical and physical features of landscape and climate. Although useful, this physical-chemical paradigm may fail to account for ecosystem variability due to biotic influences, particularly those associated with presence of fish. Spatial and temporal variability in fish populations, in turn, may reflect anthropogenic activities, landscape characteristics, and climate-mediated effects on water levels, surface connectivity, and hydroperiods. We reviewed studies assessing influences of fish on prairie wetlands and examined precipitation patterns and biological data from PPR wetlands in east-central North Dakota and western Minnesota, USA. Our review and analysis indicated that native fish influence many characteristics of permanently flooded prairie wetlands, including water clarity and abundance of phytoplankton, submerged macrophytes, and aquatic invertebrates. We suggest that ecologists and managers will benefit from conceptual paradigms that better meld biotic interactions associated with fish, and perhaps other organisms, with chemical and physical influences on prairie wetland communities. ?? 2005, The Society of Wetland Scientists.

  9. Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height.

    PubMed

    Davière, Jean-Michel; Wild, Michael; Regnault, Thomas; Baumberger, Nicolas; Eisler, Herfried; Genschik, Pascal; Achard, Patrick

    2014-08-18

    Regulation of plant height, one of the most important agronomic traits, is the focus of intensive research for improving crop performance. Stem elongation takes place as a result of repeated cell divisions and subsequent elongation of cells produced by apical and intercalary meristems. The gibberellin (GA) phytohormones have long been known to control stem and internodal elongation by stimulating the degradation of nuclear growth-repressing DELLA proteins; however, the mechanism allowing GA-responsive growth is only slowly emerging. Here, we show that DELLAs directly regulate the activity of the plant-specific class I TCP transcription factor family, key regulators of cell proliferation. Our results demonstrate that class I TCP factors directly bind the promoters of core cell-cycle genes in Arabidopsis inflorescence shoot apices while DELLAs block TCP function by binding to their DNA-recognition domain. GAs antagonize such repression by promoting DELLA destruction and therefore cause a concomitant accumulation of TCP factors on promoters of cell-cycle genes. Consistent with this model, the quadruple mutant tcp8 tcp14 tcp15 tcp22 exhibits severe dwarfism and reduced responsiveness to GA action. Altogether, we conclude that GA-regulated DELLA-TCP interactions in inflorescence shoot apex provide a novel mechanism to control plant height.

  10. Sexually-trimorphic interactions with colour polymorphism determine nectar quality in a herbaceous perennial

    PubMed Central

    Varga, Sandra; Soulsbury, Carl D.

    2017-01-01

    Amongst gynodioecious plant breeding systems, there can exist intermediate morphs with a reduction in their male function (i.e. reduced number of functional anthers). Along with this sexual trimorphism, plants can also show floral colour polymorphism. Such intricate mixtures of phenotypes within a species may have complex effects on floral rewards. Floral rewards are known to vary between sexually dimorphic species and to a lesser extent between colour morphs. However, the interactive effect of sexual trimorphism and colour polymorphism is unexplored. We measured nectar’s sugar content in the sexually trimorphic Geranium sylvaticum, a gynodioecious plant with a light/dark floral polymorphism. We found that nectar reward differed across genders and colour morphs. Results were not however consistent within the three genders; dark female and hermaphrodite flowers had higher sugar content than light morphs, whereas intermediate flowers did not. As expected, females and hermaphrodites had different nectar reward, with intermediate morphs being midway between the other genders. In intermediates, the sugar content was not related to the number of functional stamens. We show for the first time the existence of sex-specific differences between flower gender and colour morphs in nectar rewards. Our results demonstrate the importance of considering multiple and conflicting selection pressures to explain rewards. PMID:28374829

  11. Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.

    PubMed

    Lee, Hochan; Lee, Gayeon; Jeon, Jonggu; Cho, Minhaeng

    2012-01-12

    IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

  12. [Effect of ligand concentration on the precision of determining the parameters of ligand-receptor interaction by serial dilution methods].

    PubMed

    Bobrovnik, S A

    2004-01-01

    Earlier we suggested the method of serial dilution, which allows one to determine the parameters of ligand-receptor interaction even if the reactants are in a mixture and their concentrations are unknown. The method is especially useful if the liability of studied receptor does not allow its separation from corresponding ligand. The important prerequisite of the method's precision is that the concentration of the ligand should be sufficiently high comparing to the concentration of the receptor. In the present paper it was demonstrated that the method allows one to obtain sufficiently good precision even in the case when the concentration of the ligand is only one tenth of the receptor concentration.

  13. Rapid hydrophilic interaction chromatography determination of lysine in pharmaceutical preparations with fluorescence detection after postcolumn derivatization with o-phtaldialdehyde.

    PubMed

    Douša, Michal; Břicháč, Jiří; Gibala, Petr; Lehnert, Petr

    2011-04-05

    A rapid procedure for the determination of lysine based on hydrophilic interaction chromatography (HILIC) separation of arginine and lysine with fluorescence detection has been developed. The separation conditions and parameters of lysine postcolumn derivatization with o-phtaldialdehyde (OPA)/2-mercaptoethanol were studied. The various HILIC columns were employed using isocratic elution. Fluorescence detection was performed at excitation and emission wavelength of 345 nm and 450 nm, respectively. An advantage of the reported method is a simple sample pre-treatment and a quick and very sensitive HPLC method. The developed method was successfully applied for analysis of commercial samples of Ibalgin Fast tablets (Zentiva, Czech Republic).

  14. A new predictive model for determining solar wind-terrestrial planet interactions

    NASA Technical Reports Server (NTRS)

    Spreiter, J. R.; Stahara, S. S.

    1980-01-01

    A computational model has been developed for the determination of the gasdynamic and magnetic field properties of the solar wind flow around a magnetic planet, such as the earth, or a nonmagnetic planet, such as Venus. The procedures are based on an established single-fluid, steady, dissipationless, magnetogasdynamic model and are appropriate for the calculation of axisymmetric, supersonic, super-Alfvenic solar wind flow past a planetary magneto/ionosphere. Sample results are reported for a variety of solar wind and planetary conditions. Some of these are new applications; others are included to show that the new procedures produce the same results as previous procedures when applied to the same conditions. The new methods are completely automated and much more efficient and versatile than those employed heretofore.

  15. Tree species identity and interactions with neighbors determine nutrient leaching in model tropical forests.

    PubMed

    Ewel, John J; Bigelow, Seth W

    2011-12-01

    An ecosystem containing a mixture of species that differ in phenology, morphology, and physiology might be expected to resist leaching of soil nutrients to a greater extent than one composed of a single species. We tested the effects of species identity and plant-life-form richness on nutrient leaching at a lowland tropical site where deep infiltration averages >2 m year(-1). Three indigenous tree species with contrasting leafing phenologies (evergreen, dry-season deciduous, and wet-season deciduous) were grown in monoculture and together with two other life-forms with which they commonly occur in tropical forests: a palm and a giant, perennial herb. To calculate nutrient leaching over an 11-year period, concentrations of nutrients in soil water were multiplied by drainage rates estimated from a water balance. The effect of plant-life-form richness on retention differed according to tree species identity and nutrient. Nitrate retention was greater in polycultures of the dry-season deciduous tree species (mean of 7.4 kg ha(-1) year(-1) of NO(3)-N lost compared to 12.7 in monoculture), and calcium and magnesium retention were greater in polycultures of the evergreen and wet-season deciduous tree species. Complementary use of light led to intensification of soil exploitation by roots, the main agent responsible for enhanced nutrient retention in some polycultures. Other mechanisms included differences in nutrient demand among species, and avoidance of catastrophic failure due to episodic weather events or pest outbreaks. Even unrealistically simple multi-life-form mimics of tropical forest can safeguard a site's nutrient capital if careful attention is paid to species' characteristics and temporal changes in interspecific interactions.

  16. Determination of the Dzyaloshinskii Moriya interaction for various hetero-structure (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    You, Chun-Yeol

    2016-10-01

    We investigated non-reciprocal spin wave (SW) dispersion relations by using Brillouin Light Scattering (BLS) in inversion symmetry breaking heterostructures. The non-reciprocal SW dispersion relation is a fingerprint of the existence of asymmetric exchange coupling, Dzyaloshinskii-Moriya Interaction (DMI). The quantification of DMI is important, because it is an essential ingredient of the domain wall motion and skyrmion based logic devices. We obtained DMI energy densities of various NM1/ferromagnetic(Co, CoFeB)/NM2 structures, where NM1,2 are non-magnetic heavy metals (Pt, Ir, Ta) or insulators (MgO, AlOx). We revealed that DMI is proportional to the inverse of ferromagnetic layer thickness, which strong evidence of interface nature of DMI in the heterostructure. In order to exclude the possible source of non-reciprocal SW dispersions, we carefully examined DMI with three independent measurement methods, field strength dependence, SW wave vector magnitude dependence, and SW propagating angle dependences, and found all three measurements gave the same results. It implies our measurement results are more reliable compared with other methods. We also found that sign and strength are sensitive function of materials, interface qualities, layer orders, and annealing conditions. Since the strong spin-orbit coupling (SOC) between ferromagnetic and the heavy metal layers is a source DMI, we also investigated SOC related quantities such as perpendicular magnetic anisotropy, magneto-optical Kerr effect, and spin pumpings. And we found that the relation between SOC and DMI is not the same with other SOC-related physical quantities.

  17. Interactive effects of herbivory and competition intensity determine invasive plant performance.

    PubMed

    Huang, Wei; Carrillo, Juli; Ding, Jianqing; Siemann, Evan

    2012-10-01

    Herbivory can reduce plant fitness, and its effects can be increased by competition. Though numerous studies have examined the joint effects of herbivores and competitors on plant performance, these interactive effects are seldom considered in the context of plant invasions. Here, we examined variation in plant performance within a competitive environment in response to both specialist and generalist herbivores using Chinese tallow as a model species. We combined tallow plants from native and invasive populations to form all possible pairwise combinations, and designated invasive populations as stronger neighbours and native populations as weaker neighbours. We found that when no herbivory was imposed, invasive populations always had higher total biomass than natives, regardless of their neighbours, which is consistent with our assumption of increased competitive ability. Defoliation by either generalist or specialist herbivores suppressed plant growth but the effects of specialists were generally stronger for invasive populations. Invasive populations had their lowest biomass when fed upon by specialists while simultaneously competing with stronger neighbours. The root/shoot ratios of invasive populations were lower than those of native populations under almost all conditions, and invasive plants were taller than native plants overall, especially when herbivores were present, suggesting that invasive populations may adopt an "aboveground first" strategy to cope with herbivory and competition. These results suggest that release from herbivores, especially specialists, improves an invader's performance and helps to increase its competitive ability. Therefore, increasing interspecific competition intensity by planting a stronger neighbour while simultaneously releasing a specialist herbivore may be an especially effective method of managing invasive plants.

  18. Spectroscopic studies on the interaction between norfloxacin and p-amino benzoic acid: Analytical application on determination of norfloxacin

    NASA Astrophysics Data System (ADS)

    More, V. R.; Mote, U. S.; Patil, S. R.; Kolekar, G. B.

    2009-10-01

    Fluorescence (Förster) Resonance Energy Transfer (FRET) between norfloxacin (NF) and p-amino benzoic acid (PABA) has been investigated by fluorescence and UV-vis absorption spectroscopy. It was found that the quenching of fluorescence of PABA is followed by simultaneous sensitization of NF fluorescence. The hydrophobic and electrostatic interaction plays an important role to stabilize the complex. The binding constant ( K), binding site number ( n) and corresponding thermodynamic parameters like free energy change (Δ G), enthalpy change (Δ H) and entropy change (Δ S) were determined according to van't Hoff equation. Using FRET, the distance ( r) between donor (PABA) and acceptor (NF) was obtained. This method is simple, selective and relatively free of interference from co-existing substances. The method was successfully applied to the determination of norfloxacin from pharmaceutical tablets.

  19. The behavior of multiple independent managers and ecological traits interact to determine prevalence of weeds.

    PubMed

    Coutts, Shaun R; Yokomizo, Hiroyuki; Buckley, Yvonne M

    2013-04-01

    Management of damaging invasive plants is often undertaken by multiple decision makers, each managing only a small part of the invader's population. As weeds can move between properties and re-infest eradicated sites from unmanaged sources, the dynamics of multiple decision makers plays a significant role in weed prevalence and invasion risk at the landscape scale. We used a spatially explicit agent-based simulation to determine how individual agent behavior, in concert with weed population ecology, determined weed prevalence. We compared two invasive grass species that differ in ecology, control methods, and costs: Nassella trichotoma (serrated tussock) and Eragrostis curvula (African love grass). The way decision makers reacted to the benefit of management had a large effect on the extent of a weed. If benefits of weed control outweighed the costs, and either net benefit was very large or all agents were very sensitive to net benefits, then agents tended to act synchronously, reducing the pool of infested agents available to spread the weed. As N. trichotoma was more damaging than E. curvula and had more effective control methods, agents chose to manage it more often, which resulted in lower prevalence of N. trichotoma. A relatively low number of agents who were intrinsically less motivated to control weeds led to increased prevalence of both species. This was particularly apparent when long-distance dispersal meant each infested agent increased the invasion risk for a large portion of the landscape. In this case, a small proportion of land mangers reluctant to control, regardless of costs and benefits, could lead to the whole landscape being infested, even when local control stopped new infestations. Social pressure was important, but only if it was independent of weed prevalence, suggesting that early access to information, and incentives to act on that information, may be crucial in stopping a weed from infesting large areas. The response of our model to both

  20. Determining Phosphorus-sediment Interactions in a Groundwater-fed River through In Situ Measurement

    NASA Astrophysics Data System (ADS)

    Mullinger, N. J.; Heathwaite, L.; Zhang, H.; Keenan, P. O.

    2011-12-01

    In stream processing is potentially important in the regulation and availability of nutrients to riverine flora and also in attenuating point and non-point source inputs to rivers, such as wastewater outflows and agricultural runoff. Phosphorus is an important macronutrient and often cited as a limiting factor to plant and algal growth in freshwater systems. The particle-reactive nature of the orthophosphate anion means that river sediments can play an important role in phosphorus attenuation and availability in rivers. However, it is also known that plant root exudates can also affect the mobilisation of sediment adsorbed phosphorus. Results are presented from high resolution (centimetre) measurements of vertical riverbed pore water profiles at a field site in the River Leith, Cumbria, UK. The River Leith is a sub-catchment of the River Eden and is characterised by significant groundwater-surface water interactions at the monitoring site. In situ measurements of soluble reactive phosphorus (SRP) in riverbed pore waters were made using passive sampling diffusive gradient and diffusive equilibration in thin film (DGT and DET) probes. These probes allow in situ measurements of riverbed pore waters to be made to a depth of 30 cm below the riverbed at centimetre resolution. The resulting profiles provide information on the variability in phosphorus pore waters for vegetated and non-vegetated regions of the riverbed. The impact of vegetated root zones in riverbed sediments is poorly characterised for hyporheic exchanges. Comparison of the vertical profiles obtained by DGT and DET probes identifies the potential of sediments to act sources or sinks of in stream phosphorus. Simultaneous analysis for redox sensitive elements provides additional information on the redox status of riverbed sediments. Initial results show spatial and temporal variability of phosphorus in different sedimentary environments and also between vegetated and non-vegetated areas of the riverbed

  1. Genetic determinants of cardiometabolic risk: a proposed model for phenotype association and interaction.

    PubMed

    Blackett, Piers R; Sanghera, Dharambir K

    2013-01-01

    This review provides a translational and unifying summary of metabolic syndrome genetics and highlights evidence that genetic studies are starting to unravel and untangle origins of the complex and challenging cluster of disease phenotypes. The associated genes effectively express in the brain, liver, kidney, arterial endothelium, adipocytes, myocytes, and β cells. Progression of syndrome traits has been associated with ectopic lipid accumulation in the arterial wall, visceral adipocytes, myocytes, and liver. Thus, it follows that the genetics of dyslipidemia, obesity, and nonalcoholic fatty liver disease are central in triggering progression of the syndrome to overt expression of disease traits and have become a key focus of interest for early detection and for designing prevention and treatments. To support the "birds' eye view" approach, we provide a road-map depicting commonality and interrelationships between the traits and their genetic and environmental determinants based on known risk factors, metabolic pathways, pharmacologic targets, treatment responses, gene networks, pleiotropy, and association with circadian rhythm. Although only a small portion of the known heritability is accounted for and there is insufficient support for clinical application of gene-based prediction models, there is direction and encouraging progress in a rapidly moving field that is beginning to show clinical relevance.

  2. Epithelial-macrophage interactions determine pulmonary fibrosis susceptibility in Hermansky-Pudlak syndrome

    PubMed Central

    Young, Lisa R.; Gulleman, Peter M.; Short, Chelsi W.; Tanjore, Harikrishna; Sherrill, Taylor; Qi, Aidong; McBride, Andrew P.; Zaynagetdinov, Rinat; Benjamin, John T.; Lawson, William E.; Novitskiy, Sergey V.; Blackwell, Timothy S.

    2016-01-01

    Alveolar epithelial cell (AEC) dysfunction underlies the pathogenesis of pulmonary fibrosis in Hermansky-Pudlak syndrome (HPS) and other genetic syndromes associated with interstitial lung disease; however, mechanisms linking AEC dysfunction and fibrotic remodeling are incompletely understood. Since increased macrophage recruitment precedes pulmonary fibrosis in HPS, we investigated whether crosstalk between AECs and macrophages determines fibrotic susceptibility. We found that AECs from HPS mice produce excessive MCP-1, which was associated with increased macrophages in the lungs of unchallenged HPS mice. Blocking MCP-1/CCR2 signaling in HPS mice with genetic deficiency of CCR2 or targeted deletion of MCP-1 in AECs normalized macrophage recruitment, decreased AEC apoptosis, and reduced lung fibrosis in these mice following treatment with low-dose bleomycin. We observed increased TGF-β production by HPS macrophages, which was eliminated by CCR2 deletion. Selective deletion of TGF-β in myeloid cells or of TGF-β signaling in AECs through deletion of TGFBR2 protected HPS mice from AEC apoptosis and bleomycin-induced fibrosis. Together, these data reveal a feedback loop in which increased MCP-1 production by dysfunctional AECs results in recruitment and activation of lung macrophages that produce TGF-β, thus amplifying the fibrotic cascade through AEC apoptosis and stimulation of fibrotic remodeling. PMID:27777976

  3. Human and Helicobacter pylori Interactions Determine the Outcome of Gastric Diseases

    PubMed Central

    Gobert, Alain P.; Wilson, Keith T.

    2017-01-01

    The innate immune response is a critical hallmark of Helicobacter pylori infection. Epithelial and myeloid cells produce effectors, including the chemokine CXCL8, reactive oxygen species (ROS), and nitric oxide (NO), in response to bacterial components. Mechanistic and epidemiologic studies have emphasized that dysregulated and persistent release of these products leads to the development of chronic inflammation and to the molecular and cellular events related to carcinogenesis. Moreover, investigations in H. pylori-infected patients about polymorphisms of the genes encoding CXCL8 and inducible NO synthase, and epigenetic control of the ROS-producing enzyme spermine oxidase, have further proven that overproduction of these molecules impacts the severity of gastric diseases. Lastly, the critical effect of the crosstalk between the human host and the infecting bacterium in determining the severity of H. pylori-related diseases has been supported by phylogenetic analysis of the human population and their H. pylori isolates in geographic areas with varying clinical and pathologic outcomes of the infection. PMID:28124148

  4. Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript.

    PubMed Central

    Tomizawa, J; Itoh, T

    1981-01-01

    Mutants of plasmid pNT7 that can coexist with plasmid pMB9 in growing bacteria have been isolated. These mutants show altered incompatibility properties and increased copy numbers. Each mutant has a single base change at or near the center of one of the three palindromes in the region that specifies two RNA species: a larger one (primer transcripts) that provides a primer for DNA replication and a smaller one (RNA I) that is the incompatibility-specific inhibitor of primer formation. In vitro transcription studies show that the single base changes affect both the ability of RNA I to inhibit primer formation and the sensitivity of primer formation to inhibition by RNA I. RNA I hybridizes to the primer transcript, and the rate of hybridization is reduced by the single base changes. Based on analyses of inhibition of in vitro primer formation by RNA I and of in vivo properties of the mutant plasmids, we conclude that incompatibility between two plasmids can be attributed to inhibition of primer formation on one of the plasmids by the RNA I of the other. Inhibition of primer formation by RNA I appears to be the mechanism that determines the copy number of pNT7 and its derivatives. Images PMID:6171811

  5. Questioning the answer: questioning style, choice and self-determination in interactions with young people with intellectual disabilities.

    PubMed

    Pilnick, Alison; Clegg, Jennifer; Murphy, Elizabeth; Almack, Kathryn

    2010-03-01

    For young people with intellectual disabilities (ID), the transition from children's to adult services has long been recognised as a challenging move. One of the aims of the White Paper Valuing People (2001) was to address some of the problems associated with this transition. This paper reports on data from a project which examines the impact of these service changes, and the ways in which transition is negotiated by carers, professionals and users. It presents a conversation analysis of eight tape-recorded formal review meetings at which transition to adult services is discussed. It takes as its starting point the existing interactional work on ID and the way in which this demonstrates the effects of the local and contextual specifics of particular kinds of interaction on the eventual outcomes (e.g. Rapley 2004, Antaki 2001, Maynard and Marlaire 1992). We show that an attempt to allow self-determination in the context of transitions can paradoxically result in undermining user choice and control. We also argue that, while a rule-based approach to practice may offer moral clarity for professionals, it can result in interactional and practical difficulties which cannot be easily reconciled.

  6. Discovery of potent Keap1-Nrf2 protein-protein interaction inhibitor based on molecular binding determinants analysis.

    PubMed

    Jiang, Zheng-Yu; Lu, Meng-Chen; Xu, Li Li; Yang, Ting-Ting; Xi, Mei-Yang; Xu, Xiao-Li; Guo, Xiao-Ke; Zhang, Xiao-Jin; You, Qi-Dong; Sun, Hao-Peng

    2014-03-27

    Keap1 is known to mediate the ubiquitination of Nrf2, a master regulator of the antioxidant response. Directly interrupting the Keap1-Nrf2 interaction has been emerged as a promising strategy to develop novel class of antioxidant, antiinflammatory, and anticancer agents. On the basis of the molecular binding determinants analysis of Keap1, we successfully designed and characterized the most potent protein-protein interaction (PPI) inhibitor of Keap1-Nrf2, compound 2, with K(D) value of 3.59 nM binding to Keap1 for the first time to single-digit nanomolar. Compound 2 can effectively disrupt the Nrf2-Keap1 interaction with an EC50 of 28.6 nM in the fluorescence polarization assay. It can also activate the Nrf2 transcription activity in the cell-based ARE-luciferase reporter assay in a dose-dependent manner. The qRT-PCR results of Nrf2 transcription targets gave the consistent results. These results confirm direct and highly efficient interruption of the Keap1-Nrf2 PPI can be fully achieved by small molecules.

  7. Reliable Determinations of Protein-Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

    NASA Astrophysics Data System (ADS)

    Kitova, Elena N.; El-Hawiet, Amr; Schnier, Paul D.; Klassen, John S.

    2012-03-01

    The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein-ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein-ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.

  8. Pharmacogenetic determination of the effects of codeine and prediction of drug interactions.

    PubMed

    Caraco, Y; Sheller, J; Wood, A J

    1996-09-01

    To define the differences in codeine pharmacodynamics in extensive (EMs) and poor (PMs) metabolizers of debrisoquin and to determine whether the inhibition of codeine's metabolism by quinidine produces phenotypically dependent pharmacodynamic changes, we studied 16 healthy nonsmoking males, 10 EMs and 6 PMs of debrisoquin. The subjects received in random double-blind fashion 120 mg of codeine plus placebo, 120 mg of codeine plus 100 mg of quinidine and 100 mg of quinidine plus placebo. Blood was obtained over 24 hr and urine was collected for 48 hr. Respiratory, psychomotor and pupillary effects of codeine were greater in the EMs than in the PMs (P < .01). Morphine and morphine metabolites were detectable only in plasma from EMs. Codeine metabolic clearance by O-demethylation was almost 200-fold greater in the EMs than in the PMs. After coadministration of quinidine, morphine and morphine metabolites were not detectable in the plasma of either phenotype and mean (+/- S.E.M.) O-demethylation clearance was reduced in the EMs from 162.7 +/- 36.6 to 17.0 +/- 5.0 ml/min (P < .003), but not in the PMs. The diminished production of morphine in the EMs was associated with significantly reduced respiratory, psychomotor and pupillary effects (P < .01). Thus, CYP2D6 mediated O-demethylation of codeine to morphine is central to its pharmacodynamic effects. Patients who lack CYP2D6 or whose CYP2D6 is inhibited would not be expected to benefit from codeine. Thus, phenotyping for CYP2D6 and the avoidance of CYP2D6 inhibitors is justified in patients with chronic path before initiating long-term therapy with analgesics whose in vivo activation is dependent on CYP2D6 activity (i.e., codeine, hydrocodone and oxycodone.

  9. Determination of dopamine hydrochloride by host-guest interaction based on water-soluble pillar[5]arene

    NASA Astrophysics Data System (ADS)

    Xiao, Xue-Dong; Shi, Lin; Guo, Li-Hui; Wang, Jun-Wen; Zhang, Xiang

    2017-02-01

    The supramolecular interaction between the water-soluble pillar[5]arene (WP[5]) as host and dopamine hydrochloride (DH) as guest was studied by spectrofluorometry. The fluorescence intensity of DH gradually decreased with increasing WP[5] concentration, and the possible interaction mechanism between WP[5] and DH was confirmed by 1H NMR, 2D NOESY, and molecular modelling. Based on significant DH fluorescence, a highly sensitive and selective method for DH determination was developed for the first time. The fluorescence intensity was measured at 312 nm, with excitation at 285 nm. The effects of pH, temperature, and reaction time on the fluorescence spectra of the WP[5]-DH complex were investigated. A linear relationship between fluorescence intensity and DH concentration in the range of 0.07-6.2 μg mL- 1 was obtained. The corresponding linear regression equation is ΔF = 25.76 C + 13.56 (where C denotes the concentration in μg mL- 1), with the limit of detection equal to 0.03 μg mL- 1 and the correlation coefficient equal to 0.9996. This method can be used for the determination of dopamine in injection and urine samples. In addition, the WP[5]-DH complex has potential applications in fluorescent sensing and pharmacokinetics studies of DH.

  10. Determination of rate constants and equilibrium constants for solution-phase drug-protein interactions by ultrafast affinity extraction.

    PubMed

    Zheng, Xiwei; Li, Zhao; Podariu, Maria I; Hage, David S

    2014-07-01

    A method was created on the basis of ultrafast affinity extraction to determine both the dissociation rate constants and equilibrium constants for drug-protein interactions in solution. Human serum albumin (HSA), an important binding agent for many drugs in blood, was used as both a model soluble protein and as an immobilized binding agent in affinity microcolumns for the analysis of free drug fractions. Several drugs were examined that are known to bind to HSA. Various conditions to optimize in the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered, and several approaches for these measurements were examined. The dissociation rate constants obtained for soluble HSA with each drug gave good agreement with previous rate constants reported for the same drugs or other solutes with comparable affinities for HSA. The equilibrium constants that were determined also showed good agreement with the literature. The results demonstrated that ultrafast affinity extraction could be used as a rapid approach to provide information on both the kinetics and thermodynamics of a drug-protein interaction in solution. This approach could be extended to other systems and should be valuable for high-throughput drug screening or biointeraction studies.

  11. Determination of Rate Constants and Equilibrium Constants for Solution-Phase Drug–Protein Interactions by Ultrafast Affinity Extraction

    PubMed Central

    2015-01-01

    A method was created on the basis of ultrafast affinity extraction to determine both the dissociation rate constants and equilibrium constants for drug–protein interactions in solution. Human serum albumin (HSA), an important binding agent for many drugs in blood, was used as both a model soluble protein and as an immobilized binding agent in affinity microcolumns for the analysis of free drug fractions. Several drugs were examined that are known to bind to HSA. Various conditions to optimize in the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered, and several approaches for these measurements were examined. The dissociation rate constants obtained for soluble HSA with each drug gave good agreement with previous rate constants reported for the same drugs or other solutes with comparable affinities for HSA. The equilibrium constants that were determined also showed good agreement with the literature. The results demonstrated that ultrafast affinity extraction could be used as a rapid approach to provide information on both the kinetics and thermodynamics of a drug–protein interaction in solution. This approach could be extended to other systems and should be valuable for high-throughput drug screening or biointeraction studies. PMID:24911267

  12. Development and validation of a hydrophilic interaction liquid chromatographic method for determination of aromatic amines in environmental water.

    PubMed

    Li, Ruiping; Zhang, Yi; Lee, Charles C; Lu, Rongrong; Huang, Yingping

    2010-03-12

    A simple, precise, and accurate hydrophilic interaction liquid chromatographic (HILIC) method has been developed for the determination of five aromatic amines in environmental water samples. Chromatography was carried out on a bare silica column, using a mixture of acetonitrile and a buffer of NaH(2)PO(4)-H(3)PO(4) (pH 1.5, containing 10mM NaH(2)PO(4)) (85:15, v/v) as a mobile phase at a flow rate of 1 mL min(-1). Aromatic amines were detected by UV absorbance at 254 nm. The linear range of amines was good (r(2)>0.998) and limit of detection (LOD) within 0.02-0.2 mg L(-1) (S/N=3). The retention mechanism for the analytes under the optimum conditions was determined to be a combination of adsorption, partition and ionic interactions. The proposed method was applied to the environmental water samples. Aromatic amines were isolated from aqueous samples using solid-phase extraction (SPE) with Oasis HLB cartridges. Recoveries of greater than 75% with precision (RSD) less than 12% were obtained at amine concentrations of 5-50 microg L(-1) from 100mL river water and influents from a wastewater treatment plant (WWTP). The present HILIC technique proved to be a viable method for the analysis of aromatic amines in the environmental water samples.

  13. A truly human interface: interacting face-to-face with someone whose words are determined by a computer program

    PubMed Central

    Corti, Kevin; Gillespie, Alex

    2015-01-01

    We use speech shadowing to create situations wherein people converse in person with a human whose words are determined by a conversational agent computer program. Speech shadowing involves a person (the shadower) repeating vocal stimuli originating from a separate communication source in real-time. Humans shadowing for conversational agent sources (e.g., chat bots) become hybrid agents (“echoborgs”) capable of face-to-face interlocution. We report three studies that investigated people’s experiences interacting with echoborgs and the extent to which echoborgs pass as autonomous humans. First, participants in a Turing Test spoke with a chat bot via either a text interface or an echoborg. Human shadowing did not improve the chat bot’s chance of passing but did increase interrogators’ ratings of how human-like the chat bot seemed. In our second study, participants had to decide whether their interlocutor produced words generated by a chat bot or simply pretended to be one. Compared to those who engaged a text interface, participants who engaged an echoborg were more likely to perceive their interlocutor as pretending to be a chat bot. In our third study, participants were naïve to the fact that their interlocutor produced words generated by a chat bot. Unlike those who engaged a text interface, the vast majority of participants who engaged an echoborg did not sense a robotic interaction. These findings have implications for android science, the Turing Test paradigm, and human–computer interaction. The human body, as the delivery mechanism of communication, fundamentally alters the social psychological dynamics of interactions with machine intelligence. PMID:26042066

  14. USING MULTIPLE-VIEWPOINT OBSERVATIONS TO DETERMINE THE INTERACTION OF THREE CORONAL MASS EJECTIONS OBSERVED ON 2012 MARCH 5

    SciTech Connect

    Colaninno, Robin C.; Vourlidas, Angelos E-mail: angelos.vourlidas@jhuapl.edu

    2015-12-10

    We examine the interaction of three coronal mass ejections (CMEs) that took place on 2012 March 5 at heights less than 20 R{sub ⊙} in the corona. We used a forward fitting model to reconstruct the three-dimensional trajectories and kinematics of the CMEs and determine their interaction in the observations from three viewpoints: Solar and Heliospheric Observatory (SOHO), STEREO-A, and STEREO-B. The first CME (CME-1), a slow-rising eruption near disk center, is already in progress at 02:45 UT when the second CME (CME-2) erupts from AR 11429 on the east limb. These two CMEs are present in the corona not interacting when a third CME (CME-3) erupts from AR 11429 at 03:34 UT. CME-3 has a constant velocity of 1456[±31] km s{sup −1} and drives a shock that is observed as a halo from all viewpoints. We find that the shock driven by CME-3 passed through CME-1 with no observable change in the geometry, trajectory, or velocity of CME-1. However, the elevated temperatures detected in situ when CME-1 reached Earth indicate that the plasma inside CME-1 may have been heated by the passage of the shock. CME-2 is accelerated by CME-3 to more than twice its initial velocity and remains a separate structure ahead of the CME-3 front. CME-2 is deflected 24° northward by CME-3 for a total deflection of 40° from its source region. These results suggest that the collision of CME-2 and CME-3 is superelastic. This work demonstrates the capability and utility of fitting forward models to complex and interacting CMEs observed in the corona from multiple viewpoints.

  15. Characterizing the Coding Region Determinant-Binding Protein (CRD-BP)-Microphthalmia-associated Transcription Factor (MITF) mRNA interaction.

    PubMed

    Rensburg, Gerrit van; Mackedenski, Sebastian; Lee, Chow H

    2017-01-01

    Coding region determinant-binding protein (CRD-BP) binds to the 3'-UTR of microphthalmia-associated transcription factor (MITF) mRNA to prevent its targeted degradation by miR-340. Here, we aim to further understand the molecular interaction between CRD-BP and MITF RNA. Using point mutation in the GXXG motif of each KH domains, we showed that all four KH domains of CRD-BP are important for their physical association with MITF RNA. We mapped the CRD-BP-binding site in the 3'-UTR of MITF RNA from nts 1330-1740 and showed that the 49-nt fragment 1621-1669 is the minimal size MITF RNA for binding. Upon deletion of nts 1621-1669 within the nts1550-1740 of MITF RNA, there was a 3-fold increase in dissociation constant Kd, which further confirms the critical role sequences within nts 1621-1669 in binding to CRD-BP. Amongst the eight antisense oligonucleotides designed against MITF RNA 1550-1740, we found MHO-1 and MHO-7 as potent inhibitors of the CRD-BP-MITF RNA interaction. Using RNase protection and fluorescence polarization assays, we showed that both MHO-1 and MHO-7 have affinity for the MITF RNA, suggesting that both antisense oligonucleotides inhibited CRD-BP-MITF RNA interaction by directly binding to MITF RNA. The new molecular insights provided in this study have important implications for understanding the oncogenic function of CRD-BP and development of specific inhibitors against CRD-BP-MITF RNA interaction.

  16. A truly human interface: interacting face-to-face with someone whose words are determined by a computer program.

    PubMed

    Corti, Kevin; Gillespie, Alex

    2015-01-01

    We use speech shadowing to create situations wherein people converse in person with a human whose words are determined by a conversational agent computer program. Speech shadowing involves a person (the shadower) repeating vocal stimuli originating from a separate communication source in real-time. Humans shadowing for conversational agent sources (e.g., chat bots) become hybrid agents ("echoborgs") capable of face-to-face interlocution. We report three studies that investigated people's experiences interacting with echoborgs and the extent to which echoborgs pass as autonomous humans. First, participants in a Turing Test spoke with a chat bot via either a text interface or an echoborg. Human shadowing did not improve the chat bot's chance of passing but did increase interrogators' ratings of how human-like the chat bot seemed. In our second study, participants had to decide whether their interlocutor produced words generated by a chat bot or simply pretended to be one. Compared to those who engaged a text interface, participants who engaged an echoborg were more likely to perceive their interlocutor as pretending to be a chat bot. In our third study, participants were naïve to the fact that their interlocutor produced words generated by a chat bot. Unlike those who engaged a text interface, the vast majority of participants who engaged an echoborg did not sense a robotic interaction. These findings have implications for android science, the Turing Test paradigm, and human-computer interaction. The human body, as the delivery mechanism of communication, fundamentally alters the social psychological dynamics of interactions with machine intelligence.

  17. Characterizing the Coding Region Determinant-Binding Protein (CRD-BP)-Microphthalmia-associated Transcription Factor (MITF) mRNA interaction

    PubMed Central

    2017-01-01

    Coding region determinant-binding protein (CRD-BP) binds to the 3’-UTR of microphthalmia-associated transcription factor (MITF) mRNA to prevent its targeted degradation by miR-340. Here, we aim to further understand the molecular interaction between CRD-BP and MITF RNA. Using point mutation in the GXXG motif of each KH domains, we showed that all four KH domains of CRD-BP are important for their physical association with MITF RNA. We mapped the CRD-BP-binding site in the 3’-UTR of MITF RNA from nts 1330–1740 and showed that the 49-nt fragment 1621–1669 is the minimal size MITF RNA for binding. Upon deletion of nts 1621–1669 within the nts1550-1740 of MITF RNA, there was a 3-fold increase in dissociation constant Kd, which further confirms the critical role sequences within nts 1621–1669 in binding to CRD-BP. Amongst the eight antisense oligonucleotides designed against MITF RNA 1550–1740, we found MHO-1 and MHO-7 as potent inhibitors of the CRD-BP-MITF RNA interaction. Using RNase protection and fluorescence polarization assays, we showed that both MHO-1 and MHO-7 have affinity for the MITF RNA, suggesting that both antisense oligonucleotides inhibited CRD-BP-MITF RNA interaction by directly binding to MITF RNA. The new molecular insights provided in this study have important implications for understanding the oncogenic function of CRD-BP and development of specific inhibitors against CRD-BP-MITF RNA interaction. PMID:28182633

  18. Gα12 Structural Determinants of Hsp90 Interaction Are Necessary for Serum Response Element–Mediated Transcriptional Activation

    PubMed Central

    Montgomery, Ellyn R.; Temple, Brenda R. S.; Peters, Kimberly A.; Tolbert, Caitlin E.; Booker, Brandon K.; Martin, Joseph W.; Hamilton, Tyler P.; Tagliatela, Alicia C.; Smolski, William C.; Rogers, Stephen L.; Jones, Alan M.

    2014-01-01

    The G12/13 class of heterotrimeric G proteins, comprising the α-subunits Gα12 and Gα13, regulates multiple aspects of cellular behavior, including proliferation and cytoskeletal rearrangements. Although guanine nucleotide exchange factors for the monomeric G protein Rho (RhoGEFs) are well characterized as effectors of this G protein class, a variety of other downstream targets has been reported. To identify Gα12 determinants that mediate specific protein interactions, we used a structural and evolutionary comparison between the G12/13, Gs, Gi, and Gq classes to identify “class-distinctive” residues in Gα12 and Gα13. Mutation of these residues in Gα12 to their deduced ancestral forms revealed a subset necessary for activation of serum response element (SRE)–mediated transcription, a G12/13-stimulated pathway implicated in cell proliferative signaling. Unexpectedly, this subset of Gα12 mutants showed impaired binding to heat-shock protein 90 (Hsp90) while retaining binding to RhoGEFs. Corresponding mutants of Gα13 exhibited robust SRE activation, suggesting a Gα12-specific mechanism, and inhibition of Hsp90 by geldanamycin or small interfering RNA–mediated lowering of Hsp90 levels resulted in greater downregulation of Gα12 than Gα13 signaling in SRE activation experiments. Furthermore, the Drosophila G12/13 homolog Concertina was unable to signal to SRE in mammalian cells, and Gα12:Concertina chimeras revealed Gα12-specific determinants of SRE activation within the switch regions and a C-terminal region. These findings identify Gα12 determinants of SRE activation, implicate Gα12:Hsp90 interaction in this signaling mechanism, and illuminate structural features that arose during evolution of Gα12 and Gα13 to allow bifurcated mechanisms of signaling to a common cell proliferative pathway. PMID:24435554

  19. Social determinants of health--a question of social or economic capital? Interaction effects of socioeconomic factors on health outcomes.

    PubMed

    Ahnquist, Johanna; Wamala, Sarah P; Lindstrom, Martin

    2012-03-01

    Social structures and socioeconomic patterns are the major determinants of population health. However, very few previous studies have simultaneously analysed the "social" and the "economic" indicators when addressing social determinants of health. We focus on the relevance of economic and social capital as health determinants by analysing various indicators. The aim of this paper was to analyse independent associations, and interactions, of lack of economic capital (economic hardships) and social capital (social participation, interpersonal and political/institutional trust) on various health outcomes. Data was derived from the 2009 Swedish National Survey of Public Health, based on a randomly selected representative sample of 23,153 men and 28,261 women aged 16-84 year, with a participation rate of 53.8%. Economic hardships were measured by a combined economic hardships measure including low household income, inability to meet expenses and lacking cash reserves. Social capital was measured by social participation, interpersonal (horizontal) trust and political (vertical/institutional trust) trust in parliament. Health outcomes included; (i) self-rated health, (i) psychological distress (GHQ-12) and (iii) musculoskeletal disorders. Results from multivariate logistic regression show that both measures of economic capital and low social capital were significantly associated with poor health status, with only a few exceptions. Significant interactive effects measured as synergy index were observed between economic hardships and all various types of social capital. The synergy indices ranged from 1.4 to 2.3. The present study adds to the evidence that both economic hardships and social capital contribute to a range of different health outcomes. Furthermore, when combined they potentiate the risk of poor health.

  20. A fast, simple, and reliable hydrophilic interaction liquid chromatography method for the determination of ascorbic and isoascorbic acids.

    PubMed

    Barros, Ana I R N A; Silva, Ana P; Gonçalves, Berta; Nunes, Fernando M

    2010-03-01

    A reliable method for the determination of total vitamin C must be able to resolve ascorbic acid (AA) and the epimeric isoascorbic acid (IAA) and determine the sum of AA and its oxidized form dehydroascorbic acid. AA and IAA are polar molecules with a low retention time in conventional reversed phase systems, and hence of difficult resolution. Hydrophilic interaction chromatography using a TSKgel Amide-80 stationary phase with isocratic elution was successful in resolving the two epimers. The column was compatible with injections of high concentrations of metaphosphoric acid, tris(2-carboxyethyl)-phosphine, and EDTA without drift of baseline and retention time. Total AA and IAA were extracted, stabilized, and reduced in one step at 40 °C, using 5% m-phosphoric acid, 2 mM of EDTA, and 2 mM of tris(2-carboxyethyl)-phosphine as reducing agent. This simple, fast, and robust hydrophilic interaction chromatography-DAD method was applied for the analysis of food products namely fruit juices, chestnut, and ham and also in pharmaceutical and multivitamin tablets. Method validation was performed on the food products, including parameters of precision, accuracy, linearity, limit of detection, and quantification (LOQ). The absence of matrix interferences was assessed by the standard addition method and Youden calibration. The method was fast, accurate, and precise with a LOQ(AA) of 1.5 mg/L and LOQ(IAA) of 3.7 mg/L. The simple experimental procedure, completed in 1 h, the possibility of using IAA as an internal standard, and low probability of artifacts are the major advantages of the proposed method for the routine determination of these compounds in a large number of samples.

  1. Study of photorespiration in marine microalgae through the determination of glycolic acid using hydrophilic interaction liquid chromatography.

    PubMed

    Rigobello-Masini, Marilda; Penteado, José C P; Tiba, Maurício; Masini, Jorge C

    2012-01-01

    Determination of organic acids in intracellular extracts and in the cultivation media of marine microalgae aid investigations about metabolic routes related to assimilation of atmospheric carbon by these organisms, which are known by their role in the carbon dioxide sink. The separation of these acids was investigated by hydrophilic interaction liquid chromatography (HILIC) using isocratic elution with a mobile phase composed of 70:30 v/v acetonitrile/20 mmol/L ammonium acetate buffer (pH 6.8) and detection at 220 nm. HILIC allowed the determinations of glycolic acid, the most important metabolite for the evaluation of the photorespiration process in algae, to be made with better selectivity than that achieved by reversed phase liquid chromatography, but with less detectability. The concentration of glycolic acid was determined in the cultivation media and in intracellular extracts of the algae Tetraselmis gracilis and Phaeodactylum tricornutum submitted to different conditions of aeration: (i) without forced aeration, (ii) aeration with atmospheric air, and (iii) bubbling with N(2). The concentration of glycolic acid had a higher increase as the cultures were aerated with nitrogen, showing higher photorespiratory flux than that occurring in the cultures aerated with atmospheric air.

  2. Relative importance of phenotypic trait matching and species' abundances in determining plant-avian seed dispersal interactions in a small insular community.

    PubMed

    González-Castro, Aarón; Yang, Suann; Nogales, Manuel; Carlo, Tomás A

    2015-03-05

    Network theory has provided a general way to understand mutualistic plant-animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor 'animal species'.

  3. Relative importance of phenotypic trait matching and species' abundances in determining plant–avian seed dispersal interactions in a small insular community

    PubMed Central

    González-Castro, Aarón; Yang, Suann; Nogales, Manuel; Carlo, Tomás A.

    2015-01-01

    Network theory has provided a general way to understand mutualistic plant–animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor ‘animal species’. PMID:25750409

  4. Thermodynamic study of rhodamine 123-calf thymus DNA interaction: determination of calorimetric enthalpy by optical melting study.

    PubMed

    Masum, Abdulla Al; Chakraborty, Maharudra; Pandya, Prateek; Halder, Umesh Chandra; Islam, Md Maidul; Mukhopadhyay, Subrata

    2014-11-20

    In this paper, the interaction of rhodamine123 (R123) with calf thymus DNA has been studied using molecular modeling and other biophysical methods like UV-vis spectroscopy, fluoremetry, optical melting, isothermal titration calorimetry, and circular dichroic studies. Results showed that the binding energy is about -6 to -8 kcal/mol, and the binding process is favored by both negative enthalpy change and positive entropy change. A new method to determine different thermodynamic properties like calorimetric enthalpy and heat capacity change has been introduced in this paper. The obtained data has been crossed-checked by other methods. After dissecting the free-energy contribution, it was observed that the binding was favored by both negative hydrophobic free energy and negative molecular free energy which compensated for the positive free energies due to the conformational change loss of rotational and transitional freedom of the DNA helix.

  5. The Determination of the Spectrum Energy on the model of DNA-protein interactions using WKB approximation method

    NASA Astrophysics Data System (ADS)

    Syahroni, Edy; Suparmi, A.; Cari, C.

    2017-01-01

    The spectrum energy’s equation for Killingback potential on the model of DNA and protein interactions was obtained using WKB approximation method. The Killingbeck potential was substituted into the general equation of WKB approximation method to determine the energy. The general equation required the value of critical turning point to complete the form equation. In this research, the general form of Killingbeck potential was causing the equation of critical turning point turn into cube equation. In this case we take the value of critical turning point only with the real value. In mathematical condition, it was satisfied with requirement Discriminant was less than or equal to 0. If D=0, it would give two values of critical turning point and if D<0, it would give three values of critical turning point. In this research we present both of those requirements to complete the general Equation of Energy.

  6. Analysis of Performance of Jet Engine from Characteristics of Components II : Interaction of Components as Determined from Engine Operation

    NASA Technical Reports Server (NTRS)

    Goldstein, Arthur W; Alpert, Sumner; Beede, William; Kovach, Karl

    1949-01-01

    In order to understand the operation and the interaction of jet-engine components during engine operation and to determine how component characteristics may be used to compute engine performance, a method to analyze and to estimate performance of such engines was devised and applied to the study of the characteristics of a research turbojet engine built for this investigation. An attempt was made to correlate turbine performance obtained from engine experiments with that obtained by the simpler procedure of separately calibrating the turbine with cold air as a driving fluid in order to investigate the applicability of component calibration. The system of analysis was also applied to prediction of the engine and component performance with assumed modifications of the burner and bearing characteristics, to prediction of component and engine operation during engine acceleration, and to estimates of the performance of the engine and the components when the exhaust gas was used to drive a power turbine.

  7. Aerosol-Cloud Interaction Determined by Both in Situ and Satellite Data Over a Northern High-Latitude Site

    NASA Technical Reports Server (NTRS)

    Lihavainen, H.; Kerminen, V.-M.; Remer, L. A.

    2009-01-01

    The first aerosol indirect effect over a clean, northern high-latitude site was investigated by determining the aerosol cloud interaction (ACI) using three different approaches; ground-based in situ measurements, combined ground-based in situ measurements 5 and satellite retrievals and using only satellite retrievals. The obtained values of ACI were highest for in situ ground-based data, clearly lower for combined ground-based and satellite data, and lowest for data relying solely on satellite retrievals. One of the key findings of this study was the high sensitivity of ACI to the definition of the aerosol burden. We showed that at least a part of the variability in ACI can be explained by 10 how different investigators have related dierent cloud properties to "aerosol burden".

  8. Food Web Architecture and Basal Resources Interact to Determine Biomass and Stoichiometric Cascades along a Benthic Food Web

    PubMed Central

    Guariento, Rafael D.; Carneiro, Luciana S.; Caliman, Adriano; Leal, João J. F.; Bozelli, Reinaldo L.; Esteves, Francisco A.

    2011-01-01

    Understanding the effects of predators and resources on primary producers has been a major focus of interest in ecology. Within this context, the trophic cascade concept especially concerning the pelagic zone of lakes has been the focus of the majority of these studies. However, littoral food webs could be especially interesting because base trophic levels may be strongly regulated by consumers and prone to be light limited. In this study, the availability of nutrients and light and the presence of an omnivorous fish (Hyphessobrycon bifasciatus) were manipulated in enclosures placed in a humic coastal lagoon (Cabiúnas Lagoon, Macaé – RJ) to evaluate the individual and interactive effects of resource availability (nutrients and light) and food web configuration on the biomass and stoichiometry of periphyton and benthic grazers. Our findings suggest that light and nutrients interact to determine periphyton biomass and stoichiometry, which propagates to the consumer level. We observed a positive effect of the availability of nutrients on periphytic biomass and grazers' biomass, as well as a reduction of periphytic C∶N∶P ratios and an increase of grazers' N and P content. Low light availability constrained the propagation of nutrient effects on periphyton biomass and induced higher periphytic C∶N∶P ratios. The effects of fish presence strongly interacted with resource availability. In general, a positive effect of fish presence was observed for the total biomass of periphyton and grazer's biomass, especially with high resource availability, but the opposite was found for periphytic autotrophic biomass. Fish also had a significant effect on periphyton stoichiometry, but no effect was observed on grazers' stoichiometric ratios. In summary, we observed that the indirect effect of fish predation on periphyton biomass might be dependent on multiple resources and periphyton nutrient stoichiometric variation can affect consumers' stoichiometry. PMID:21789234

  9. Determination of TNT explosive based on its selectively interaction with creatinine-capped CdSe/ZnS quantum dots.

    PubMed

    Carrillo-Carrión, Carolina; Simonet, Bartolomé M; Valcárcel, Miguel

    2013-08-20

    Here, a creatinine-modified CdSe/ZnS quantum dots fluorescent probe has been prepared and used for sensing 2,4,6,-trinitrotoluene explosive (TNT). The proposed method is based on the selective interaction between creatinine and nitroaromatic compounds according to the well-known Jaffé reaction. The procedure for the synthesis of creatinine-CdSe/ZnS reagent is very simple and reproducible and its fluorescent characteristics are reported. We found that the presence of TNT quenches the original fluorescence of creatinine-QD according to the Stern-Volmer model. Under the working conditions, the calibration plot of Io/I versus concentration of TNT was linear in the range 10-300μg L(-1) (R(2)=0.996). The mechanism interaction is discussed. The selectivity of fluorescence quenching of creatinine-QD for TNT has been evaluated. Finally, the potential application of the proposed methodology for the determination of TNT in spiked soils is demonstrated. For the analysis of soil samples a solid-liquid extraction is carried out and a four-point standard addition protocol is used to correct the matrix effect. The method, which is simple and rapid, allows the detection of 0.057μg g(-1) of TNT in soil samples. This sensor could be a useful tool for environmental studies, a crucial topic for nanotechnology nowadays.

  10. A model-based approach to determine the long-term effects of multiple interacting stressors on coral reefs.

    PubMed

    Blackwood, Julie C; Hastings, Alan; Mumby, Peter J

    2011-10-01

    The interaction between multiple stressors on Caribbean coral reefs, namely, fishing effort and hurricane impacts, is a key element in the future sustainability of reefs. We develop an analytic model of coral-algal interactions and explicitly consider grazing by herbivorous reef fish. Further, we consider changes in structural complexity, or rugosity, in addition to the direct impacts of hurricanes, which are implemented as stochastic jump processes. The model simulations consider various levels of fishing effort corresponding to' several hurricane frequencies and impact levels dependent on geographic location. We focus on relatively short time scales so we do not explicitly include changes in ocean temperature, chemistry, or sea level rise. The general features of our approach would, however, apply to these other stressors and to the management of other systems in the face of multiple stressors. It is determined that the appropriate management policy, either local reef restoration or fisheries management, greatly depends on hurricane frequency and impact level. For sufficiently low hurricane impact and macroalgal growth rate, our results indicate that regions with lower-frequency hurricanes require stricter fishing regulations, whereas management in regions with higher-frequency hurricanes might be less concerned with enhancing grazing and instead consider whether local-scale restorative activities to increase vertical structure are cost-effective.

  11. Two SERK Receptor-Like Kinases Interact with EMS1 to Control Anther Cell Fate Determination1[OPEN

    PubMed Central

    Wang, Yao; Ahsan, Nagib; Biener, Gabriel; Paprocki, Joel

    2017-01-01

    Cell signaling pathways mediated by leucine-rich repeat receptor-like kinases (LRR-RLKs) are essential for plant growth, development, and defense. The EMS1 (EXCESS MICROSPOROCYTES1) LRR-RLK and its small protein ligand TPD1 (TAPETUM DETERMINANT1) play a fundamental role in somatic and reproductive cell differentiation during early anther development in Arabidopsis (Arabidopsis thaliana). However, it is unclear whether other cell surface molecules serve as coregulators of EMS1. Here, we show that SERK1 (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1) and SERK2 LRR-RLKs act redundantly as coregulatory and physical partners of EMS1. The SERK1/2 genes function in the same genetic pathway as EMS1 in anther development. Bimolecular fluorescence complementation, Förster resonance energy transfer, and coimmunoprecipitation approaches revealed that SERK1 interacted biochemically with EMS1. Transphosphorylation of EMS1 by SERK1 enhances EMS1 kinase activity. Among 12 in vitro autophosphorylation and transphosphorylation sites identified by tandem mass spectrometry, seven of them were found to be critical for EMS1 autophosphorylation activity. Furthermore, complementation test results suggest that phosphorylation of EMS1 is required for its function in anther development. Collectively, these data provide genetic and biochemical evidence of the interaction and phosphorylation between SERK1/2 and EMS1 in anther development. PMID:27920157

  12. A turn-on fluorescence-sensing technique for glucose determination based on graphene oxide-DNA interaction.

    PubMed

    Zhang, Hao; Huang, Hui; Lin, Zihan; Su, Xingguang

    2014-11-01

    Graphene is a two-dimensional carbon nanomaterial one atom thick. Interactions between graphene oxide (GO) and ssDNA containing different numbers of bases have been proved to be remarkably different. In this paper we propose a novel approach for turn-on fluorescence sensing determination of glucose. Hydrogen peroxide (H2O2) is produced by glucose oxidase-catalysed oxidation of glucose. In the presence of ferrous iron (Fe(2+)) the hydroxyl radical (•OH) is generated from H2O2 by the Fenton reaction. This attacks FAM-labelled long ssDNA causing irreversible cleavage, as a result of the oxidative effect of •OH, producing an FAM-linked DNA fragment. Because of the weak interaction between GO and short FAM-linked DNA fragments, restoration of DNA fluorescence can be achieved by addition of glucose. Due to the excellent fluorescence quenching efficiency of GO and the specific catalysis of glucose oxidase, the sensitivity and selectivity of this method for GO-DNA sensing are extremely high. The linear range is from 0.5 to 10 μmol L(-1) and the detection limit for glucose is 0.1 μmol L(-1). The method has been successfully used for analysis of glucose in human serum.

  13. Delay-specific stimuli and genotype interact to determine temporal discounting in a rapid-acquisition procedure.

    PubMed

    Pope, Derek A; Newland, M Christopher; Hutsell, Blake A

    2015-05-01

    The importance of delay discounting to many socially important behavior problems has stimulated investigations of biological and environmental mechanisms responsible for variations in the form of the discount function. The extant experimental research, however, has yielded disparate results, raising important questions regarding Gene X Environment interactions. The present study determined the influence of stimuli that uniquely signal delays to reinforcement on delay discounting in two inbred mouse strains using a rapid-acquisition procedure. BALB/c and C57BL/6 mice responded under a six-component, concurrent-chained schedule in which the terminal-link delays preceding the larger-reinforcer were presented randomly across components of an individual session. Across conditions, components were presented either with or without delay-specific auditory stimuli, i.e., as multiple or mixed schedules. A generalized matching-based model was used to incorporate the impact of current and previous component reinforcer-delay ratios on current component response allocation. Sensitivity to reinforcer magnitude and delay were higher for BALB/c mice, but within-component preference reached final levels faster for C57Bl/6 mice. For BALB/c mice, acquisition of preference across blocks of a component was faster under the multiple than the mixed schedule, but final levels of sensitivity to reinforcement were unaffected by schedule. The speed of acquisition of preference was not different across schedules for C57Bl/6 mice, but sensitivity to reinforcement was higher under the multiple than the mixed schedule. Overall, differences in the acquisition and final form of the discount function were determined by a Gene X Environment interaction, but the presence of delay-specific stimuli attenuated genotype-dependent differences in magnitude and delay sensitivity.

  14. Membrane skeleton-bilayer interaction is not the major determinant of membrane phospholipid asymmetry in human erythrocytes.

    PubMed

    Gudi, S R; Kumar, A; Bhakuni, V; Gokhale, S M; Gupta, C M

    1990-03-30

    Transbilayer phospholipid distribution, membrane skeleton dissociation/association, and spectrin structure have been analysed in human erythrocytes after subjecting them to heating at 50 degrees C for 15 min. The membrane skeleton dissociation/association was determined by measuring the Tris-induced dissociation of Triton-insoluble membrane skeletons (Triton shells), the spectrin-actin extractability under low ionic conditions, and the binding of spectrin-actin with normal erythrocyte membrane inside-out vesicles (IOVs). The spectrin structure was ascertained by measuring the spectrin dimer-to-tetramer ratio as well as the spectrin tryptophan fluorescence. Both the Tris-induced Triton shell dissociation and the spectrin-actin extractability under low ionic conditions were considerably reduced by the heat treatment. Also, the binding of heated erythrocyte spectrin-actin to IOVs was significantly smaller than that observed with the normal cell spectrin-actin. Further, the quantity of spectrin dimers was appreciably increased in heat-treated erythrocytes as compared to the normal cells. This change in the spectrin dimer-to-tetramer ratio was accompanied by marked changes in the spectrin tryptophan fluorescence. In spite of these heat-induced alterations in structure and bilayer interactions of the membrane skeleton, the inside-outside glycerophospholipid distribution remained virtually unaffected in the heat-treated cells, as judged by employing bee venom and pancreatic phospholipase A2, fluorescamine and Merocyanine 540 as the external membrane probes. These results strongly indicate that membrane bilayer-skeleton interaction is not the major factor in determining the transbilayer phospholipid asymmetry in human erythrocyte membrane.

  15. When sad groups expect to meet again: interactive affective sharing and future interaction expectation as determinants of work groups' analytical and creative task performance.

    PubMed

    Klep, Annefloor H M; Wisse, Barbara; van der Flier, Henk

    2013-12-01

    The present study examines the moderating role of future interaction expectation in the relationship between affective sharing and work groups' task performance. We argue that group affect, a group defining characteristic, becomes more salient to its members when it is interactively shared, and that the anticipation of future interaction may strengthen the effects of group defining characteristics on subsequent group member behaviour. As a consequence, interactive sharing (vs. non-interactive sharing) of negative affect is more likely to influence work group outcomes when group members expect to meet again. Results from a laboratory experiment with 66 three-person work groups indeed show that interactively shared (vs. non-interactively shared) negative affect facilitated work groups' analytical task performance, whereas it inhibited performance on a creative fluency task when groups have expectations of future interaction and not when they do not have such expectations. The discussion focuses on how these results add to theory on group affect and contribute to insights in the effects of future interaction expectation.

  16. Determination of nicotine and its metabolites accumulated in fish tissue using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Chang, Yun-Wei; Nguyen, Hien P; Chang, Mike; Burket, S Rebekah; Brooks, Bryan W; Schug, Kevin A

    2015-07-01

    The determination of nicotine and its major metabolites (cotinine and anabasine) in fish tissue was performed using liquid chromatography and tandem mass spectrometry. Marine and freshwater fish were purchased from local grocery stores and were prepared based on a quick, easy, cheap, effective, rugged, and safe sample preparation protocol. To determine the highly polar compounds, hydrophilic interaction liquid chromatography was also used. There were modest suppressions on measured nicotine signals (10%) due to the matrix effects from marine fish but no obvious effects on freshwater fish signals. Method validation was incorporated with internal standards and carried out with matrix-matched calibration. The detection limits for nicotine, cotinine, and anabasine were 9.4, 3.0, and 1.5 ng/g in fish, respectively. Precision was quite acceptable returning less than 8% RSD at low, medium, and high concentrations. Acceptable and reproducible extraction recoveries (70-120%) of all three compounds were achieved, except for anabasine at low concentration (61%). The method was then applied to define nicotine bioaccumulation in a fathead minnow model, which resulted in rapid uptake with steady state internal tissue levels, reached within 12 h. This developed method offers a fast, easy, and sensitive way to evaluate nicotine and its metabolite residues in fish tissues.

  17. Supramolecular interaction of 18-crown-6 ether with mesalazine and spectrofluorimetric determination of mesalazine in pharmaceutical formulations.

    PubMed

    Elbashir, Abdalla A; Abdalla, Fatima Altayib Alasha; Aboul-Enein, Hassan Y

    2015-12-01

    The supramolecular interaction of protonated mesalazine (MSZ) and 18-crown-6 ether (18C6) has been examined by Ultraviolet-visible, FT-IR and fluorescence spectroscopy. The formation of the inclusion complex has been confirmed based on the changes of the spectral properties. The MSZ-18C6 host-guest complex formed in (1:1) stoichiometry and the inclusion constant (K = 1.411 × 10(2) L mol(-1)) was ascertained by the typical double reciprocal plots. Furthermore, the thermodynamic parameters (ΔG°, ΔH° and ΔS°) of (MSZ-18C6) were obtained. Based on the remarkable enhancement of the fluorescence intensity of MSZ produced through complex formation, a simple, accurate, rapid and highly sensitive spectrofluorometric method for the determination of MSZ in aqueous solution in the presence of 18C6 was developed. The measurement of relative fluorescence intensity was carried with excitation at 298 nm, emission 410 nm. All variables affecting the reactions were studied and optimized. Beer's law was obeyed in the concentration range of 0.1-0.9 µg/mL. The absorbance was found to increase linearly with increasing concentration of MSZ. The molar absorptivity, Sandell sensitivity, limit of detection (LOD) and limit of quantification (LOQ) were calculated. The validity of the described method was assessed, and the method was successfully applied to the determination of MSZ in its pharmaceutical formulation. In addition, a solid inclusion complex was synthesized by the coprecipitation method.

  18. Hydrophilic interaction liquid chromatography-solid phase extraction directly combined with protein precipitation for the determination of triptorelin in plasma.

    PubMed

    Wang, Jixia; Kong, Song; Yan, Jingyu; Jin, Gaowa; Guo, Zhimou; Shen, Aijin; Xu, Junyan; Zhang, Xiuli; Zou, Lijuan; Liang, Xinmiao

    2014-06-01

    Peptide drugs play a critical role in therapeutic treatment. However, as the complexity of plasma, determination of peptide drugs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a daunting task. To solve this problem, hydrophilic interaction liquid chromatography-solid phase extraction (HILIC-SPE) directly combined with protein precipitation (PPT) was developed for the selective extraction of triptorelin from plasma. The extracts were analyzed by reversed-phase liquid chromatography (RPLC). Proteins, phospholipids and highly polar interferences could be removed from plasma by the efficient combination of PPT, HILIC-SPE and RPLC-MS/MS. This method was evaluated by matrix effect, recovery and process efficiency at different concentration levels (50, 500 and 5,000 ng/mL) of triptorelin. Furthermore, the performance of HILIC-SPE was compared with that of reversed-phase C18 SPE and hydrophilic lipophilic balance (Oasis HLB) SPE. Among them, HILIC-SPE provided the minimum matrix effect (ranging from 96.02% to 103.41%), the maximum recovery (ranging from 80.68% to 90.54%) and the satisfactory process efficiency (ranging from 82.83% to 92.95%). The validated method was successfully applied to determine triptorelin in rat plasma.

  19. Surface Energy Determined by Inverse Gas Chromatography as a Tool to Investigate Particulate Interactions in Dry Powder Inhalers.

    PubMed

    Das, Shyamal C; Tucker, Ian G; Stewart, Peter J

    2015-01-01

    Dry powder inhalers (DPIs) usually contain drug particles <6 µm which agglomerate and/ or adhere on the surfaces of large carriers particles. The detachment of drug particles from carriers and de-agglomeration of drug particles into primary particles is essential for drug deposition in the deep lung. These processes are influenced by the surface energy of particles. Inverse gas chromatography (IGC) has been used to determine the surface energy of powder particles used in DPI to characterize materials and to understand aerosolization behaviour. Early studies used an infinite dilution technique to determine nonpolar surface energy and free energy of adsorption for polar interactions separately. Although some correlations were observed with the change in nonpolar surface energy before and after micronization, milling and storage, a lack of consistency in the change of free energy of adsorption was common. Moreover, a consistent relationship between complex de-agglomeration behaviour and surface energy has not been established and there are even some examples of negative correlation. In fact, nonpolar surface energy at infinite dilution is an incomplete representation of powder surface characteristics. The techniques for measuring polar surface energy, total surface energy and surface energy distribution have provided more revealing information about surface energetics of powders. Surface energy distributions determined by IGC or surface energy analyser have been successfully used to understand energetic heterogeneity of surfaces, characterize different polymorphs and understand changes due to micronization, structural relaxation, dry coating and storage. Efforts have been made to utilize surface energy distribution data to calculate powder strength distribution and to explain complex de-agglomeration behaviour of DPI formulations.

  20. Determinants and Outcomes of Decision-Making, Group Coordination and Social Interactions during a Foraging Experiment in a Wild Primate

    PubMed Central

    Pyritz, Lennart W.; Fichtel, Claudia; Huchard, Elise; Kappeler, Peter M.

    2013-01-01

    Social animals have to coordinate joint movements to maintain group cohesion, but the latter is often compromised by diverging individual interests. A widespread behavioral mechanism to achieve coordination relies on shared or unshared consensus decision-making. If consensus costs are high, group fission represents an alternative tactic. Exploring determinants and outcomes of spontaneous group decisions and coordination of free-ranging animals is methodologically challenging. We therefore conducted a foraging experiment with a group of wild redfronted lemurs (Eulemur rufifrons) to study decision outcomes, coordination of movements, individual foraging benefits and social interactions in response to the presentation of drinking platforms with varying baiting patterns. Behavioral observations were complemented with data from recordings of motion detector cameras installed at the platforms. The animal's behavior in the experimental conditions was compared to natural group movements. We could not determine the type of consensus decision-making because the group visited platforms randomly. The group fissioned during 23.3% of platform visits, and fissioning resulted in more individuals drinking simultaneously. As under natural conditions, adult females initiated most group movements, but overtaking by individuals of different age and sex classes occurred in 67% of movements to platforms, compared to only 18% during other movements. As a result, individual resource intake at the platforms did not depend on departure position, age or sex, but on arrival order. Aggression at the platforms did not affect resource intake, presumably due to low supplanting rates. Our findings highlight the diversity of coordination processes and related consequences for individual foraging benefits in a primate group living under natural conditions. PMID:23326392

  1. Characterization of CD4 glycoprotein determinant-HIV envelope protein interactions: perspectives for analog and vaccine development.

    PubMed

    Farrar, W L; Harel-Bellan, A; Ferris, D K

    1988-01-01

    The CD4 surface determinant, previously associated as a phenotypic marker for helper/inducer subsets of T lymphocytes, has now been critically identified as the binding/entry protein for human immunodeficiency viruses (HIV). The human CD4 molecule is readily detectable on monocytes, T lymphocytes, and brain tissues. Soluble HIV (HTLV IIIB) envelope protein (gp120) binds native or recombinant CD4 with equal affinity estimated to be 4 to 8 nM kDa. All human tissue sources of CD4 bind radiolabeled gp120 to the same relative degree; however, the murine homologous protein, L3T4, does not bind the HIV envelope protein. Lack of sufficient recognition by the recombinant L3T4 molecule suggests divergence in the gp120-binding epitope. The binding of gp120 to CD4 is dependent upon intact sulfhydryl bonds within cysteine residues and glycosylation. Deglycosylated native gp120 is unable to bind CD4 under physiological conditions. Recombinant deglycosylated fragments cannot bind to the CD4 receptor, although they serve as immunogen for neutralizing antibody development. A number of synthetic peptides to putative critical domains of gp120 have been studied for their antagonism of native gp120 binding. Peptide T analogs or synthetic cogeners of Neuroleukin proposed to bind the CD4 determinant involved in gp120 binding had no competitive displacement of native gp120 binding as assessed by two independent methods that measure gp120 interaction with CD4. Recombinant C-terminal fragments, also containing other putative domains, did not displace native gp120 from CD4. Glycosylation appears to be critical in the maintenance of the structure of the binding domain of gp120. Native gp120 binding to CD4 is sufficient for the activation of cellular metabolism that alters target cell gene expression and differentiation, suggesting that the virus binding contributes to the activation of the host cell.

  2. Determinants and outcomes of decision-making, group coordination and social interactions during a foraging experiment in a wild primate.

    PubMed

    Pyritz, Lennart W; Fichtel, Claudia; Huchard, Elise; Kappeler, Peter M

    2013-01-01

    Social animals have to coordinate joint movements to maintain group cohesion, but the latter is often compromised by diverging individual interests. A widespread behavioral mechanism to achieve coordination relies on shared or unshared consensus decision-making. If consensus costs are high, group fission represents an alternative tactic. Exploring determinants and outcomes of spontaneous group decisions and coordination of free-ranging animals is methodologically challenging. We therefore conducted a foraging experiment with a group of wild redfronted lemurs (Eulemur rufifrons) to study decision outcomes, coordination of movements, individual foraging benefits and social interactions in response to the presentation of drinking platforms with varying baiting patterns. Behavioral observations were complemented with data from recordings of motion detector cameras installed at the platforms. The animal's behavior in the experimental conditions was compared to natural group movements. We could not determine the type of consensus decision-making because the group visited platforms randomly. The group fissioned during 23.3% of platform visits, and fissioning resulted in more individuals drinking simultaneously. As under natural conditions, adult females initiated most group movements, but overtaking by individuals of different age and sex classes occurred in 67% of movements to platforms, compared to only 18% during other movements. As a result, individual resource intake at the platforms did not depend on departure position, age or sex, but on arrival order. Aggression at the platforms did not affect resource intake, presumably due to low supplanting rates. Our findings highlight the diversity of coordination processes and related consequences for individual foraging benefits in a primate group living under natural conditions.

  3. Non-Linear Interactions Determine the Impact of Sea-Level Rise on Estuarine Benthic Biodiversity and Ecosystem Processes

    PubMed Central

    Yamanaka, Tsuyuko; Raffaelli, David; White, Piran C. L.

    2013-01-01

    Sea-level rise induced by climate change may have significant impacts on the ecosystem functions and ecosystem services provided by intertidal sediment ecosystems. Accelerated sea-level rise is expected to lead to steeper beach slopes, coarser particle sizes and increased wave exposure, with consequent impacts on intertidal ecosystems. We examined the relationships between abundance, biomass, and community metabolism of benthic fauna with beach slope, particle size and exposure, using samples across a range of conditions from three different locations in the UK, to determine the significance of sediment particle size beach slope and wave exposure in affecting benthic fauna and ecosystem function in different ecological contexts. Our results show that abundance, biomass and oxygen consumption of intertidal macrofauna and meiofauna are affected significantly by interactions among sediment particle size, beach slope and wave exposure. For macrofauna on less sloping beaches, the effect of these physical constraints is mediated by the local context, although for meiofauna and for macrofauna on intermediate and steeper beaches, the effects of physical constraints dominate. Steeper beach slopes, coarser particle sizes and increased wave exposure generally result in decreases in abundance, biomass and oxygen consumption, but these relationships are complex and non-linear. Sea-level rise is likely to lead to changes in ecosystem structure with generally negative impacts on ecosystem functions and ecosystem services. However, the impacts of sea-level rise will also be affected by local ecological context, especially for less sloping beaches. PMID:23861863

  4. Non-linear interactions determine the impact of sea-level rise on estuarine benthic biodiversity and ecosystem processes.

    PubMed

    Yamanaka, Tsuyuko; Raffaelli, David; White, Piran C L

    2013-01-01

    Sea-level rise induced by climate change may have significant impacts on the ecosystem functions and ecosystem services provided by intertidal sediment ecosystems. Accelerated sea-level rise is expected to lead to steeper beach slopes, coarser particle sizes and increased wave exposure, with consequent impacts on intertidal ecosystems. We examined the relationships between abundance, biomass, and community metabolism of benthic fauna with beach slope, particle size and exposure, using samples across a range of conditions from three different locations in the UK, to determine the significance of sediment particle size beach slope and wave exposure in affecting benthic fauna and ecosystem function in different ecological contexts. Our results show that abundance, biomass and oxygen consumption of intertidal macrofauna and meiofauna are affected significantly by interactions among sediment particle size, beach slope and wave exposure. For macrofauna on less sloping beaches, the effect of these physical constraints is mediated by the local context, although for meiofauna and for macrofauna on intermediate and steeper beaches, the effects of physical constraints dominate. Steeper beach slopes, coarser particle sizes and increased wave exposure generally result in decreases in abundance, biomass and oxygen consumption, but these relationships are complex and non-linear. Sea-level rise is likely to lead to changes in ecosystem structure with generally negative impacts on ecosystem functions and ecosystem services. However, the impacts of sea-level rise will also be affected by local ecological context, especially for less sloping beaches.

  5. Bottom-up determination of soil collembola diversity and population dynamics in response to interactive climatic factors.

    PubMed

    A'Bear, A Donald; Boddy, Lynne; Jones, T Hefin

    2013-11-01

    Soil invertebrate contributions to decomposition are climate dependent. Understanding the influence of abiotic factors on soil invertebrate population dynamics will strengthen predictions regarding ecosystem functioning under climate change. As well as being important secondary decomposers, mycophagous collembola exert a strong influence on the growth and activity of primary decomposers, particularly fungi. Species-specific grazing preferences for different fungi enable fungal community composition to influence the direct impacts of climate change on collembola populations. We investigate the interactive roles of altered abiotic conditions (warming, wetting and drying) and the identity of the dominant decomposer fungus in determining collembola community dynamics in woodland soil mesocosms. The bottom-up influence of the dominant component of the fungal resource base was an important mediator of the direct climatic impacts on collembola populations. The positive influences of warming and wetting, and the negative influence of drying, on collembola abundance and diversity were much less pronounced in fungal-inoculation treatments, in which populations were reduced compared with uninoculated mesocosms. We conclude that the thick, sclerotised cords of the competitively dominant decomposer fungi reduced the biomass of smaller, more palatable soil fungi, limiting the size of collembola populations and their ability to respond to altered abiotic conditions.

  6. Determination of aminoglycoside residues in kidney and honey samples by hydrophilic interaction chromatography-tandem mass spectrometry.

    PubMed

    Kumar, Praveen; Rúbies, Antoni; Companyó, Ramon; Centrich, Francesc

    2012-10-01

    Two methods based on liquid chromatography-tandem mass spectrometry were developed for the determination of ten aminoglycosides (streptomycin, dihydrostreptomycin, spectinomycin, apramycin, paromomycin, kanamycin A, gentamycin C1, gentamycin C2/C2a, gentamycin C1a, and neomycin B) in kidney samples from food-producing animals and in honey samples. The methods involved extraction with an aqueous solution (for the kidney samples) or sample dissolution in water (for the honey samples), solid-phase extraction with a weak cation exchange cartridge and injection of the eluate into a liquid chromatography-tandem mass spectrometry system. A zwitterionic hydrophilic interaction chromatography column was used for separation of aminoglycosides and a triple quadrupole mass analyzer was used for detection. The methods were validated according to Decision 2002/657/EC. The limits of quantitation ranged from 2 to 125 μg/kg in honey and 25 to 264 μg/kg in the kidney samples. Interday precision (RSD%) ranged from 6 to 26% in honey and 2 to 21% in kidney. Trueness, expressed as the percentage of error, ranged from 7 to 20% in honey and 1 to 11% in kidney.

  7. Path integral Monte Carlo determination of the fourth-order virial coefficient for unitary two-component Fermi gas with zero-range interactions

    NASA Astrophysics Data System (ADS)

    Yan, Yangqian; Blume, D.

    2016-05-01

    The unitary equal-mass Fermi gas with zero-range interactions constitutes a paradigmatic model system that is relevant to atomic, condensed matter, nuclear, particle, and astro physics. This work determines the fourth-order virial coefficient b4 of such a strongly-interacting Fermi gas using a customized ab inito path integral Monte Carlo (PIMC) algorithm. In contrast to earlier theoretical results, which disagreed on the sign and magnitude of b4, our b4 agrees with the experimentally determined value, thereby resolving an ongoing literature debate. Utilizing a trap regulator, our PIMC approach determines the fourth-order virial coefficient by directly sampling the partition function. An on-the-fly anti-symmetrization avoids the Thomas collapse and, combined with the use of the exact two-body zero-range propagator, establishes an efficient general means to treat small Fermi systems with zero-range interactions. We gratefully acknowledge support by the NSF.

  8. Path-Integral Monte Carlo Determination of the Fourth-Order Virial Coefficient for a Unitary Two-Component Fermi Gas with Zero-Range Interactions

    NASA Astrophysics Data System (ADS)

    Yan, Yangqian; Blume, D.

    2016-06-01

    The unitary equal-mass Fermi gas with zero-range interactions constitutes a paradigmatic model system that is relevant to atomic, condensed matter, nuclear, particle, and astrophysics. This work determines the fourth-order virial coefficient b4 of such a strongly interacting Fermi gas using a customized ab initio path-integral Monte Carlo (PIMC) algorithm. In contrast to earlier theoretical results, which disagreed on the sign and magnitude of b4 , our b4 agrees within error bars with the experimentally determined value, thereby resolving an ongoing literature debate. Utilizing a trap regulator, our PIMC approach determines the fourth-order virial coefficient by directly sampling the partition function. An on-the-fly antisymmetrization avoids the Thomas collapse and, combined with the use of the exact two-body zero-range propagator, establishes an efficient general means to treat small Fermi systems with zero-range interactions.

  9. Foraging modality and plasticity in foraging traits determine the strength of competitive interactions among carnivorous plants, spiders and toads.

    PubMed

    Jennings, David E; Krupa, James J; Rohr, Jason R

    2016-07-01

    Foraging modalities (e.g. passive, sit-and-wait, active) and traits are plastic in some species, but the extent to which this plasticity affects interspecific competition remains unclear. Using a long-term laboratory mesocosm experiment, we quantified competition strength and the plasticity of foraging traits in a guild of generalist predators of arthropods with a range of foraging modalities. Each mesocosm contained eight passively foraging pink sundews, and we employed an experimental design where treatments were the presence or absence of a sit-and-wait foraging spider and actively foraging toad crossed with five levels of prey abundance. We hypothesized that actively foraging toads would outcompete the other species at low prey abundance, but that spiders and sundews would exhibit plasticity in foraging traits to compensate for strong competition when prey were limited. Results generally supported our hypotheses. Toads had a greater effect on sundews at low prey abundances, and toad presence caused spiders to locate webs higher above the ground. Additionally, the closer large spider webs were to the ground, the greater the trichome densities produced by sundews. Also, spider webs were larger with than without toads and as sundew numbers increased, and these effects were more prominent as resources became limited. Finally, spiders negatively affected toad growth only at low prey abundance. These findings highlight the long-term importance of foraging modality and plasticity of foraging traits in determining the strength of competition within and across taxonomic kingdoms. Future research should assess whether plasticity in foraging traits helps to maintain coexistence within this guild and whether foraging modality can be used as a trait to reliably predict the strength of competitive interactions.

  10. LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype Determinants Fezf2 and Sox11

    PubMed Central

    Muralidharan, Bhavana; Khatri, Zeba; Maheshwari, Upasana; Gupta, Ritika; Roy, Basabdatta; Pradhan, Saurabh J.; Karmodiya, Krishanpal; Padmanabhan, Hari; Shetty, Ashwin S.; Balaji, Chinthapalli; Kolthur-Seetharam, Ullas; Macklis, Jeffrey D.; Galande, Sanjeev

    2017-01-01

    In the developing cerebral cortex, sequential transcriptional programs take neuroepithelial cells from proliferating progenitors to differentiated neurons with unique molecular identities. The regulatory changes that occur in the chromatin of the progenitors are not well understood. During deep layer neurogenesis, we show that transcription factor LHX2 binds to distal regulatory elements of Fezf2 and Sox11, critical determinants of neuron subtype identity in the mouse neocortex. We demonstrate that LHX2 binds to the nucleosome remodeling and histone deacetylase histone remodeling complex subunits LSD1, HDAC2, and RBBP4, which are proximal regulators of the epigenetic state of chromatin. When LHX2 is absent, active histone marks at the Fezf2 and Sox11 loci are increased. Loss of LHX2 produces an increase, and overexpression of LHX2 causes a decrease, in layer 5 Fezf2 and CTIP2-expressing neurons. Our results provide mechanistic insight into how LHX2 acts as a necessary and sufficient regulator of genes that control cortical neuronal subtype identity. SIGNIFICANCE STATEMENT The functional complexity of the cerebral cortex arises from an array of distinct neuronal subtypes with unique connectivity patterns that are produced from common progenitors. This study reveals that transcription factor LHX2 regulates the numbers of specific cortical output neuron subtypes by controlling the genes that are required to produce them. Loss or increase in LHX2 during neurogenesis is sufficient to increase or decrease, respectively, a particular subcerebrally projecting population. Mechanistically, LHX2 interacts with chromatin modifying protein complexes to edit the chromatin landscape of its targets Fezf2 and Sox11, which regulates their expression and consequently the identities of the neurons produced. Thus, LHX2 is a key component of the control network for producing neurons that will participate in cortical circuitry. PMID:28053041

  11. Land-use history, historical connectivity, and land management interact to determine longleaf pine woodland understory richness and composition.

    SciTech Connect

    Brudvig, Lars A.; Damschen, Ellen L.

    2010-08-13

    Restoration and management activities targeted at recovering biodiversity can lead to unexpected results. In part, this is due to a lack of understanding of how site-level characteristics, landscape factors, and land-use history interact with restoration and management practices to determine patterns of diversity. For plants, such factors may be particularly important since plant populations often exhibit lagged responses to habitat loss and degradation. Here, we assess the importance of site-level, landscape, and historical effects for understory plant species richness and composition across a set of 40 longleaf pine Pinus palustris woodlands undergoing restoration for the federally endangered red-cockaded woodpecker in the southeastern United States. Land-use history had an overarching effect on richness and composition. Relative to historically forested sites, sites with agricultural histories (i.e. former pastures or cultivated fields) supported lower species richness and an altered species composition due to fewer upland longleaf pine woodland community members. Landscape effects did not influence the total number of species in either historically forested or post-agricultural sites; however, understory species composition was affected by historical connectivity, but only for post-agricultural sites. The influences of management and restoration activities were only apparent once land-use history was accounted for. Prescribed burning and mechanical overstory thinning were key drivers of understory composition and promoted understory richness in post-agricultural sites. In historically forested sites these activities had no impact on richness and only prescribed fire influenced composition. Our findings reveal complex interplays between site-level, landscape, and historical effects, suggest fundamentally different controls over plant communities in longleaf pine woodlands with varying land-use history, and underscore the importance of considering land

  12. [Determination of melamine residue in raw milk and dairy products using hydrophilic interaction chromatography-electrospray ionization tandem mass spectrometry].

    PubMed

    Yan, Lijuan; Wu, Min; Zhang, Zhigang; Zhou, Yu; Lin, Liyi; Fang, Enhua; Xu, Dunming; Chen, Luping

    2008-11-01

    A method for the determination of melamine residue in raw milk and dairy products was developed using hydrophilic interaction chromatography-electrospray ionization tandem mass spectrometry (HILIC-ESI-MS/MS). The melamine residue in the test sample was extracted with 1% trichloroacetic acid-acetonitrile (1 : 1, v/v) solution. The homogenate was centrifuged and the supernatant was collected. The extract was cleaned up using a mixed-mode cation exchange (MCX) solid-phase extraction cartridge and then concentrated, and analyzed by HILIC-ESI-MS/MS. The gradient chromatographic separation was performed using a hydrophilic silica column (250 mm x 4.6 mm, 5 microm) with 10 mmol/L ammonium acetate buffer (pH 3.0) and acetonitrile as the mobile phases. Due to its hydrophilic property, melamine was well retained on the column and seperated from other compounds. It effectively reduced matrix effect. A triple quadruple mass spectrometer equipped with an electrospray ionization source was employed for the qualitative and quantitative measurement of melamine. The melamine was quantified using the fragments produced from the protonated melamine ion through multiple reaction monitoring (MRM) in positive ion mode. Two MRM transitions from the protonated melamine ion (m/z 127 --> 85 and m/z 127 --> 68) were monitored. The average recoveries were between 76.3% and 98.7% in the spiked range of 0.5 to 10 mg/kg in raw milk and dairy products, and the relative standard deviations were less than 6.8%. The linear range was from 0.05 to 10.0 mg/L. The limit of quantification (S/N > 10) was 0.05 mg/kg. The method is highly selective and sensitive for the measurements of melamine and adequate for the analysis of melamine in raw milk and dairy products.

  13. Hydrophilic interaction liquid chromatography coupled to high-resolution mass spectrometry to determine artificial sweeteners in environmental waters.

    PubMed

    Salas, Daniela; Borrull, Francesc; Fontanals, Núria; Marcé, Rosa Maria

    2015-06-01

    Artificial sweeteners are food additives employed as sugar substitutes which are now considered to be emerging organic contaminants. In the present study, a method is developed for the determination of a group of artificial sweeteners in environmental waters. Considering the polar and hydrophilic character of these compounds, hydrophilic interaction liquid chromatography is proposed for their separation as an alternative to traditional reversed-phase liquid chromatography. Two stationary phases with different chemistry were compared for this purpose. For the detection of the analytes, high-resolution mass spectrometry (Orbitrap) was employed to take advantage of its benefits in terms of reliable quantification and confirmation for the measurement of accurate masses. Solid-phase extraction was chosen as the sample treatment, in which the extract in a mixture of NH4OH:MeOH:ACN (1:4:15) was directly injected into the chromatographic system, simplifying the analytical procedure. The optimized method was validated on river and waste water samples. For example, in the case of effluent water samples, limits of detection ranged from 0.002 to 0.7 μg/L and limits of quantification ranged from 0.004 to 1.5 μg/L. Apparent (whole method) recoveries ranged from 57 to 74% with intra-day precision (%RSD, n = 5) ranging from 6 to 25%. The method was successfully applied to water samples from different rivers in Catalonia and different waste water treatment plants in Tarragona. Acesulfame, cyclamate, saccharine and sucralose were found in several samples.

  14. Interaction of cosmic ray muons with spent nuclear fuel dry casks and determination of lower detection limit

    NASA Astrophysics Data System (ADS)

    Chatzidakis, S.; Choi, C. K.; Tsoukalas, L. H.

    2016-08-01

    The potential non-proliferation monitoring of spent nuclear fuel sealed in dry casks interacting continuously with the naturally generated cosmic ray muons is investigated. Treatments on the muon RMS scattering angle by Moliere, Rossi-Greisen, Highland and, Lynch-Dahl were analyzed and compared with simplified Monte Carlo simulations. The Lynch-Dahl expression has the lowest error and appears to be appropriate when performing conceptual calculations for high-Z, thick targets such as dry casks. The GEANT4 Monte Carlo code was used to simulate dry casks with various fuel loadings and scattering variance estimates for each case were obtained. The scattering variance estimation was shown to be unbiased and using Chebyshev's inequality, it was found that 106 muons will provide estimates of the scattering variances that are within 1% of the true value at a 99% confidence level. These estimates were used as reference values to calculate scattering distributions and evaluate the asymptotic behavior for small variations on fuel loading. It is shown that the scattering distributions between a fully loaded dry cask and one with a fuel assembly missing initially overlap significantly but their distance eventually increases with increasing number of muons. One missing fuel assembly can be distinguished from a fully loaded cask with a small overlapping between the distributions which is the case of 100,000 muons. This indicates that the removal of a standard fuel assembly can be identified using muons providing that enough muons are collected. A Bayesian algorithm was developed to classify dry casks and provide a decision rule that minimizes the risk of making an incorrect decision. The algorithm performance was evaluated and the lower detection limit was determined.

  15. Determination of partial unfolding enthalpy for lysozyme upon interaction with dodecyltrimethylammonium bromide using an extended solvation model.

    PubMed

    Behbehani, G Rezaei; Saboury, A A; Taleshi, E

    2008-01-01

    The interactions of dodecyltrimethylammonium bromides (DTABs) with hen egg lysozyme have been investigated at pH = 7.0 and 27 degrees C in phosphate buffer by isothermal titration calorimetry. DTAB interacts endothermically and activate lysozyme. The endothermicity of the lysozyme-DTAB interaction is in marked contrast to the exothermic interactions between sodium dodecyl sulphate (SDS) and lysozyme which have been attributed to specific binding between the anionic sulphate head groups and cationic amino acid residues. The enthalpies of interaction between the cationic surfactant (DTAB) and lysozyme are dominated by the endothermic unfolding of the native structure followed by an exothermic solvation of the lysozyme-DTAB complex by the addition of extra DTAB. A new direct calorimetric method to follow protein denaturation, and the effect of surfactants on the stability of proteins was introduced. The extended solvation model was used to reproduce the enthalpies of lysozyme-DTAB interaction over the whole range of DTAB concentrations. The solvation parameters recovered from the new equation, attributed to the structural change of lysozyme and its biological activity. At low concentrations of DTAB, the binding is mainly electrostatic, with some simultaneous interaction of the hydrophobic tail with nearby hydrophobic patches on the lysozyme. These initial interactions presumably cause some protein unfolding and expose additional hydrophobic sites. The DTAB-induced denaturation enthalpy of lysozyme is 86.46 +/- 0.02 kJ mol(-1).

  16. Multivalent interactions of the SUMO-interaction motifs in RING finger protein 4 determine the specificity for chains of the SUMO.

    PubMed

    Keusekotten, Kirstin; Bade, Veronika N; Meyer-Teschendorf, Katrin; Sriramachandran, Annie Miriam; Fischer-Schrader, Katrin; Krause, Anke; Horst, Christiane; Schwarz, Günter; Hofmann, Kay; Dohmen, R Jürgen; Praefcke, Gerrit J K

    2014-01-01

    RNF4 (RING finger protein 4) is a STUbL [SUMO (small ubiquitin-related modifier)-targeted ubiquitin ligase] controlling PML (promyelocytic leukaemia) nuclear bodies, DNA double strand break repair and other nuclear functions. In the present paper, we describe that the sequence and spacing of the SIMs (SUMO-interaction motifs) in RNF4 regulate the avidity-driven recognition of substrate proteins carrying SUMO chains of variable length.

  17. Prevalence, Specificity and Determinants of Lipid-Interacting PDZ Domains from an In-Cell Screen and In Vitro Binding Experiments

    PubMed Central

    Kashyap, Rudra; Polanowska, Jolanta; Betzi, Stéphane; Lembo, Frédérique; Vermeiren, Elke; Chiheb, Driss; Lenfant, Nicolas; Morelli, Xavier; Borg, Jean-Paul; Reboul, Jérôme; Zimmermann, Pascale

    2013-01-01

    Background PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited. Methodology/Principal Findings We screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands. Conclusions/Significance Our screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands. PMID:23390500

  18. Pharmacokinetic drug–drug interactions between 1,4-dihydropyridine calcium channel blockers and statins: factors determining interaction strength and relevant clinical risk management

    PubMed Central

    Zhou, Yi-Ting; Yu, Lu-Shan; Zeng, Su; Huang, Yu-Wen; Xu, Hui-Min; Zhou, Quan

    2014-01-01

    Background Coadministration of 1,4-dihydropyridine calcium channel blockers (DHP-CCBs) with statins (or 3-hydroxy-3-methylglutaryl-coenzyme A [HMG-CoA] reductase inhibitors) is common for patients with hypercholesterolemia and hypertension. To reduce the risk of myopathy, in 2011, the US Food and Drug Administration (FDA) Drug Safety Communication set a new dose limitation for simvastatin, for patients taking simvastatin concomitantly with amlodipine. However, there is no such dose limitation for atorvastatin for patients receiving amlodipine. The combination pill formulation of amlodipine/atorvastatin is available on the market. There been no systematic review of the pharmacokinetic drug–drug interaction (DDI) profile of DHP-CCBs with statins, the underlying mechanisms for DDIs of different degree, or the corresponding management of clinical risk. Methods The relevant literature was identified by performing a PubMed search, covering the period from January 1987 to September 2013. Studies in the field of drug metabolism and pharmacokinetics that described DDIs between DHP-CCB and statin or that directly compared the degree of DDIs associated with cytochrome P450 (CYP)3A4-metabolized statins or DHP-CCBs were included. The full text of each article was critically reviewed, and data interpretation was performed. Results There were three circumstances related to pharmacokinetic DDIs in the combined use of DHP-CCB and statin: 1) statin is comedicated as the precipitant drug (pravastatin–nimodipine and lovastatin–nicardipine); 2) statin is comedicated as the object drug (isradipine–lovastatin, lacidipine–simvastatin, amlodipine–simvastatin, benidipine-simvastatin, azelnidipine– simvastatin, lercanidipine–simvastatin, and amlodipine–atorvastatin); and 3) mutual interactions (lercanidipine–fluvastatin). Simvastatin has an extensive first-pass effect in the intestinal wall, whereas atorvastatin has a smaller intestinal first-pass effect. The interaction

  19. INTERACTION OF LASER RADIATION WITH MATTER: Absorption of a femtosecond laser pulse by metals and the possibility of determining effective electron—electron collision frequencies

    NASA Astrophysics Data System (ADS)

    Isakov, Vladimir A.; Kanavin, Andrey P.; Uryupin, Sergey A.

    2006-10-01

    A method is proposed for describing absorption of an electron-heating femtosecond laser pulse that interacts with a metal under conditions of high-frequency skin effect. It is shown that the effective frequencies of electron—electron collisions accompanied by umklapp processes can be determined by measuring the absorption or reflection coefficients of a femtosecond pulse.

  20. Interactive Whiteboard Technologies in High School: A Comparison of Their Impact on the Levels of Measure That Determine a Return on Investment

    ERIC Educational Resources Information Center

    Schipper, Joseph M.; Yocum, Russell G.

    2016-01-01

    This quantitative, quasi-experimental, nonequivalent group study examined the impact on levels of measure that determine a return on investment of differing forms of interactive whiteboard (IWB) technology used at a high school in a suburban school district in southeastern Virginia. Three forms of IWB were compared: a full-screen IWB, a mobile…

  1. Simultaneous determination of four local anesthetics by CE with ECL and study on interaction between procainamide and human serum albumin.

    PubMed

    Duan, Hong-Bing; Cao, Jun-Tao; Yang, Jiu-Jun; Wang, Hui; Liu, Yan-Ming

    2016-07-01

    A new method of capillary electrophoresis (CE) coupled with tris(2, 2'-bipyridyl) ruthenium(II) electrochemiluminescence (ECL) detection has been developed to detect four local anesthetics procainamide (PAH), tetracaine (TCH), proparacaine (PCH) and cinchocaine (CIN) simultaneously. An europium (III)-doped prussian blue analogue film (Eu-PB) modified platinum electrode was prepared and applied to improve the detection sensitivity. The parameters including additives, concentration and pH of the running buffer, separation voltage and detection potential that affect CE separation and ECL detection were optimized in detail. The four local anesthetics were baseline separated and detected within 10min under the optimized conditions. The detection limits (LOD) of PAH, TCH, PCH and CIN are 5.5×10(-8), 9.6×10(-8), 2.5×10(-8) and 3.5×10(-8)molL(-1) (S/N=3), respectively. RSDs of the migration time for four analytes range from 1.2% to 2.5% within intraday and from 2.4% to 4.9% in interday, RSDs of the peak area for four analytes are from 1.7% to 3.3% within intraday and from 2.2% to 5.6% in interday, respectively. The limits of quantitation (LOQ) (S/N=10) for PAH, TCH, PCH and CIN in human urine sample are 5.9×10(-7), 9.2×10(-7), 8.3×10(-7) and 5.0×10(-7)molL(-1), separately. The recoveries (n=3) of four analytes in human urine are from 87.6% to 107.7% with less than 5.9% in RSDs. The developed method was used to determine four local anesthetics in human urine samples and investigate the interaction between PAH and human serum albumin (HSA). The number of binding sites and the binding constant of PAH with HSA were calculated to be 1.03 and 2.4×10(4)Lmol(-1), respectively.

  2. Simultaneous determination of erlotinib and tamoxifen in rat plasma using UPLC-MS/MS: Application to pharmacokinetic interaction studies.

    PubMed

    Maher, Hadir M; Alzoman, Nourah Z; Shehata, Shereen M

    2016-08-15

    Tamoxifen (TAM) is a non-steroidal estrogen receptor antagonist that enhances erlotinib (ERL)-induced cytotoxicity in the treatment of NSCLC. ERL and TAM are metabolized by CYP3A4 enzymes. In addition, both drugs have the potential of altering the enzymatic activity through either inhibition (ERL) or induction (TAM). Thus it was expected that pharmacokinetics (PK) drug-drug interactions (DDIs) could be encountered following their co-administration. In this respect, a bioanalytical UPLC-MS/MS method has been developed and validated for the simultaneous determination of ERL and TAM in rat plasma samples, using ondansetron (OND) as an internal standard (IS). Plasma samples were prepared using mixed mode cationic solid phase extraction (SPE) STRATA™ -X-C 33μm cartridges with good extraction recovery of both drugs from rat plasma (Er% from -13.92 to -3.32). The drugs were separated on a Waters BEH™ C18 column with an isocratic elution using a mobile phase composed of a mixture of acetonitrile and water, each with 0.15% formic acid, in the ratio of 80: 20, v/v. Quantitation was carried out using the positive ionization mode with multiple reaction monitoring (MRM) at m/z 394.20>278.04 (ERL), m/z 372.25>72.01 (TAM), and m/z 294.18>170.16 (OND). The method was fully validated as per the FDA guidelines over the concentration range of 0.2-50ng/mL with very low lower limit of quantification (LLOQ) of 0.2ng/mL for both ERL and TAM. The intra- and inter-day assay precision (in terms of relative standard deviation, RSD) and accuracy (in terms of percentage relative error, % Er) were evaluated for both drugs and the calculated values evaluated at four different concentration levels were within the acceptable limits (<15%) for concentrations other than LLOQ and 20% for LLOQ. The method was successfully applied to the study of possible PK-DDI following the oral administration of ERL and TAM in a combination, compared to their single administration.

  3. Simultaneous determination of gastrodin and puerarin in rat plasma by HPLC and the application to their interaction on pharmacokinetics.

    PubMed

    Jiang, Li; Dai, Jundong; Huang, Zhenlin; Du, Qinghua; Lin, Jiahao; Wang, Yurong

    2013-02-01

    Gastrodin (Gas) and puerarin (Pur) are bioactive substances derived from traditional Chinese medicine Gastrodia elata and Radix Puerariae, respectively, which were often used together in Chinese clinical prescriptions. Their injections were used in combined way for treatment of some cardiocerebrovascular diseases in clinic, especially for vertigo due to vertebrobasilar ischemia. In this paper, interaction of gastrodin and puerarin in rat plasma pharmacokinetics via intragastic (i.g.)/intravenous (i.v.) administration was investigated. A reliable HPLC method was developed for simultaneous determination of Gas and Pur in rat plasma with a linear range of 0.101-101 μg/mL for Gas and 0.0500-5.98 μg/mL for Pur (r(2)>0.993). The LLOQ, LOD of Gas and Pur were determined to be 0.101, 0.0486 μg/mL, and 0.05, 0.0245 μg/mL, respectively. The intra-day and inter-day precision were all less than 12.0%, whilst the accuracy were all within 96.4±6.00%. The proposed method has been successfully applied to the pharmacokinetic study of the analytes in rats after i.g./i.v. administration of Gas and Pur alone or combined with each other (i.g.: 40 mg/kg Gas, 400 mg/kg Pur; i.v.: 20 mg/kg Gas, 20 mg/kg Pur). Blood samples were collected from retinal vein plexus of rats at predetermined time points and plasma containing the internal standard tyrosol (IS) were precipitated by methanol and chromatography was carried out on a C(18) column with a gradient mobile phase of ACN-H(2)O with 0.05% phosphoric acid as a modifier. The pharmacokinetic profiles of combined administration were found to be distinct from those of given alone. The C(max), T(max), T(1/2), MRT of Gas administrated alone or combined with Pur via i.g. were 21.7 μg/mL, 0.250 h, 2.81 h, 0.830 h and 18.4 μg/mL, 0.550 h, 0.970 h, 1.37 h, respectively, of Pur administrated alone or combined with Gas via i.g. were 0.490 μg/mL, 1.95 h, 1.33 h, 2.10 h and 2.01 μg/mL, 0.570 h, 4.00 h, 5.10 h, respectively. The relative oral

  4. Real-time non-invasive eyetracking and gaze-point determination for human-computer interaction and biomedicine

    NASA Technical Reports Server (NTRS)

    Talukder, Ashit; Morookian, John-Michael; Monacos, S.; Lam, R.; Lebaw, C.; Bond, A.

    2004-01-01

    Eyetracking is one of the latest technologies that has shown potential in several areas including human-computer interaction for people with and without disabilities, and for noninvasive monitoring, detection, and even diagnosis of physiological and neurological problems in individuals.

  5. Role of Dispersive Interactions in Determining Structural Properties of Organic-Inorganic Halide Perovskites: Insights from First-Principles Calculations.

    PubMed

    Egger, David A; Kronik, Leeor

    2014-08-07

    A microscopic picture of structure and bonding in organic-inorganic perovskites is imperative to understanding their remarkable semiconducting and photovoltaic properties. On the basis of a density functional theory treatment that includes both spin-orbit coupling and dispersive interactions, we provide detailed insight into the crystal binding of lead-halide perovskites and quantify the effect of different types of interactions on the structural properties. Our analysis reveals that cohesion in these materials is characterized by a variety of interactions that includes important contributions from both van der Waals interactions among the halide atoms and hydrogen bonding. We also assess the role of spin-orbit coupling and show that it causes slight changes in lead-halide bonding that do not significantly affect the lattice parameters. Our results establish that consideration of dispersive effects is essential for understanding the structure and bonding in organic-inorganic perovskites in general and for providing reliable theoretical predictions of structural parameters in particular.

  6. Determination of tetrodotoxin and its analogs in the puffer fish Takifugu oblongus from Bangladesh by hydrophilic interaction chromatography and mass-spectrometric detection.

    PubMed

    Diener, Marc; Christian, Bernd; Ahmed, M Sagir; Luckas, Bernd

    2007-11-01

    Tetrodotoxin (TTX) and its analogs (TTXs), widely distributed among marine as well as terrestrial animals, induce dangerous intoxications. These highly potential toxins are also known as the causative agent of puffer fish poisoning. A newly developed highly sensitive method for determination of TTXs based on hydrophilic interaction chromatography and mass-spectrometric detection is presented. TTX, anhydrotetrodotoxin, 11-deoxytetrodotoxin and trideoxytetrodotoxin were determined in separated tissues of Bangladeshi marine puffers, Takifugu oblongus. TTX was predominant in skin, muscle and liver, whereas trideoxytetrodotoxin preponderated in the ovary. The toxicity of the various tissues was determined by a mouse bioassay.

  7. Separating the role of biotic interactions and climate in determining adaptive response of plants to climate change.

    PubMed

    Tomiolo, Sara; Van der Putten, Wim H; Tielbörger, Katja

    2015-05-01

    Altered rainfall regimes will greatly affect the response of plant species to climate change. However, little is known about how direct effects of changing precipitation on plant performance may depend on other abiotic factors and biotic interactions. We used reciprocal transplants between climatically very different sites with simultaneous manipulation of soil, plant population origin, and neighbor conditions to evaluate local adaptation and possible adaptive response of four Eastern Mediterranean annual plant species to climate change. The effect of site on plant performance was negligible, but soil origin had a strong effect on fecundity, most likely due to differential water retaining ability. Competition by neighbors strongly reduced fitness. We separated the effects of the abiotic and biotic soil properties on plant performance by repeating the field experiment in a greenhouse under homogenous environmental conditions and including a soil biota manipulation treatment. As in the field, plant performance differed among soil origins and neighbor treatments. Moreover, we found plant species-specific responses to soil biota that may be best explained by the differential sensitivity to negative and positive soil biota effects. Overall, under the conditions of our experiment with two contrasting sites, biotic interactions had a strong effect on plant fitness that interacted with and eventually overrode climate. Because climate and biotic interactions covary, reciprocal transplants and climate gradient studies should consider soil biotic interactions and abiotic conditions when evaluating climate change effects on plant performance.

  8. [Determining the parameters for receptor-ligand interaction by serial dilution method for the case when the ligand and receptor are in a pre-existing mixture].

    PubMed

    Bobrovnik, S A

    2005-01-01

    New methods of determining the binding parameters for ligand-receptor interaction are considered. The considered approaches are based on the earlier suggested method of serial dilution and application of so-called coordinates of dilution. It was shown that the suggested methods allow to evaluate affinity constant and ligand concentration even for the case, when the receptor and corresponding ligand of unknown concentration are in a mixture and their separation from each other is impossible. In this connection the suggested methods are especially useful for studying the ligand-receptor interaction if the receptor is very liable and its purification from the ligand would cause drastic changes of its binding properties.

  9. Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC.

    PubMed

    Khusainov, Rustem; Moll, Gert N; Kuipers, Oscar P

    2013-01-01

    Nisin is the most prominent and applied bacteriocin that serves as a model for class I lantibiotics. The nisin leader peptide importantly determines interactions between precursor nisin and its modification enzymes NisB and NisC that mature nisin posttranslationally. NisB dehydrates serines and threonines, while NisC catalyzes the subsequent coupling of the formed dehydroamino acids to form lanthionines. Currently, little is known about how the nisin leader interacts with NisB and even less is known about its interactions with NisC. To investigate the nisin leader peptide requirements for functional interaction with the modification enzymes NisB and NisC, we systematically replaced six regions, of 2-4 amino acids each, with all-alanine regions. By performing NisB and NisC co-purification studies with these mutant leader peptides, we demonstrate that the nisin leader regions STKD(-22-19), FNLD(-18-15) and PR(-2-1) importantly contribute to the interactions of precursor nisin with both NisB and NisC, whereas the nisin leader region LVSV(-14-11) additionally contributes to the interaction of precursor nisin with NisC.

  10. Determination of the enthalpy of solute-solvent interaction from the enthalpy of solution: aqueous solutions of erythritol and L-threitol.

    PubMed

    Lopes Jesus, A J; Tomé, Luciana I N; Eusébio, M Ermelinda S; Redinha, J S

    2006-05-11

    In this work the enthalpy of the solute-solvent interaction of erythritol and L-threitol in aqueous solution was determined from the values obtained for the enthalpy of solvation. The values for this property were calculated from those determined for the enthalpies of solution and sublimation. To determine the values of the enthalpy of solute-solvent interaction, the solvation process is considered as taking place in three steps: opening a cavity in the solvent to hold the solute molecule, changing the solute conformation when it passes from the gas phase into solution, and interaction between the solute and the solvent molecules. The cavity enthalpy was calculated by the scaled particle theory and the conformational enthalpy change was estimated from the value of this function in the gas phase and in solution. Both terms were determined by DFT calculations. The solvent effect on the solute conformation in solution was estimated using the CPCM solvation model. The importance of the cavity and conformational terms in the interpretation of the enthalpy of solvation is noted. While the cavity term has been used by some authors, the conformational term is considered for the first time. The structural features in aqueous solution of erythritol and L-threitol are discussed.

  11. Exercisers' perceptions of their fitness instructor's interacting style, perceived competence, and autonomy as a function of self-determined regulation to exercise, enjoyment, affect, and exercise frequency.

    PubMed

    Puente, Rogelio; Anshel, Mark H

    2010-02-01

    The primary purpose of the present investigation was to test the hypothesis, derived from Self-Determination Theory (SDT), that an individual's perceived competence and autonomy mediate the relationship between the exercisers' perception of their instructor's interaction style and the exercisers' motivation to exercise. A secondary purpose was to identify the affective and behavioral outcomes derived from self-determined regulation. It was hypothesized that SDT would significantly explain and predict exercise behavior. Participants consisted of 238 college students, 103 males and 135 females (M age = 20.4 years, SD = 2.16), who volunteered to participate in the study. They were asked to complete a battery of questionnaires measuring instructor's interacting style, self-regulation to exercise, perceived autonomy and competence, enjoyment, positive and negative affect, and exercise frequency. Using structural equation modeling with observed variables, the results showed that perceived competence and autonomy mediated the relationship between perceived instructor's interacting style and self-determined regulation. It was also found that self-determined regulation was significantly related to exercise enjoyment, positive affect, and exercise frequency. It was concluded that understanding the motivational factors and emotional and behavioral consequences of physical activity will partially explain an individual's motives to engage regularly in exercise.

  12. Supply determines demand: influence of partner quality and quantity on the interactions between bats and pitcher plants.

    PubMed

    Schöner, Caroline R; Schöner, Michael G; Kerth, Gerald; Grafe, T Ulmar

    2013-09-01

    Interspecific relationships such as mutualism and parasitism are major drivers of biodiversity. Because such interactions often comprise more than two species, ecological studies increasingly focus on complex multispecies systems. However, the spatial heterogeneity of multi-species interactions is often poorly understood. Here, we investigate the unusual interaction of a bat (Kerivoula hardwickii hardwickii) and two pitcher plant species (Nepenthes hemsleyana and N. bicalcarata) whose pitchers serve as roost for bats. Nepenthes hemsleyana offers roosts of higher quality, indicated by a more stable microclimate compared to N. bicalcarata but occurs at lower abundance and is less common than the latter. Whereas N. hemsleyana benefits from the roosting bats by gaining nitrogen from their feces, the bats' interaction with N. bicalcarata seems to be commensal or even parasitic. Bats stayed longer in roosts of higher quality provided by N. hemsleyana and preferred them to pitchers of N. bicalcarata in a disturbance experiment. Moreover, bats roosting only in pitchers of N. hemsleyana had a higher body condition and were less infested with parasites compared to bats roosting in pitchers of N. bicalcarata. Our study shows how the local supply of roosts with different qualities affects the behavior and status of their inhabitants and-as a consequence-how the demand of the inhabitants can influence evolutionary adaptations of the roost providing species.

  13. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    PubMed

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments.

  14. A binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function

    PubMed Central

    Zeng, Menglong; Shang, Yuan; Guo, Tingfeng; He, Qinghai; Yung, Wing-Ho; Liu, Kai; Zhang, Mingjie

    2016-01-01

    Shank and SAPAP (synapse-associated protein 90/postsynaptic density-95–associated protein) are two highly abundant scaffold proteins that directly interact with each other to regulate excitatory synapse development and plasticity. Mutations of SAPAP, but not other reported Shank PDZ domain binders, share a significant overlap on behavioral abnormalities with the mutations of Shank both in patients and in animal models. The molecular mechanism governing the exquisite specificity of the Shank/SAPAP interaction is not clear, however. Here we report that a sequence preceding the canonical PDZ domain of Shank, together with the elongated PDZ BC loop, form another binding site for a sequence upstream of the SAPAP PDZ-binding motif, leading to a several hundred-fold increase in the affinity of the Shank/SAPAP interaction. We provide evidence that the specific interaction afforded by this newly identified site is required for Shank synaptic targeting and the Shank-induced synaptic activity increase. Our study provides a molecular explanation of how Shank and SAPAP dosage changes due to their gene copy number variations can contribute to different psychiatric disorders. PMID:27185935

  15. On their best behavior: how animal behavior can help determine the combined effects of species interactions and climate change.

    PubMed

    Harmon, Jason P; Barton, Brandon T

    2013-09-01

    The increasingly appreciated link between climate change and species interactions has the potential to help us understand and predict how organisms respond to a changing environment. As this connection grows, it becomes even more important to appreciate the mechanisms that create and control the combined effect of these factors. However, we believe one such important set of mechanisms comes from species' behavior and the subsequent trait-mediated interactions, as opposed to the more often studied density-mediated effects. Behavioral mechanisms are already well appreciated for mitigating the separate effects of the environment and species interactions. Thus, they could be at the forefront for understanding the combined effects. In this review, we (1) show some of the known behaviors that influence the individual and combined effects of climate change and species interactions; (2) conceptualize general ways behavior may mediate these combined effects; and (3) illustrate the potential importance of including behavior in our current tools for predicting climate change effects. In doing so, we hope to promote more research on behavior and other mechanistic factors that may increase our ability to accurately predict climate change effects.

  16. The calculation of electrostatic interactions and their role in determining the energies and geometries of explosive molecular crystals

    SciTech Connect

    Ritchie, J.P.; Kober, E.M.; Copenhaver, A.S.

    1993-01-01

    Three different procedures were used to calculate electrostatic interactions in explosive molecular crystals. The use of Potential Derived Charges (PDC's) and atom-centered multipole expansions (ACME's) provides reasonable fits of the molecular electrostatic potential. The ability of these approaches to reproduce observed crystal structures was also evaluated.

  17. Do intraspecific or interspecific interactions determine responses to predators feeding on a shared size-structured prey community?

    PubMed

    ten Brink, Hanna; Mazumdar, Abul Kalam Azad; Huddart, Joseph; Persson, Lennart; Cameron, Tom C

    2015-03-01

    Coexistence of predators that share the same prey is common. This is still the case in size-structured predator communities where predators consume prey species of different sizes (interspecific prey responses) or consume different size classes of the same species of prey (intraspecific prey responses). A mechanism has recently been proposed to explain coexistence between predators that differ in size but share the same prey species, emergent facilitation, which is dependent on strong intraspecific responses from one or more prey species. Under emergent facilitation, predators can depend on each other for invasion, persistence or success in a size-structured prey community. Experimental evidence for intraspecific size-structured responses in prey populations remains rare, and further questions remain about direct interactions between predators that could prevent or limit any positive effects between predators [e.g. intraguild predation (IGP)]. Here, we provide a community-wide experiment on emergent facilitation including natural predators. We investigate both the direct interactions between two predators that differ in body size (fish vs. invertebrate predator), and the indirect interaction between them via their shared prey community (zooplankton). Our evidence supports the most likely expectation of interactions between differently sized predators that IGP rates are high, and interspecific interactions in the shared prey community dominate the response to predation (i.e. predator-mediated competition). The question of whether emergent facilitation occurs frequently in nature requires more empirical and theoretical attention, specifically to address the likelihood that its pre-conditions may co-occur with high rates of IGP.

  18. Groucho is required for Drosophila neurogenesis, segmentation, and sex determination and interacts directly with hairy-related bHLH proteins.

    PubMed

    Paroush, Z; Finley, R L; Kidd, T; Wainwright, S M; Ingham, P W; Brent, R; Ish-Horowicz, D

    1994-12-02

    We have used the interaction trap, a yeast two-hybrid system, to identify proteins interacting with hairy, a basic-helix-loop-helix (bHLH) protein that represses transcription during Drosophila embryonic segmentation. We find that the groucho (gro) protein binds specifically to hairy and also to hairy-related bHLH proteins encoded by deadpan and the Enhancer of split complex. The C-terminal WRPW motif present in all these bHLH proteins is essential for this interaction. We demonstrate that these associations reflect in vivo maternal requirements for gro during neurogenesis, segmentation, and sex determination, three processes regulated by the above bHLH proteins, and we propose that gro is a transcriptional corepressor recruited to specific target promoters by hairy-related bHLH proteins.

  19. Identification of Regions Interacting with Ovo(d) Mutations: Potential New Genes Involved in Germline Sex Determination or Differentiation in Drosophila Melanogaster

    PubMed Central

    Pauli, D.; Oliver, B.; Mahowald, A. P.

    1995-01-01

    Only a few Drosophila melanogaster germline sex determination genes are known, and there have been no systematic screens to identify new genes involved in this important biological process. The ovarian phenotypes produced by females mutant for dominant alleles of the ovo gene are modified in flies with altered doses of other loci involved in germline sex determination in Drosophila (Sex-lethal(+), sans fille(+) and ovarian tumor(+)). This observation constitutes the basis for a screen to identify additional genes required for proper establishment of germline sexual identity. We tested 300 deletions, which together cover ~58% of the euchromatic portion of the genome, for genetic interactions with ovo(D). Hemizygosity for more than a dozen small regions show interactions that either partially suppress or enhance the ovarian phenotypes of females mutant for one or more of the three dominant ovo mutations. These regions probably contain genes whose products act in developmental hierarchies that include ovo(+) protein. PMID:7713427

  20. Antigen availability determines CD8⁺ T cell-dendritic cell interaction kinetics and memory fate decisions.

    PubMed

    Henrickson, Sarah E; Perro, Mario; Loughhead, Scott M; Senman, Balimkiz; Stutte, Susanne; Quigley, Michael; Alexe, Gabriela; Iannacone, Matteo; Flynn, Michael P; Omid, Shaida; Jesneck, Jonathan L; Imam, Sabrina; Mempel, Thorsten R; Mazo, Irina B; Haining, W Nicholas; von Andrian, Ulrich H

    2013-09-19

    T cells are activated by antigen (Ag)-bearing dendritic cells (DCs) in lymph nodes in three phases. The duration of the initial phase of transient, serial DC-T cell interactions is inversely correlated with Ag dose. The second phase, characterized by stable DC-T cell contacts, is believed to be necessary for full-fledged T cell activation. Here we have shown that this is not the case. CD8⁺ T cells interacting with DCs presenting low-dose, short-lived Ag did not transition to phase 2, whereas higher Ag dose yielded phase 2 transition. Both antigenic constellations promoted T cell proliferation and effector differentiation but yielded different transcriptome signatures at 12 hr and 24 hr. T cells that experienced phase 2 developed long-lived memory, whereas conditions without stable contacts yielded immunological amnesia. Thus, T cells make fate decisions within hours after Ag exposure, resulting in long-term memory or abortive effector responses, correlating with T cell-DCs interaction kinetics.

  1. Voltammetric method for determining the trace moisture content of organic solvents based on hydrogen-bonding interactions with quinones.

    PubMed

    Hui, Yanlan; Chng, Elaine Lay Khim; Chua, Louisa Pei-Lyn; Liu, Wan Zhen; Webster, Richard D

    2010-03-01

    Voltammetry experiments were performed on the natural quinone, vitamin K(1) (VK(1)), in a range of organic solvents of varying dielectric constant that are commonly used for electrochemical measurements [dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetonitrile (MeCN), propionitrile (EtCN), butyronitrile (PrCN), 1,2-dichloroethane (DCE), dichloromethane (DCM), and 1,1,2,2-tetrachloroethane (TCE)]. The water content of the solvents was accurately measured using Karl Fischer (KF) coulometric titrations, and the voltammetric data were used to estimate the degree of hydrogen-bonding interactions between the reduced forms of VK(1) and variable levels of water, thereby allowing a ranking of water-substrate interactions in the different solvents. The voltammetric data were analyzed based on interactions that occur between reduced forms of VK(1) and the water, the solvent, and the supporting electrolyte. Calibration data were obtained that are independent of the nature of the reference electrode and allow the water content of the solvents to be calculated by performing a single voltammetric scan in the presence of VK(1) and 0.2 M supporting electrolyte (Bu(4)NPF(6)).

  2. Visualization of CD2 interaction with LFA-3 and determination of the two-dimensional dissociation constant for adhesion receptors in a contact area

    PubMed Central

    1996-01-01

    Many adhesion receptors have high three-dimensional dissociation constants (Kd) for counter-receptors compared to the KdS of receptors for soluble extracellular ligands such as cytokines and hormones. Interaction of the T lymphocyte adhesion receptor CD2 with its counter- receptor, LFA-3, has a high solution-phase Kd (16 microM at 37 degrees C), yet the CD2/LFA-3 interaction serves as an effective adhesion mechanism. We have studied the interaction of CD2 with LFA-3 in the contact area between Jurkat T lymphoblasts and planar phospholipid bilayers containing purified, fluorescently labeled LFA-3. Redistribution and lateral mobility of LFA-3 were measured in contact areas as functions of the initial LFA-3 surface density and of time after contact of the cells with the bilayers. LFA-3 accumulated at sites of contact with a half-time of approximately 15 min, consistent with the previously determined kinetics of adhesion strengthening. The two-dimensional Kd for the CD2/LFA-3 interaction was 21 molecules/microns 2, which is lower than the surface densities of CD2 on T cells and LFA-3 on most target or stimulator cells. Thus, formation of CD2/LFA-3 complexes should be highly favored in physiological interactions. Comparison of the two-dimensional (membrane- bound) and three-dimensional (solution-phase) KdS suggest that cell- cell contact favors CD2/LFA-3 interaction to a greater extent than that predicted by the three-dimensional Kd and the intermembrane distance at the site of contact. LFA-3 molecules in the contact site were capable of lateral diffusion in the plane of the phospholipid bilayer and did not appear to be irreversibly trapped in the contact area, consistent with a rapid off-rate. These data provide insights into the function of low affinity interactions in adhesion. PMID:8636222

  3. Protein folding rates and thermodynamic stability are key determinants for interaction with the Hsp70 chaperone system

    PubMed Central

    Sekhar, Ashok; Lam, Hon Nam; Cavagnero, Silvia

    2012-01-01

    The Hsp70 family of molecular chaperones participates in vital cellular processes including the heat shock response and protein homeostasis. E. coli's Hsp70, known as DnaK, works in concert with the DnaJ and GrpE co-chaperones (K/J/E chaperone system), and mediates cotranslational and post-translational protein folding in the cytoplasm. While the role of the K/J/E chaperones is well understood in the presence of large substrates unable to fold independently, it is not known if and how K/J/E modulates the folding of smaller proteins able to fold even in the absence of chaperones. Here, we combine experiments and computation to evaluate the significance of kinetic partitioning as a model to describe the interplay between protein folding and binding to the K/J/E chaperone system. First, we target three nonobligatory substrates, that is, proteins that do not require chaperones to fold. The experimentally observed chaperone association of these client proteins during folding is entirely consistent with predictions from kinetic partitioning. Next, we develop and validate a computational model (CHAMP70) that assumes kinetic partitioning of substrates between folding and interaction with K/J/E. CHAMP70 quantitatively predicts the experimentally measured interaction of RNase HD as it refolds in the presence of various chaperones. CHAMP70 shows that substrates are posed to interact with K/J/E only if they are slow-folding proteins with a folding rate constant kf <50 s−1, and/or thermodynamically unstable proteins with a folding free energy ΔG0UN ≥−2 kcal mol−1. Hence, the K/J/E system is tuned to use specific protein folding rates and thermodynamic stabilities as substrate selection criteria. PMID:22886941

  4. Chemical interactions in complex matrices: Determination of polar impurities in biofuels and fuel contaminants in building materials

    NASA Astrophysics Data System (ADS)

    Baglayeva, Ganna

    The solutions to several real-life analytical and physical chemistry problems, which involve chemical interactions in complex matrices are presented. The possible interferences due to the analyte-analyte and analyte-matrix chemical interactions were minimized on each step of the performed chemical analysis. Concrete and wood, as major construction materials, typically become contaminated with fuel oil hydrocarbons during their spillage. In the catastrophic scenarios (e.g., during floods), fuel oil mixes with water and then becomes entrained within the porous structure of wood or concrete. A strategy was proposed for the efficient extraction of fuel oil hydrocarbons from concrete to enable their monitoring. The impacts of sample aging and inundation with water on the extraction efficiency were investigated to elucidate the nature of analytematrix interactions. Two extraction methods, 4-days cold solvent extraction with shaking and 24-hours Soxhlet extraction with ethylacetate, methanol or acetonitrile yielded 95-100 % recovery of fuel oil hydrocarbons from concrete. A method of concrete remediation after contamination with fuel oil hydrocarbons using activated carbon as an adsorbent was developed. The 14 days remediation was able to achieve ca. 90 % of the contaminant removal even from aged water-submerged concrete samples. The degree of contamination can be qualitatively assessed using transport rates of the contaminants. Two models were developed, Fickian and empirical, to predict long-term transport behavior of fuel oil hydrocarbons under flood representative scenarios into wood. Various sorption parameters, including sorption rate, penetration degree and diffusion coefficients were obtained. The explanations to the observed three sorption phases are provided in terms of analyte-matrix interactions. The detailed simultaneous analysis of intermediate products of the cracking of triacylglycerol oils, namely monocarboxylic acids, triacyl-, diacyl- and

  5. Determination of atropine sulfate using a novel sensitive DNA-biosensor based on its interaction on a modified pencil graphite electrode.

    PubMed

    Ensafi, Ali A; Nasr-Esfahani, Parisa; Heydari-Bafrooei, Esmaeil; Rezaei, B

    2015-01-01

    A novel, selective, rapid and simple electrochemical method is developed for the determination of atropine sulfate. UV-Vis and differential pulse voltammetry are used to study the interaction of atropine sulfate with salmon sperm ds-DNA on the surface of salmon sperm ds-DNA modified-pencil graphite electrode (PGE). For this purpose, a pencil graphite electrode (PGE) modified with multiwall carbon nanotubes (MWCNTs), titanium dioxide nanoparticles (TiO2NPs), and poly-dialyldimethylammonium chloride (PDDA) decorated with ds-DNA is tested for the determination of atropine sulfate. The electrochemical oxidation peak current of adenine and guanine bonded on the surface of ds-DNA/PDDA-TiO2NPs-MWCNTs/PGE is used to obtain the analytical signal. Decreases in the intensities of guanine and adenine oxidation signals after their interaction with atropine sulfate are used as indicator signals for the sensitive determination of atropine sulfate. Using ds-DNA/PDDA-TiO2NPs-MWCNTs/PGE and based on the guanine signal, linear calibration curves were obtained in the range of 0.6 to 30.0 μmol L(-1) and 30.0 to 600.0 μmol L(-1) atropine sulfate with low detection limits of 30.0 nmol L(-1). The biosensor shows a good selectivity for the determination of atropine sulfate. Finally, the applicability of the biosensor is evaluated by measuring atropine sulfate in real samples with good accuracy.

  6. Genomic and p16-specific DNA methylation of the mouse colon: elder age and dietary folate as interactive determinants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Elder age and inadequate folate intake are strongly implicated as important risk factors for colon cancer and each is associated with altered DNA methylation. This study was designed to determine the effect of aging and dietary folate on select features of DNA methylation in the colon that are relev...

  7. Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

    SciTech Connect

    Sundlov, Jesse A.; Gulick, Andrew M.

    2013-08-01

    The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.

  8. Determining Wheel-Soil Interaction Loads Using a Meshfree Finite Element Approach Assisting Future Missions with Rover Wheel Design

    NASA Technical Reports Server (NTRS)

    Contreras, Michael T.; Peng, Chia-Yen; Wang, Dongdong; Chen, Jiun-Shyan

    2012-01-01

    A wheel experiencing sinkage and slippage events poses a high risk to rover missions as evidenced by recent mobility challenges on the Mars Exploration Rover (MER) project. Because several factors contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc., there are significant benefits to modeling these events to a sufficient degree of complexity. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree finite element approaches enable simulations that capture sufficient detail of wheel-soil interaction while remaining computationally feasible. This study demonstrates some of the large deformation modeling capability of meshfree methods and the realistic solutions obtained by accounting for the soil material properties. A benchmark wheel-soil interaction problem is developed and analyzed using a specific class of meshfree methods called Reproducing Kernel Particle Method (RKPM). The benchmark problem is also analyzed using a commercially available finite element approach with Lagrangian meshing for comparison. RKPM results are comparable to classical pressure-sinkage terramechanics relationships proposed by Bekker-Wong. Pending experimental calibration by future work, the meshfree modeling technique will be a viable simulation tool for trade studies assisting rover wheel design.

  9. A hierarchical network of interreceptor interactions determines signal transduction by Neu differentiation factor/neuregulin and epidermal growth factor.

    PubMed Central

    Tzahar, E; Waterman, H; Chen, X; Levkowitz, G; Karunagaran, D; Lavi, S; Ratzkin, B J; Yarden, Y

    1996-01-01

    The ErbB family includes four homologous transmembrane tyrosine kinases. Whereas ErbB-1 binds to the epidermal growth factor (EGF), both ErbB-3 and ErbB-4 bind to the Neu differentiation factors (NDFs, or neuregulins), and ErbB-2, the most oncogenic family member, is an orphan receptor whose function is still unknown. Because previous lines of evidence indicated the existence of interreceptor interactions, we used ectopic expression of individual ErbB proteins and their combinations to analyze the details of receptor cross talks. We show that 8 of 10 possible homo-and heterodimeric complexes of ErbB proteins can be hierarchically induced by ligand binding. Although ErbB-2 binds neither ligand, even in a heterodimeric receptor complex, it is the preferred heterodimer partner of the three other members, and it favors interaction with ErbB-3. Selective receptor overexpression in human tumor cells appears to bias the hierarchical relationships. The ordered network is reflected in receptor transphosphorylation, ErbB-2-mediated enhancement of ligand affinities, and remarkable potentiation of mitogenesis by a coexpressed ErbB-2. The observed superior ability of ErbB-2 to form heterodimers, in conjunction with its uniquely high basal tyrosine kinase activity, may explain why ErbB-2 overexpression is associated with poor prognosis. PMID:8816440

  10. Structure of the bacterial cell division determinant GpsB and its interaction with penicillin-binding proteins.

    PubMed

    Rismondo, Jeanine; Cleverley, Robert M; Lane, Harriet V; Großhennig, Stephanie; Steglich, Anne; Möller, Lars; Mannala, Gopala Krishna; Hain, Torsten; Lewis, Richard J; Halbedel, Sven

    2016-03-01

    Each bacterium has to co-ordinate its growth with division to ensure genetic stability of the population. Consequently, cell division and growth are tightly regulated phenomena, albeit different bacteria utilise one of several alternative regulatory mechanisms to maintain control. Here we consider GpsB, which is linked to cell growth and division in Gram-positive bacteria. ΔgpsB mutants of the human pathogen Listeria monocytogenes show severe lysis, division and growth defects due to distortions of cell wall biosynthesis. Consistent with this premise, GpsB interacts both in vitro and in vivo with the major bi-functional penicillin-binding protein. We solved the crystal structure of GpsB and the interaction interfaces in both proteins are identified and validated. The inactivation of gpsB results in strongly attenuated virulence in animal experiments, comparable in degree to classical listerial virulence factor mutants. Therefore, GpsB is essential for in vitro and in vivo growth of a highly virulent food-borne pathogen, suggesting that GpsB could be a target for the future design of novel antibacterials.

  11. Functional traits determine formation of mutualism and predation interactions in seed-rodent dispersal system of a subtropical forest

    NASA Astrophysics Data System (ADS)

    Chang, Gang; Zhang, Zhibin

    2014-02-01

    Network structure in plant-animal systems has been widely investigated but the roles of functional traits of plants and animals in formation of mutualism and predation interactions and community structure are still not fully understood. In this study, we quantitatively assessed interaction strength of mutualism and predation between 5 tree species and 7 rodent species by using semi-natural enclosures in a subtropical forest in southwest China. Seeds with high handling-time and nutrition traits (for both rat and mouse species) or high tannin trait (for mouse species) show high mutualism but low predation with rodents; while seeds with low handling-time and low nutrition traits show high predation but low mutualism with rodents. Large-sized rat species are more linked to seeds with high handling-time and high nutrition traits, while small-sized mouse species are more connected with seeds with low handling-time, low nutrition value and high tannin traits. Anti-predation seed traits tend to increase chance of mutualism instead of reducing predation by rodents, suggesting formation of mutualism may be connected with that of predation. Our study demonstrates that seed and animal traits play significant roles in the formation of mutualism and predation and network structure of the seed-rodent dispersal system.

  12. Yeast TATA Binding Protein Interaction with DNA: Fluorescence Determination of Oligomeric State, Equilibrium Binding, On-Rate, and Dissociation Kinetics†

    PubMed Central

    Perez-Howard, Gina M.; Weil, P. Anthony

    2010-01-01

    A combination of steady-state, stopped-flow, and time-resolved fluorescence of intrinsic tryptophan and extrinsically labeled fluorescent DNA is utilized to examine the interaction of yeast TATA binding protein (TBP) with DNA. TBP is composed of two structural domains, the carboxy domain (residues 61–240), which is responsible for DNA binding and initiation of basal level transcription, and an amino terminal domain (residues 1–60), whose function is currently unknown. The steady-state fluorescence emission spectrum of the single tryptophan in the amino terminal domain of TBP undergoes a huge (30–40 nm) red-shift upon interaction with stoichiometric amounts of TATA box containing DNA. From time-resolved tryptophan fluorescence anisotropy studies, we demonstrate that, in the absence of DNA, the protein exists as a multimer in solution and it contains (at least) two primary conformations, one with the amino terminus associated tightly with the protein(s) in a hydrophobic environment and one with the amino terminus decoupled away from the rest of the protein and solvent-exposed. Upon binding DNA, the protein dissociates into a monomeric complex, upon which only the solvent-exposed amino terminus conformation remains. Kinetic and equilibrium binding studies were performed on TATA box containing DNA which was extrinsically labeled with a fluorescent probe Rhodamine-X at the 5′-end. This “fluorescent” DNA allowed for the collection of quantitative spectroscopic binding, kinetic on-rate, and kinetic off-rate data at physiological concentrations. Global analysis of equilibrium binding studies performed from 500 pM to 50 nM DNA reveals a single dissociation constant (Kd) of approximately 5 nM. Global analysis of stopped-flow anisotropy on-rate experiments, with millisecond timing resolution and TBP concentrations ranging from 20 to 600 nM (20 nM DNA), can be perfectly described by a single second-order rate constant of 1.66 × 105 M−1 s−1. These measurements

  13. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    PubMed Central

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  14. Interactions between the dietary polyunsaturated fatty acid ratio and genetic factors determine susceptibility to pediatric Crohn's disease.

    PubMed

    Costea, Irina; Mack, David R; Lemaitre, Rozenn N; Israel, David; Marcil, Valerie; Ahmad, Ali; Amre, Devendra K

    2014-04-01

    Increased dietary ratios of ω6/ω3 polyunsaturated fatty acids have been implicated in the pathogenesis of Crohn's disease (CD), but epidemiologic data are limited. We investigated whether variants of genes that control polyunsaturated fatty acid metabolism (CYP4F3, FADS1, and FADS2), along with the dietary ratio of ω6/ω3, confers susceptibility to CD. Based on data from 182 children newly diagnosed with CD and 250 controls, we found that children who consumed a higher dietary ratio of ω6/ω3 were susceptible for CD if they were also carriers of specific variants of CYP4F3 and FADS2 genes. Our findings implicate diet-gene interactions in the pathogenesis of CD.

  15. Concomitant Action of Structural Elements and Receptor Phosphorylation Determines Arrestin-3 Interaction with the Free Fatty Acid Receptor FFA4*

    PubMed Central

    Butcher, Adrian J.; Hudson, Brian D.; Shimpukade, Bharat; Alvarez-Curto, Elisa; Prihandoko, Rudi; Ulven, Trond; Milligan, Graeme; Tobin, Andrew B.

    2014-01-01

    In addition to being nutrients, free fatty acids act as signaling molecules by activating a family of G protein-coupled receptors. Among these is FFA4, previously called GPR120, which responds to medium and long chain fatty acids, including health-promoting ω-3 fatty acids, which have been implicated in the regulation of metabolic and inflammatory responses. Here we show, using mass spectrometry, mutagenesis, and phosphospecific antibodies, that agonist-regulated phosphorylation of the human FFA4 receptor occurred primarily at five residues (Thr347, Thr349, Ser350, Ser357, and Ser360) in the C-terminal tail. Mutation of these residues reduced both the efficacy and potency of ligand-mediated arrestin-3 recruitment as well as affecting recruitment kinetics. Combined mutagenesis of all five of these residues was insufficient to fully abrogate interaction with arrestin-3, but further mutagenesis of negatively charged residues revealed additional structural components for the interaction with arrestin-3 within the C-terminal tail of the receptor. These elements consist of the acidic residues Glu341, Asp348, and Asp355 located close to the phosphorylation sites. Receptor phosphorylation thus operates in concert with structural elements within the C-terminal tail of FFA4 to allow for the recruitment of arrestin-3. Importantly, these mechanisms of arrestin-3 recruitment operate independently from Gq/11 coupling, thereby offering the possibility that ligands showing stimulus bias could be developed that exploit these differential coupling mechanisms. Furthermore, this provides a strategy for the design of biased receptors to probe physiologically relevant signaling. PMID:24817122

  16. Past agricultural land use and present-day fire regimes can interact to determine the nature of seed predation.

    PubMed

    Stuhler, John D; Orrock, John L

    2016-06-01

    Historical agriculture and present-day fire regimes can have significant effects on contemporary ecosystems. Although past agricultural land use can lead to long-term changes in plant communities, it remains unclear whether these persistent land-use legacies alter plant-consumer interactions, such as seed predation, and whether contemporary disturbance (e.g., fire) alters the effects of historical agriculture on these interactions. We conducted a study at 27 sites distributed across 80,300 ha in post-agricultural and non-agricultural longleaf pine woodlands with different degrees of fire frequency to test the hypothesis that past and present-day disturbances that alter plant communities can subsequently alter seed predation. We quantified seed removal by arthropods and rodents for Tephrosia virginiana and Vernonia angustifolia, species of conservation interest. We found that the effects of land-use history and fire frequency on seed removal were contingent on granivore guild and microhabitat characteristics. Tephrosia virginiana removal was greater in low fire frequency sites, due to greater seed removal by rodents. Although overall removal of V. angustifolia did not differ among habitats, rodents removed more seeds than arthropods at post-agricultural sites and non-agricultural sites with low fire frequencies, but not at non-agricultural sites with high fire frequencies. Land-use history and fire frequency also affected the relationship between microhabitat characteristics and removal of V. angustifolia. Our results suggest that historical agriculture and present-day fire regimes may alter seed predation by shifting the impact of rodent and arthropod seed predators among habitats, with potential consequences for the establishment of rare plant species consumed by one or both predators.

  17. NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein

    PubMed Central

    Haba, Noam Y.; Gross, Renana; Novacek, Jiri; Shaked, Hadassa; Zidek, Lukas; Barda-Saad, Mira; Chill, Jordan H.

    2013-01-01

    WASp-interacting protein (WIP) is a 503-residue proline-rich polypeptide expressed in human T cells. The WIP C-terminal domain binds to Wiskott-Aldrich syndrome protein (WASp) and regulates its activation and degradation, and the WIP-WASp interaction has been shown to be critical for actin polymerization and implicated in the onset of WAS and X-linked thrombocytopenia. WIP is predicted to be an intrinsically disordered protein, a class of polypeptides that are of great interest because they violate the traditional structure-function paradigm. In this first (to our knowledge) study of WIP in its unbound state, we used NMR to investigate the biophysical behavior of WIPC, a C-terminal domain fragment of WIP that includes residues 407–503 and contains the WASp-binding site. In light of the poor spectral dispersion exhibited by WIPC and the high occurrence (25%) of proline residues, we employed 5D-NMR13C-detected NMR experiments with nonuniform sampling to accomplish full resonance assignment. Secondary chemical-shift analysis, 15N relaxation rates, and protection from solvent exchange all concurred in detecting transient structure located in motifs that span the WASp-binding site. Residues 446–456 exhibited a propensity for helical conformation, and an extended conformation followed by a short, capped helix was observed for residues 468–478. The 13C-detected approach allows chemical-shift assignment in the WIPC polyproline stretches and thus sheds light on their conformation and dynamics. The effects of temperature on chemical shifts referenced to a denatured sample of the polypeptide demonstrate that heating reduces the structural character of WIPC. Thus, we conclude that the disordered WIPC fragment is comprised of regions with latent structure connected by flexible loops, an architecture with implications for binding affinity and function. PMID:23870269

  18. Interaction between sulfonephthalein dyes and chitosan in aqueous solution and its application to the determination of surfactants.

    PubMed

    Yamamoto, Koichi; Adachi, Kana

    2003-08-01

    A spectrophotometric method for the determination of ionic surfactants with Bromophenol Blue (BPB) based on incorporation into a precipitated chitosan was studied. Cationic surfactants (CS+), such as a quaternary ammonium ion containing a long-chain alkyl group, associate with BPB2- buffered at about pH 9 to form the ion associate (CS+)2 x BPB2-. CS+ associates with anionic surfactants (AS-). In the presence of a definite amount of CS+, an increase in the amount of AS- leads to a decrease in the amount of excess CS+, and therefore to a decrease in the amount of the ion associate of CS+ with BPB2-. The addition of a chitosan dissolved in acetic acid to a solution containing these ion associates leads immediately to precipitation of the chitosan and the incorporation of the ion associates (CS+)2 x BPB2- or CS+ x AS- into the precipitated chitosan. After centrifuging, ionic surfactants can be determined by the following two methods: (1) the absorbance of the supernatant solution is measured at 590 nm. (2) After the supernatant solution is separated, the precipitate is dissolved in an acetic acid solution and the absorbance is measured at 625 nm. Because the color of the precipitate is judged by the naked eye, this can be applied to the visual method. This is a simple and rapid method for the determination of a 10(-6) M order of ionic surfactants.

  19. A major determinant for gliding motility in Mycoplasma genitalium: the interaction between the terminal organelle proteins MG200 and MG491.

    PubMed

    Martinelli, Luca; Lalli, Daniela; García-Morales, Luis; Ratera, Mercè; Querol, Enrique; Piñol, Jaume; Fita, Ignacio; Calisto, Bárbara M

    2015-01-16

    Several mycoplasmas, such as the emergent human pathogen Mycoplasma genitalium, developed a complex polar structure, known as the terminal organelle (TO), responsible for a new type of cellular motility, which is involved in a variety of cell functions: cell division, adherence to host cells, and virulence. The TO cytoskeleton is organized as a multisubunit dynamic motor, including three main ultrastructures: the terminal button, the electrodense core, and the wheel complex. Here, we describe the interaction between MG200 and MG491, two of the main components of the TO wheel complex that connects the TO with the cell body and the cell membrane. The interaction between MG200 and MG491 has a KD in the 80 nm range, as determined by surface plasmon resonance. The interface between the two partners was confined to the "enriched in aromatic and glycine residues" (EAGR) box of MG200, previously described as a protein-protein interaction domain, and to a 25-residue-long peptide from the C-terminal region of MG491 by surface plasmon resonance and NMR spectroscopy studies. An atomic description of the MG200 EAGR box binding surface was also provided by solution NMR. An M. genitalium mutant lacking the MG491 segment corresponding to the peptide reveals specific alterations in cell motility and cell morphology indicating that the MG200-MG491 interaction plays a key role in the stability and functioning of the TO.

  20. Dual isotopic approach for determining groundwater origin and water-rock interactions in over exploited watershed in India

    NASA Astrophysics Data System (ADS)

    Negrel, Philippe; Pauwels, Hélène; Millot, Romain; Roy, Stéphane; Guerrot, Catherine

    2010-05-01

    Groundwater flow and storage in hard rock areas is becoming a matter of great interest and importance to researchers and water managers either with regards to the quantity, quality of water as well as delimitation of resources and aquifers. Degradation of groundwater resources by abstraction, contamination, ... has been increasing in many areas and is of growing concern for few decades. In terms of hydrogeology, hard rocks represent a quite heterogeneous and anisotropic media with irregular distribution of pathways of groundwater flow, typically consisting of three vertical zones, upper weathered, middle fractured and lower massive bedrock. Aim of this work is dual and the Maheshwaram watershed (53 km2, Andhra Pradesh, India) representative of watersheds in southern India in terms of geology, overpumping of its hard-rock aquifer (more than 700 classical open end wells in use), its cropping pattern (rice dominating), and its rural socio-economy mainly based on traditional agriculture is investigated through stable isotopes of the water molecule and lead isotopes in groundwater. The overall objective is to incorporate isotopic- and chemical-tracing data and constraints into methods for evaluating groundwater circulation. It divides into fingerprinting the groundwater recharge processes (e.g. the input by the monsoon) and the water use in such agricultural watershed, which is of primary importance in such semi-arid context and investigating the processes of water-rock interactions (e.g. granite-water interaction). In the frame of delimitation of resources and aquifers and long-term sustainability, we monitored the input from monsoon-precipitation over 2 years, and measured spatial and temporal variations in δ18O and δ2H in the groundwater and in precipitation. Individual recharge from the two monsoon periods was identified. This led to identification of periods during which evaporation affects groundwater quality through a higher concentration of salts and stable

  1. Cell surface-mediated cellular interactions: effects of B104 neuroblastoma surface determinants on C6 glioma cellular properties.

    PubMed

    Ciment, G; de Vellis, J

    1982-01-01

    To study the influence of cell surface-associated molecules on intercellular communication, C6 glioma cells were cultured both on plastic and on substrata of paraformaldehyde-fixed B104 neuroblastoma cells. By then comparing the phenotypic expression of these "cocultured" C6 cells with cells cultured on tissue culture plastic, the influence of the cellular substratum was determined. The beta-adrenergic-responsive cyclic AMP-generating system of C6 cells was compared on these various substrata. We found that fixed beds of dibutyryl cyclic AMP (dbcAMP)-treated B104 cells uncoupled beta-receptors from adenylate cyclase, whereas fixed beds of similarly treated C6 cells did not. However, other cellular properties were not affected by growth atop fixed dbcAMP-treated B104 cell beds including the rate of C6 cellular proliferation and their rate of protein synthesis. The cell surface-associated determinant on B104 cells capable of uncoupling the beta-responsive cyclase system of C6 cells is probably a protein, as judged by its susceptibility to protease treatment. Other properties of C6 cells were also affected by the various substrata including basal and hydrocortisone-induced levels of glycerol phosphate dehydrogenase (GPDH; an oligodendroglial marker) and the rate of RNA synthesis in these cells.

  2. Analysis of the interaction of a laser pulse with a silicon wafer - Determination of bulk lifetime and surface recombination velocity

    NASA Technical Reports Server (NTRS)

    Luke, Keung L.; Cheng, Li-Jen

    1987-01-01

    The decay of excess minority carriers produced in a silicon wafer of thickness d by a laser pulse is analyzed. A comprehensive theory based on this analysis is presented for the determination of bulk lifetime Tau(b) and surface recombination velocity S. It is shown that, starting with an exponential spatial profile, the carrier profile assumes a spatially symmetrical form after approximately one time constant of the fundamental mode of decay. Expressions for the spatial average of the carrier density as a function of time are derived for three temporal laser pulse shapes: impulse, square, and Gaussian. Particular attention is paid to the time constants of the fundamental and higher modes of decay. The ratios of the time constants of the higher modes to the fundamental mode, as well as the time constant of the fundamental mode, are presented over wide ranges of values of S and d. For Sd less than about 40 sq cm/s, a two-wafer method is developed to determine Tau(b) and S; it is also shown that the requirement of d/Tau(b) greater than about 20S is sufficient to adequately guarantee that the asymptotic value of the instantaneous observed lifetime differs from the bulk lifetime by no more than 10 percent.

  3. Neighbourhood density and genetic relatedness interact to determine fruit set and abortion rates in a continuous tropical tree population.

    PubMed

    Jones, F A; Comita, L S

    2008-12-07

    Tropical trees may show positive density dependence in fruit set and maturation due to pollen limitation in low-density populations. However, pollen from closely related individuals in the local neighbourhood might reduce fruit set or increase fruit abortion in self-incompatible tree species. We investigated the role of neighbourhood density and genetic relatedness on individual fruit set and abortion in the neotropical tree Jacaranda copaia in a large forest plot in central Panama. Using nested neighbourhood models, we found a strong positive effect of increased conspecific density on fruit set and maturation. However, high neighbourhood genetic relatedness interacted with density to reduce total fruit set and increase the proportion of aborted fruit. Our results imply a fitness advantage for individuals growing in high densities as measured by fruit set, but realized fruit set is lowered by increased neighbourhood relatedness. We hypothesize that the mechanism involved is increased visitation by density-dependent invertebrate pollinators in high-density populations, which increases pollen quantity and carry-over and increases fruit set and maturation, coupled with self-incompatibility at early and late stages due to biparental inbreeding that lowers fruit set and increases fruit abortion. Implications for the reproductive ecology and conservation of tropical tree communities in continuous and fragmented habitats are discussed.

  4. Determination of the interaction second virial coefficients for the carbon dioxide-ethane system from refractive index measurements

    SciTech Connect

    Jaeschke, M.

    1987-01-01

    The compressibility behavior of the CO/sub 2/-C/sub 2/H/sub 6/ system was investigated experimentally. In this work, the refractive indexes of the pure gases and the mixtures were measured using an optical apparatus. On the basis of these data, density and compressibility factors were computed using the Lorentz-Lorenz law. For the pure components, carbon dioxide and ethane, the data from the optical system were slightly adjusted by a fit to Burnett apparatus data measured separately. The experiments produced very accurate virial coefficients and refraction virial coefficients. This paper reports on the effect of temperature on the second and third virial coefficients. For the first refraction virial coefficient, no influence of temperature was found with the equipment used. The interaction second virial coefficient B /sub 12/ (as a function of temperature) was computed from experimental data for the CO/sub 2/-C/sub 2/H/sub 6/ binary system. The data, for which an accuracy of +/- 1.5 cm/sup 3/ mol/sup -1/ was estimated, are in agreement with the data published by Holste et al.

  5. The determination of organophosphonate nerve agent metabolites in human urine by hydrophilic interaction liquid chromatography tandem mass spectrometry.

    PubMed

    Mawhinney, Douglas B; Hamelin, Elizabeth I; Fraser, Rheaclare; Silva, Sathya S; Pavlopoulos, Antonis J; Kobelski, Robert J

    2007-06-01

    A sensitive, robust isotope dilution LC/MS/MS method is presented for the quantitative analysis of human urine for the alkyl methylphosphonic acid metabolites of five organophosphorus nerve agents (VX, rVX or VR, GB or Sarin, GD or Soman, and GF or Cyclosarin). The selective sample preparation method employs non-bonded silica solid-phase extraction and is partially automated. While working with a mobile phase composition that enhances the electrospray ionization process, the hydrophilic interaction chromatography method results in a 5-min injection-to-injection cycle time, excellent peak shapes and adequate retention (k'=3.1). These factors lead to limits of detection for these metabolites as low as 30 pg/mL in a 1-mL sample of human urine. The quality control data (15 and 75 ng/mL) demonstrate accurate (-0.5 to +3.4%) and precise (coefficients of variation of 2.1-3.6%) quantitative results over the clinically relevant urine concentration range of 1-200 ng/mL for a validation set of 20 standard and quality control sets prepared by five analysts over 54 days. The selectivity of the method is demonstrated for a 100-individual reference range study, as well as the analysis of relevant biological samples. The combined sample preparation and analysis portions of this method have a throughput of 288 samples per day.

  6. Determination of dicyandiamide in infant formula by stable isotope dilution hydrophilic interaction liquid chromatography with tandem mass spectrometry.

    PubMed

    Inoue, Koichi; Sakamoto, Tasuku; Min, Jun Zhe; Todoroki, Kenichiro; Toyo'oka, Toshimasa

    2014-08-01

    Dicyandiamide is a compound for reducing the negative effects of greenhouse gas emissions and nitrate leaching into waterways. In this study, the trace contamination of dicyandiamide in infant formula was analysed by stable isotope dilution hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-MS/MS). Dicyandiamide and a stable isotope internal standard were monitored by multiple reaction-monitoring with mass transitions: m/z 85→68/43 and m/z 89→71/45 in the electrospray positive ion mode. For sample preparation of the infant formula, a diluted/filtered procedure was developed for this assay. The calculated LOD and LOQ values were 0.01 or 0.05ng/mL for the standard solution, respectively. The averaged recovery and precision were 110.8% and 7.4%, respectively. This assay was applied to monitor 23 infant formulas, and the dicyandiamide contamination in one sample was detected and quantified at 79.1±1.2ng/g (ppb) powder. We suggest that it is necessary to cautiously monitor the DCD in common products from international countries.

  7. Application of Analytical Quality by Design concept for bilastine and its degradation impurities determination by hydrophilic interaction liquid chromatographic method.

    PubMed

    Terzić, Jelena; Popović, Igor; Stajić, Ana; Tumpa, Anja; Jančić-Stojanović, Biljana

    2016-06-05

    This paper deals with the development of hydrophilic interaction liquid chromatographic (HILIC) method for the analysis of bilastine and its degradation impurities following Analytical Quality by Design approach. It is the first time that the method for bilastine and its impurities is proposed. The main objective was to identify the conditions where an adequate separation in minimal analysis duration could be achieved within a robust region. Critical process parameters which have the most influence on method performance were defined as acetonitrile content in the mobile phase, pH of the aqueous phase and ammonium acetate concentration in the aqueous phase. Box-Behnken design was applied for establishing a relationship between critical process parameters and critical quality attributes. The defined mathematical models and Monte Carlo simulations were used to identify the design space. Fractional factorial design was applied for experimental robustness testing and the method is validated to verify the adequacy of selected optimal conditions: the analytical column Luna(®) HILIC (100mm×4.6mm, 5μm particle size); mobile phase consisted of acetonitrile-aqueous phase (50mM ammonium acetate, pH adjusted to 5.3 with glacial acetic acid) (90.5:9.5, v/v); column temperature 30°C, mobile phase flow rate 1mLmin(-1), wavelength of detection 275nm.

  8. The interactions between TiO2 and graphene with surface inhomogeneity determined using density functional theory.

    PubMed

    Bukowski, Brandon; Deskins, N Aaron

    2015-11-28

    TiO2/graphene composites have shown promise as photocatalysts, leading to improved electronic properties. We have modeled using density functional theory TiO2/graphene interfaces formed between graphene with various defects/functional groups (C vacancy, epoxide, and hydroxyl) and TiO2 clusters of various sizes. We considered clusters from 3 to 45 atoms, the latter a nanoparticle of ∼1 nm in size. Our results show that binding to pristine graphene is dominated by van der Waals forces, and that C vacancies or epoxide groups lead to much stronger binding between the graphene and TiO2. Such sites may serve to anchor TiO2 to graphene. Graphene surfaces with hydroxyls however lead to OH transfer to TiO2 and weak interactions between the graphene and the hydroxylated TiO2 cluster. Charge transfer may occur between TiO2 and graphene in various directions (graphene to TiO2 or TiO2 to graphene), depending on the state of the graphene surface, based on overlap of the density of states. Our work indicates that graphene surface defects or functional groups may have a significant effect on the stability, structure, and photoactivity of these materials.

  9. Determinants of the direction illusion: motion speed and dichoptic presentation interact to reveal systematic individual differences in sign.

    PubMed

    Chen, Tony T; Maloney, Ryan T; Clifford, Colin W G

    2014-07-17

    When two fields of dots with different directions of movement are presented in tandem, the perceived direction of one is biased by the presence of the other. Although this ‘‘direction illusion’’ typically involves repulsion, with an exaggeration of the perceived angular difference in direction between the dot fields, attraction effects, where the perceived difference is reduced, have also been found under certain presentation conditions. Earlier literature has been inconsistent, and there is debate surrounding the nature of the interactions that facilitate the direction illusion, as well as whether they occur at a local or global stage of the motion processing hierarchy. Here we measured the operating characteristics of the direction illusion by parametrically varying inducer contrast and coherence while examining the effects of stimulus speed and dichoptic presentation. It was found that the magnitude and sign of the direction illusion differed substantially from earlier research. Furthermore, there appeared to be significant interindividual variability, with dichoptic presentation producing an attractive rather than repulsive direction illusion in some participants.

  10. Evolution determines how global warming and pesticide exposure will shape predator-prey interactions with vector mosquitoes.

    PubMed

    Tran, Tam T; Janssens, Lizanne; Dinh, Khuong V; Op de Beeck, Lin; Stoks, Robby

    2016-07-01

    How evolution may mitigate the effects of global warming and pesticide exposure on predator-prey interactions is directly relevant for vector control. Using a space-for-time substitution approach, we addressed how 4°C warming and exposure to the pesticide endosulfan shape the predation on Culex pipiens mosquitoes by damselfly predators from replicated low- and high-latitude populations. Although warming was only lethal for the mosquitoes, it reduced predation rates on these prey. Possibly, under warming escape speeds of the mosquitoes increased more than the attack efficiency of the predators. Endosulfan imposed mortality and induced behavioral changes (including increased filtering and thrashing and a positional shift away from the bottom) in mosquito larvae. Although the pesticide was only lethal for the mosquitoes, it reduced predation rates by the low-latitude predators. This can be explained by the combination of the evolution of a faster life history and associated higher vulnerabilities to the pesticide (in terms of growth rate and lowered foraging activity) in the low-latitude predators and pesticide-induced survival selection in the mosquitoes. Our results suggest that predation rates on mosquitoes at the high latitude will be reduced under warming unless predators evolve toward the current low-latitude phenotype or low-latitude predators move poleward.

  11. Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions

    PubMed Central

    Hussain, Rohanah; Harding, Stephen E.; Hughes, Charlotte S.; Ma, Pikyee; Patching, Simon G.; Edara, Shalini; Siligardi, Giuliano; Henderson, Peter J.F.; Phillips-Jones, Mary K.

    2016-01-01

    This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs. PMID:27284046

  12. Structure determination of three furan-substituted benzimidazoles and calculation of π-π and C-H···π interaction energies.

    PubMed

    Geiger, David K; Geiger, H Cristina; Deck, Jared M

    2014-12-01

    used to partition the interaction energies into the C-H···π and π-π components, which are 9.4 and 24.1 kJ mol(-1), respectively. Energy-minimized structures were used to determine the optimal interplanar spacing, the slip distance along the major molecular axis, and the slip distance along the minor molecular axis for 2-(furan-2-yl)-1H-benzimidazole.

  13. A native whole blood test for the evaluation of blood-surface interaction: determination of thromboxane production.

    PubMed

    Mantovani, E; Marconi, W; Cebo, B; Togna, A R; Togna, G; Caprino, L

    1984-05-01

    The method developed to evaluate the hemocompatibility of artificial materials involves the determination of thromboxane production during the clotting of rabbit blood, in test tubes of different materials. The concentration of serum TXB2 obtained after incubation of whole blood in glass test tubes, for 40 min at 37 degrees C, averaged 416.8 +/- 23.3 ng/ml (mean +/- SE). Polymethylpentene, recognised as having a relatively poor blood compatibility, elicited 309.5 +/- 17.2 ng/ml of serum TXB2, while silicone and Avcothane, considered of better hemocompatibility, showed thromboxane levels of 276.2 +/- 28.2 and 222.9 +/- 31.5 ng/ml, respectively. These values validate the usefulness of the proposed method as a preliminary in vitro screening test of artificial materials intended for biomedical application.

  14. Role of enthalpy-entropy compensation interactions in determining the conformational propensities of amino acid residues in unfolded peptides.

    PubMed

    Toal, Siobhan E; Verbaro, Daniel J; Schweitzer-Stenner, Reinhard

    2014-02-06

    The driving forces governing the unique and restricted conformational preferences of amino acid residues in the unfolded state are still not well understood. In this study, we experimentally determine the individual thermodynamic components underlying intrinsic conformational propensities of these residues. Thermodynamic analysis of ultraviolet-circular dichroism (UV-CD) and (1)H NMR data for a series of glycine capped amino acid residues (i.e., G-x-G peptides) reveals the existence of a nearly exact enthalpy-entropy compensation for the polyproline II-β strand equilibrium for all investigated residues. The respective ΔHβ, ΔSβ values exhibit a nearly perfect linear relationship with an apparent compensation temperature of 295 ± 2 K. Moreover, we identified iso-equilibrium points for two subsets of residues at 297 and 305 K. Thus, our data suggest that within this temperature regime, which is only slightly below physiological temperatures, the conformational ensembles of amino acid residues in the unfolded state differ solely with respect to their capability to adopt turn-like conformations. Such iso-equilibria are rarely observed, and their existence herein indicates a common physical origin behind conformational preferences, which we are able to assign to side-chain dependent backbone solvation. Conformational effects such as differences between the number of sterically allowed side chain rotamers can contribute to enthalpy and entropy but not to the Gibbs energy associated with conformational preferences. Interestingly, we found that alanine, aspartic acid, and threonine are the only residues which do not share these iso-equilbiria. The enthalpy-entropy compensation discovered as well as the iso-equilbrium and thermodynamics obtained for each amino acid residue provide a new and informative way of identifying the determinants of amino acid propensities in unfolded and disordered states.

  15. Determination of N-acetylglucosamine in cosmetic formulations and skin test samples by hydrophilic interaction liquid chromatography and UV detection.

    PubMed

    Pedrali, Alice; Bleve, Mariella; Capra, Priscilla; Jonsson, Tobias; Massolini, Gabriella; Perugini, Paola; Marrubini, Giorgio

    2015-03-25

    N-Acetylglucosamine is an ingredient in pharmaceuticals, nutritional supplements and in cosmetics. N-Acetylglucosamine in cosmetics is expected to improve skin hydration, reparation, and to contribute as anti-wrinkle agent. This study reports on the validation and application of an HPLC method based on HILIC and UV detection for determining N-acetylglucosamine in cosmetics and in samples obtained after testing the skin exposed to cosmetics formulations. The chromatographic column used is a ZIC(®)-pHILIC (150 mm × 4.6 mm, 5 μm particle size) on which a mobile phase containing acetonitrile-aqueous KH2PO4 (70:30, v/v) 15 mM was applied in isocratic elution mode injecting 20 μl of sample at 0.5 ml/min constant flow-rate and 10±1°C column temperature. Under these conditions the total run time was 10 min and N-acetylglucosamine eluted baseline separated from all other compounds in the samples. Calibration in the range from 40 to 80 μg/ml allowed to assess the method linearity (R(2)>0.999) in a concentration range corresponding to about 50% to 120% of the expected levels of N-acetylglucosamine in the formulations. Precision expressed by RSD% was always better than 2% in intra-day and inter-day assays of authentic samples. Accuracy was in all cases within 95-105% of the expected concentration value in formulations containing N-acetylglucosamine. The sensitivity of the method was at the level of 10 μg/ml as limit of detection, and at 40 μg/ml as limit of quantitation. The application of the method to formulations containing solid lipid nanoparticles documents its usefulness in cosmetic quality control. The results witness that the method is also suitable for the determination of N-acetylglucosamine in samples obtained from skin test strips.

  16. Implications of using transmitted vs. reflected light for determining cloud properties, cloud radiative effects and aerosol-cloud-interactions

    NASA Astrophysics Data System (ADS)

    LeBlanc, S. E.; Redemann, J.; Segal-Rosenhaimer, M.; Kacenelenbogen, M. S.; Shinozuka, Y.; Flynn, C. J.; Schmidt, S.; Pilewskie, P.; Song, S.; Woods, S.; Lawson, P.; Nenes, A.; Lin, J. J.; Ziemba, L. D.

    2015-12-01

    Light transmitted through clouds is sensitive to a different cloud volume than reflected light at cloud top. This difference in sampling volumes has implications when calculating the radiative effects of clouds (CRE) and aerosol-cloud-interactions (ACI). We present a comparison of retrieved cloud properties and the corresponding CRE and ACI based on transmitted and reflected light for a cloud sampled during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS, 2013) field campaign. Measurements of zenith radiances were obtained from the NASA DC-8 aircraft using the Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR) instrument. 4STAR was deployed on an airborne platform during SEAC4RS alongside the Solar Spectral Flux Radiometer (SSFR). To retrieve cloud properties from transmitted shortwave radiation, we use a retrieval utilizing spectrally resolved measurements. Spectral features in shortwave radiation transmitted through clouds are sensitive to changes in cloud optical thickness, effective radius, and thermodynamic phase. The spectral features due to absorption and scattering processes by liquid water and ice cloud particles include shifts in spectral slopes, curvatures, maxima, and minima of cloud-transmitted radiance. These spectral features have been quantified by 15 parameters used to retrieve cloud properties from the 4STAR zenith radiances. Retrieved cloud optical thicknesses and effective radii based on transmitted shortwave radiation are compared to their counterparts obtained from reflected shortwave radiation measured above cloud with MODIS and with the enhanced MODIS Airborne Simulator (eMAS), the Research Scanning Polarimeter (RSP), and SSFR operating aboard the NASA ER-2 aircraft. Remotely sensed cloud particle effective radius are combined with in situ measurements of cloud and aerosol particles from the NASA Langley Aerosol Research Group Experiment (LARGE) CCN Counter

  17. Structural determinants of heparin-transforming growth factor-β1 interactions and their effects on signaling.

    PubMed

    Lee, Jonathan; Wee, Sheena; Gunaratne, Jayantha; Chua, R J E; Smith, Raymond A A; Ling, Ling; Fernig, David G; Swaminathan, Kunchithapadam; Nurcombe, Victor; Cool, Simon M

    2015-12-01

    Transforming growth factor-β1 (TGF-β1, Uniprot: P01137) is a heparin-binding protein that has been implicated in a number of physiological processes, including the initiation of chondrogenesis by human mesenchymal stem cells (hMSCs). Here, we identify the molecular features in the protein and in heparin required for binding and their effects on the potentiation of TGF-β1's activity on hMSCs. Using a proteomics "Protect and Label" approach, lysines K291, K304, K309, K315, K338, K373, K375 and K388 were identified as being directly involved in binding heparin (Data are available via ProteomeXchange with identifier PXD002772). Competition assays in an optical biosensor demonstrated that TGF-β1 does require N- and 6-O-sulfate groups for binding but that 2-O-sulfate groups are unlikely to underpin the interaction. Heparin-derived oligosaccharides as short as degree of polymerization (dp) 4 have a weak ability to compete for TGF-β1 binding to heparin, which increases with the length of the oligosaccharide to reach a maximum between dp18 and dp24. In cell-based assays, heparin, 2-O-, 6-O- and N-desulfated re-N-acetylated heparin and oligosaccharides 14-24 saccharides (dp14-24) in length all increased the phosphorylation of mothers against decapentaplegic homolog 2 (SMAD2) after 6 h of stimulation with TGF-β1. The results provide the structural basis for a model of heparin/heparan sulfate binding to TGF-β1 and demonstrate that the features in the polysaccharide required for binding are not identical to those required for sustaining the signaling by TGF-β1 in hMSCs.

  18. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms.

    PubMed

    van Opijnen, Tim; Lazinski, David W; Camilli, Andrew

    2014-04-14

    The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobial agents and vaccines. This unit presents Tn-seq, a method that has made it possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies on the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated transposon insertion library. After library selection, changes in the frequency of each insertion mutant are determined by sequencing flanking regions en masse. These changes are used to calculate each mutant's fitness. The method was originally developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis, but has now been applied to several different microbial species.

  19. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms.

    PubMed

    van Opijnen, Tim; Lazinski, David W; Camilli, Andrew

    2015-02-02

    The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobial agents and vaccines. This unit presents Tn-seq, a method that has made it possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies on the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated transposon insertion library. After library selection, changes in the frequency of each insertion mutant are determined by sequencing flanking regions en masse. These changes are used to calculate each mutant's fitness. The method was originally developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis, but has now been applied to several different microbial species.

  20. In vitro interaction between alginate lyase and amphotericin B against Aspergillus fumigatus biofilm determined by different methods.

    PubMed

    Bugli, Francesca; Posteraro, Brunella; Papi, Massimiliano; Torelli, Riccardo; Maiorana, Alessandro; Paroni Sterbini, Francesco; Posteraro, Patrizia; Sanguinetti, Maurizio; De Spirito, Marco

    2013-03-01

    Aspergillus fumigatus biofilms represent a problematic clinical entity, especially because of their recalcitrance to antifungal drugs, which poses a number of therapeutic implications for invasive aspergillosis, the most difficult-to-treat Aspergillus-related disease. While the antibiofilm activities of amphotericin B (AMB) deoxycholate and its lipid formulations (e.g., liposomal AMB [LAMB]) are well documented, the effectiveness of these drugs in combination with nonantifungal agents is poorly understood. In the present study, in vitro interactions between polyene antifungals (AMB and LAMB) and alginate lyase (AlgL), an enzyme degrading the polysaccharides produced as extracellular polymeric substances (EPSs) within the biofilm matrix, against A. fumigatus biofilms were evaluated by using the checkerboard microdilution and the time-kill assays. Furthermore, atomic force microscopy (AFM) was used to image and quantify the effects of AlgL-antifungal combinations on biofilm-growing hyphal cells. On the basis of fractional inhibitory concentration index values, synergy was found between both AMB formulations and AlgL, and this finding was also confirmed by the time-kill test. Finally, AFM analysis showed that when A. fumigatus biofilms were treated with AlgL or polyene alone, as well as with their combination, both a reduction of hyphal thicknesses and an increase of adhesive forces were observed compared to the findings for untreated controls, probably owing to the different action by the enzyme or the antifungal compounds. Interestingly, marked physical changes were noticed in A. fumigatus biofilms exposed to the AlgL-antifungal combinations compared with the physical characteristics detected after exposure to the antifungals alone, indicating that AlgL may enhance the antibiofilm activity of both AMB and LAMB, perhaps by disrupting the hypha-embedding EPSs and thus facilitating the drugs to reach biofilm cells. Taken together, our results suggest that a combination

  1. Potential of Cupriavidus metallidurans CH34 for in situ resource utilization from basalt by determining the molecular micro-mineral interactions

    NASA Astrophysics Data System (ADS)

    Byloos, Bo; Van Houdt, Rob; Boon, Nico; Leys, Natalie

    In order to maintain a persistent human presence in space, materials must either be provided from Earth or generated from material already present in space, in a process referred to as 'in situ resource utilization (ISRU)'. Microorganisms can biomine useful elements from extra-terrestrial materials for use as nutrients in a life support system or to aid in the creation of soil. To effectively use bacteria in an ISRU process more needs to be known about the molecular mechanisms behind microbe-mineral interaction and the influence of microgravity and radiation that affect bioleaching. The aim of this research project is to define the microbe-mineral interactions on basalt, which is a major constituent of Lunar or Martian regolith, the mechanisms that are important in bioleaching and how this process will be altered by space flight conditions. In particular, the research will be focussed on the determination of the genes and proteins involved in the biosynthesis of metallophores and exopolysaccharides (EPS), and biofilm formation. Iron, copper and phosphate uptake mechanisms are investigated in detail because these have been shown to be essential for life and bacteria are faced with limitation of these nutrients in the environment. In this study the bacterium Cupriavidus metallidurans CH34 is used to study these interactions. C. metallidurans CH34 is a soil bacterium which is resistant to up to 20 different heavy metal ions. Its behaviour in space has already been determined with earlier flight experiments to the ISS. It was recently discovered that C. metallidurans forms a biofilm and is capable of leaching calcium, magnesium and iron from basalt to sustain its growth First, C. metallidurans was grown in conditions with and without basalt, iron, copper and phosphate and the production of EPS and metallophores was examined. The iron, copper and phosphate concentrations which are limiting and optimal to allow C. metallidurans cell proliferation could be determined as

  2. Simultaneous high-throughput determination of interaction kinetics for drugs and cyclodextrins by high performance affinity chromatography with mass spectrometry detection.

    PubMed

    Wang, Caifen; Wang, Xiaobo; Xu, Xiaonan; Liu, Botao; Xu, Xu; Sun, Lixin; Li, Haiyan; Zhang, Jiwen

    2016-02-25

    The individual determination of the apparent dissociation rate constant (kd,app) using high performance affinity chromatography (HPAC) is a tedious process requiring numerous separate tests and massive data fitting, unable to provide the apparent association rate constant (ka) and equilibrium binding constant (Ka). In this study, a HPAC with mass spectrometry detection (HPAC-MS/MS) was employed to determine the drug-cyclodextrin (CD) interaction kinetics with low sample loading quantity (<10 ng per injection for single compound) and high-throughput yield as twenty drugs determined in one injection. The kd,app measured by HPAC-MS/MS approach were 0.89 ± 0.07, 4.34 ± 0.01, 1.48 ± 0.01 and 7.77 ± 0.04 s(-1) for ketoprofen, trimethoprim, indapamide and acetaminophen, with kd,app for acetaminophen consistent with that from the HPAC method with UV detector in our previous studies. For twenty drugs with diverse structures and chemical properties, good correlationship was found between kd,app measured by single compound analysis method and high-throughput HPAC-MS/MS approach, with the correlation coefficient of 0.987 and the significance F less than 0.001. Comprehensive quantification of ka,app, kd,app and Ka values was further performed based on the measurement of kd,app by peak profiling method and Ka by the peak fitting method. And the investigation of the drug-CD interaction kinetics under different conditions indicated that the column temperature and mobile phase composition significantly affected the determination of ka,app, kd,app and Ka while also dependent on the acidity and basicity of drugs. In summary, the high-throughput HPAC-MS/MS approach has been demonstrated high efficiency in determination of the drug-CD primary interaction kinetic parameter, especially, kd,app, being proven as a novel tool in screening the right CD for the solubilization of the right drug.

  3. A new hydrophilic interaction liquid chromatography tandem mass spectrometry method for the simultaneous determination of seven biogenic amines in cheese.

    PubMed

    Gianotti, V; Chiuminatto, U; Mazzucco, E; Gosetti, F; Bottaro, M; Frascarolo, P; Gennaro, M C

    2008-03-28

    An HILIC-PI APCI MS/MS method is developed for the determination of seven biogenic amines (cadaverine, histamine, putrescine, spermidine, spermine, tryptamine and tyramine) in cheese. Their presence and relative amounts give useful information about freshness, level of maturing, quality of storage and cheese typicization. The major drawback in the analysis is represented by the relevant matrix effect and the general unbalanced concentrations of the different amines in cheese. The method proposed represents an improvement with respect to an HPLC-MS/MS method already developed in this laboratory. The new method permits better sensitivities it makes use of a Waters Atlantis HILIC (150.0 mm x 2.1 mm i.d., 3 microm) stationary phase and of a mobile phase of acetonitrile and ammonium formate 50.0 mM in ultrapure water brought to pH 4.00 for formic acid, flowing under gradient conditions. The chromatographic system is interfaced with a 3200QTrap LC-MS/MS system (Applied Biosystem, Foster City, CA, USA) by a Turbo V interface equipped with Heated Nebuliser (APCI) and Turbo Ion Spray (TIS) probes. LOQ values lower than 10 microg L(-1) are obtained. The method is applied in the analysis of Castelmagno cheese.

  4. Dorsoventral patterning of the Drosophila hindgut is determined by interaction of genes under the control of two independent gene regulatory systems, the dorsal and terminal systems.

    PubMed

    Hamaguchi, Takashi; Takashima, Shigeo; Okamoto, Aiko; Imaoka, Misa; Okumura, Takashi; Murakami, Ryutaro

    2012-01-01

    Dorsoventral (DV) patterning in the trunk region of Drosophila embryo is established through intricate molecular interactions that regulate Dpp/Scw signaling during the early blastoderm stages. The hindgut of Drosophila, which derives from posterior region of the cellular blastoderm, also shows dorsoventral patterning, being subdivided into distinct dorsal and ventral domains. engrailed (en) is expressed in the dorsal domain, which determines dorsal fate of the hindgut. Here we show that a repressor Brk restricts en expression to the dorsal domain of the hindgut. Expression domain of brk during early blastdermal stages is defined through antagonistic interaction with dpp, and expression domains of dpp and brk in the early blastoderm include prospective hindgut domain. After stage 9, dpp expression in the dorsal domain of the hindgut primordium disappears, but, the brk expression in the ventral domain continues. It was found that Dorsocross (Doc), which is a targe gene of Dpp, is responsible for restricting brk expression to the ventral domain of the hindgut. On the other hand, activation of en is under the control of brachyenteron (byn) that is regulated independently of dpp, brk, and Doc. The cooperative interaction of common DV positional cues with byn during hindgut development represents another aspect of mechanisms of DV patterning in the Drosophila embryo.

  5. Identification of a Skp1-like protein interacting with SFB, the pollen S determinant of the gametophytic self-incompatibility in Prunus.

    PubMed

    Matsumoto, Daiki; Yamane, Hisayo; Abe, Kazuyuki; Tao, Ryutaro

    2012-07-01

    Many species in Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI). In this system, the pistil and pollen specificities are determined by S-RNase and the S locus F-box protein, respectively. The pollen S determinant F-box protein in Prunus (Rosaceae) is referred to by two different terms, SFB (for S-haplotype-specific F-box protein) and SLF (for S locus F box), whereas it is called SLF in Solanaceae and Plantaginaceae. Prunus SFB is thought to be a molecule indispensable for its cognate S-RNase to exert cytotoxicity and to arrest pollen tube growth in incompatible reactions. Although recent studies have demonstrated the molecular function of SCF(SLF) in the SI reaction of Solanaceae and Plantaginaceae, how SFB participates in the Prunus SI mechanism remains to be elucidated. Here we report the identification of sweet cherry (Prunus avium) SFB (PavSFB)-interacting Skp1-like1 (PavSSK1) using a yeast (Saccharomyces cerevisiae) two-hybrid screening against the pollen cDNA library. Phylogenetic analysis showed that PavSSK1 belongs to the same clade as Antirrhinum hispanicum SLF-interacting Skp1-like1 and Petunia hybrida SLF-interacting Skp1-like1 (PhSSK1). In yeast, PavSSK1 interacted not only with PavSFBs from different S haplotypes and Cullin1-likes (PavCul1s), but also with S-locus F-box-likes. A pull-down assay confirmed the interactions between PavSSK1 and PavSFB and between PavSSK1 and PavCul1s. These results collectively indicate that PavSSK1 could be a functional component of the SCF complex and that PavSFB may function as a component of the SCF complex. We discuss the molecular function of PavSFB in self-/nonself-recognition in the gametophytic SI of Prunus.

  6. Ground-Atmosphere Interactions at Gale: Determination of the Surface Energy Budget, Thermal Inertia and Water Sorption on the Regolith

    NASA Astrophysics Data System (ADS)

    Martinez, German; Renno, Nilton; Fischer, Erik; Borlina, Caue; Hallet, Bernard; De la Torre Juarez, Manuel; Vasavada, Aswhin; Gomez-Elvira, Javier

    2014-05-01

    The analysis of the Surface Energy Budget (SEB) yields insights into the local climate and the soil-atmosphere interactions, while the analysis of the thermal inertia of the shallow subsurface augments surface observations, providing information about the local geology. The Mars Global Surveyor Thermal Emission Spectrometer and the Mars Odyssey Thermal Emission Imaging System have measured near subsurface thermal inertia from orbit at scales of ~104 m2 to ~10 km2. Here we report analysis of the thermal inertia at a few locations at Gale Crater at scales of 100 m2. The thermal inertia is calculated by solving the heat conduction equation in the soil using hourly measurements by the Rover Environmental Station (REMS) ground temperature sensor as an upper boundary condition. Three Sols representative of different environmental conditions and soil properties, namely, Sol 82 at Rocknest (RCK), Sol 112 at Point Lake (PL) and Sol 139 at Yellowknife Bay (YKB) are analyzed in detail. The largest thermal inertia (I) value is found at YKB, I = 445 J m-2 K-1 s-1/2 or 445 tiu (thermal inertia unit), followed by PL with I= 300 tiu and RCK withI = 280 tiu [1]. These values are consistent with the type of terrain imaged by MastCam and with previous satellite estimates at Gale Crater [2,3]. The SEB is calculated by using all REMS data products as well as dust opacity values derived from MastCam measurements, whereas previously, the SEB has been calculated using numerical models only [4]. At each location and during the daytime, the SEB is dominated by the downwelling shortwave (SW) solar radiation (~450-500 W/m2) and the upwelling longwave (LW) radiation emitted by the surface (~300-400 W/m2). The sum of these two terms accounts for at least 70% of the net surface heating rate between 0900 and 1400 local solar time. At nighttime, the SEB is dominated by the upwelling LW radiation emitted by the surface (~50-100 W/m2) and the downwelling LW radiation from the atmosphere (~50 W/m2

  7. Biotic and abiotic interactions in aquatic microcosms determine fate and toxicity of Ag nanoparticles: part 2-toxicity and Ag speciation.

    PubMed

    Bone, Audrey J; Colman, Benjamin P; Gondikas, Andreas P; Newton, Kim M; Harrold, Katherine H; Cory, Rose M; Unrine, Jason M; Klaine, Stephen J; Matson, Cole W; Di Giulio, Richard T

    2012-07-03

    To study the effects of complex environmental media on silver nanoparticle (AgNP) toxicity, AgNPs were added to microcosms with freshwater sediments and two species of aquatic plants (Potamogeton diversifolius and Egeria densa), followed by toxicity testing with microcosm surface water. Microcosms were designed with four environmental matrices in order to determine the contribution of each environmental compartment to changes in toxicity: water only (W), water + sediment (WS), water + plants (WP), and water + plants + sediment (WPS). Silver treatments included AgNPs with two different coatings, gum arabic (GA-AgNPs) or polyvinylpyrollidone (PVP-AgNPs), as well as AgNO(3). Water samples taken from the microcosms at 24 h postdosing were used in acute toxicity tests with two standard model organisms, early life stage zebrafish (Danio rerio) and Daphnia magna. Speciation of Ag in these samples was analyzed using Ag L3-edge X-ray absorption near edge spectroscopy (XANES). Silver speciation patterns for the nanoparticle treatments varied significantly by coating type. While PVP-AgNPs were quite stable and resisted transformation across all matrices (>92.4% Ag(0)), GA-AgNP speciation patterns suggest significantly higher transformation rates, especially in treatments with plants (<69.2% and <58.8% Ag(0) in WP and WPS, respectively) and moderately increased transformation with sediments (<85.6% Ag(0)). Additionally, the presence of plants in the microcosms (with and without sediments) reduced both the concentration of Ag in the water column and toxicity for all Ag treatments. Reductions in toxicity may have been related to decreased water column concentrations as well as changes in the surface chemistry of the particles induced by organic substances released from the plants.

  8. Non-Linear Interactions between Consumers and Flow Determine the Probability of Plant Community Dominance on Maine Rocky Shores

    PubMed Central

    Silliman, Brian R.; McCoy, Michael W.; Trussell, Geoffrey C.; Crain, Caitlin M.; Ewanchuk, Patrick J.; Bertness, Mark D.

    2013-01-01

    Although consumers can strongly influence community recovery from disturbance, few studies have explored the effects of consumer identity and density and how they may vary across abiotic gradients. On rocky shores in Maine, recent experiments suggest that recovery of plant- or animal- dominated community states is governed by rates of water movement and consumer pressure. To further elucidate the mechanisms of consumer control, we examined the species-specific and density-dependent effects of rocky shore consumers (crabs and snails) on community recovery under both high (mussel dominated) and low flow (plant dominated) conditions. By partitioning the direct impacts of predators (crabs) and grazers (snails) on community recovery across a flow gradient, we found that grazers, but not predators, are likely the primary agent of consumer control and that their impact is highly non-linear. Manipulating snail densities revealed that herbivorous and bull-dozing snails (Littorina littorea) alone can control recovery of high and low flow communities. After ∼1.5 years of recovery, snail density explained a significant amount of the variation in macroalgal coverage at low flow sites and also mussel recovery at high flow sites. These density-dependent grazer effects were were both non-linear and flow-dependent, with low abundance thresholds needed to suppress plant community recovery, and much higher levels needed to control mussel bed development. Our study suggests that consumer density and identity are key in regulating both plant and animal community recovery and that physical conditions can determine the functional forms of these consumer effects. PMID:23940510

  9. Photoaffinity approaches to determining the sequence selectivities of DNA-small molecule interactions: actinomycin D and ethidium.

    PubMed Central

    Marsch, G A; Graves, D E; Rill, R L

    1995-01-01

    The DNA photoaffinity ligands, 7-azidoactinomycin D and 8-azidoethidium, form DNA adducts that cause chain cleavage upon treatment with piperidine. Chemical DNA sequencing techniques were used to detect covalent binding. The relative preferences for modifications of all possible sites defined by a base pair step (e.g. GC) were determined within all quartet contexts such as (IGCJ). These preferences are described in terms of 'effective site occupations', which express the ability of a ligand to covalently modify some base in the binding site. Ideally, the effective site occupations measured for photoaffinity agents can also be related to site-specific, non-covalent association constants of the ligand. The sites most reactive with 7-azidoactinomycin D were those preferred for non-covalent binding of unsubstituted actinomycin D. GC sites were most reactive, but next-nearest neighbors exerted significant influences on reactivity. GC sites in 5'-(pyrimidine)GC(purine)-3' contexts, particularly TGCA, were most reactive, while reactivity was strongly suppressed for GC sites with a 5'-flanking G, or a 3'-flanking C. High reactivities were also observed for bases in the first (5') GG steps in TGGT, TGGG and TGGGT sequences recently shown to bind actinomycin D with high affinity. Pyrimidine-3',5'-purine steps and GG steps flanked by a T were most preferred by 8-azidoethidium, in agreement with the behavior of unsubstituted ethidium. The good correspondence between expected and observed covalent binding preferences of these two azide analogs demonstrates that photoaffinity labeling can identify highly preferred sites of non-covalent DNA binding by small molecules. PMID:7739904

  10. The interaction of taurine-salicylaldehyde Schiff base copper(II) complex with DNA and the determination of DNA using the complex as a fluorescence probe

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoyan; Wang, Yong; Zhang, Qianru; Yang, Zhousheng

    2010-09-01

    The interaction of taurine-salicylaldehyde Schiff base copper(II) (Cu(TSSB) 22+) complex with DNA was explored by using UV-vis, fluorescence spectrophotometry, and voltammetry. In pH 7.4 Tris-HCl buffer solution, the binding constant of the Cu(TSSB) 22+ complex interaction with DNA was 3.49 × 10 4 L mol -1. Moreover, due to the fluorescence enhancing of Cu(TSSB) 22+ complex in the presence of DNA, a method for determination of DNA with Cu(TSSB) 22+ complex as a fluorescence probe was developed. The fluorescence spectra indicated that the maximum excitation and emission wavelength were 389 nm and 512 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range of 0.03-9.03 μg mL -1 for calf thymus DNA (CT-DNA), 0.10-36 μg mL -1 for yeast DNA and 0.01-10.01 μg mL -1 for salmon DNA (SM-DNA), respectively. The corresponding detection limits are 7 ng mL -1 for CT-DNA, 3 ng mL -1 for yeast DNA and 3 ng mL -1 for SM-DNA. Using this method, DNA in synthetic samples was determined with satisfactory results.

  11. Competing Lipid-Protein and Protein-Protein Interactions Determine Clustering and Gating Patterns in the Potassium Channel from Streptomyces lividans (KcsA)*

    PubMed Central

    Molina, M. Luisa; Giudici, A. Marcela; Poveda, José A.; Fernández-Ballester, Gregorio; Montoya, Estefanía; Renart, M. Lourdes; Fernández, Asia M.; Encinar, José A.; Riquelme, Gloria; Morales, Andrés; González-Ros, José M.

    2015-01-01

    There is increasing evidence to support the notion that membrane proteins, instead of being isolated components floating in a fluid lipid environment, can be assembled into supramolecular complexes that take part in a variety of cooperative cellular functions. The interplay between lipid-protein and protein-protein interactions is expected to be a determinant factor in the assembly and dynamics of such membrane complexes. Here we report on a role of anionic phospholipids in determining the extent of clustering of KcsA, a model potassium channel. Assembly/disassembly of channel clusters occurs, at least partly, as a consequence of competing lipid-protein and protein-protein interactions at nonannular lipid binding sites on the channel surface and brings about profound changes in the gating properties of the channel. Our results suggest that these latter effects of anionic lipids are mediated via the Trp67–Glu71–Asp80 inactivation triad within the channel structure and its bearing on the selectivity filter. PMID:26336105

  12. Identification of regions interacting with ovo{sup D} mutations: Potential new genes involved in germline sex determination or differentiation in Drosophila melanogaster

    SciTech Connect

    Pauli, D.; Oliver, B.; Mahowald, A.P.

    1995-02-01

    Only a few Drosophila melanogaster germline sex determination genes are known, and there have been no systematic screens to identify new genes involved in this important biological process. The ovarian phenotypes produced by females mutant for dominant alleles of the ovo gene are modified in flies with altered doses of other loci involved in germline sex determination in Drosophila (Sex-lethal{sup +}, snas fille{sup +} and ovarian tumor{sup +}). This observation constitutes the basis for a screen to identify additional genes required for proper establishment of germline sexual identity. We tested 300 deletions, which together cover {approximately}58% of the euchromatic portion of the genome, for genetic interactions with ovo{sup D}. Hemizygosity for more than a dozen small regions show interactions that either partially suppress or enhance the ovarian phenotypes of females mutant for one or more of the three dominant ovo mutations. These regions probably contain genes whose products act in developmental heirarchies that include ovo{sup +} protein. 40 refs, 7 figs., 5 tabs.

  13. Demonstration of N- and C-terminal domain intramolecular interactions in rat liver carnitine palmitoyltransferase 1 that determine its degree of malonyl-CoA sensitivity

    PubMed Central

    Faye, Audrey; Borthwick, Karen; Esnous, Catherine; Price, Nigel T.; Gobin, Stéphanie; Jackson, Vicky N.; Zammit, Victor A.; Girard, Jean; Prip-Buus, Carina

    2004-01-01

    We have previously proposed that changes in malonyl-CoA sensitivity of rat L-CPT1 (liver carnitine palmitoyltransferase 1) might occur through modulation of interactions between its cytosolic N- and C-terminal domains. By using a cross-linking strategy based on the trypsin-resistant folded state of L-CPT1, we have now shown the existence of such N–C (N- and C-terminal domain) intramolecular interactions both in wild-type L-CPT1 expressed in Saccharomyces cerevisiae and in the native L-CPT1 in fed rat liver mitochondria. These N–C intramolecular interactions were found to be either totally (48-h starvation) or partially abolished (streptozotocin-induced diabetes) in mitochondria isolated from animals in which the enzyme displays decreased malonyl-CoA sensitivity. Moreover, increasing the outer membrane fluidity of fed rat liver mitochondria with benzyl alcohol in vitro, which induced malonyl-CoA desensitization, attenuated the N–C interactions. This indicates that the changes in malonyl-CoA sens-itivity of L-CPT1 observed in mitochondria from starved and diabetic rats, previously shown to be associated with altered membrane composition in vivo, are partly due to the disruption of N–C interactions. Finally, we show that mutations in the regulatory regions of the N-terminal domain affect the ability of the N terminus to interact physically with the C-terminal domain, irrespective of whether they increased [S24A (Ser24→Ala)/Q30A] or abrogated (E3A) malonyl-CoA sensitivity. Moreover, we have identified the region immediately N-terminal to transmembrane domain 1 (residues 40–47) as being involved in the chemical N–C cross-linking. These observations provide the first demonstration by a physico-chemical method that L-CPT1 adopts different conformational states that differ in their degree of proximity between the cytosolic N-terminal and the C-terminal domains, and that this determines its degree of malonyl-CoA sensitivity depending on the physiological state

  14. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states.

    PubMed

    Godtliebsen, Ian H; Christiansen, Ove

    2015-10-07

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  15. Determination of equilibrium constants and computational interaction energies for adducts of [Rh2(RCO2)(4-n)(PC)n] (n = 0-2) with Lewis bases.

    PubMed

    Hirva, Pipsa; Esteban, Julio; Lloret, Julio; Lahuerta, Pascual; Pérez-Prieto, Julia

    2007-04-02

    Properties of dirhodium catalysts with cyclometalated aryl phosphine ligands have been studied. We report here the study of the acid-base reaction of Rh2(RCO2)2(PC)2(H2O)2 catalysts (PC = cyclometalated aryl phosphine) with different Lewis bases. The determination of the equilibrium constants of these reactions can be used to study to which extent the properties of the axial coordination site of the catalyst, considered the active site, are affected by modification of the metalated phosphines, the carboxylate ligands, or the incoming axial ligand. The trends in the computational density functional theory interaction energies show good agreement with the major trends in the equilibrium constants, thus enabling a further study of the influence of the modification of the ligand core.

  16. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states

    NASA Astrophysics Data System (ADS)

    Godtliebsen, Ian H.; Christiansen, Ove

    2015-10-01

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  17. Determination of nucleosides and nucleotides in baby foods by hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of hydrophilic ion-pairing reagents.

    PubMed

    Mateos-Vivas, María; Rodríguez-Gonzalo, Encarnación; Domínguez-Álvarez, Javier; García-Gómez, Diego; Carabias-Martínez, Rita

    2016-11-15

    In this work we propose a rapid and efficient method for the joint determination of nucleosides and nucleotides in dairy and non-dairy baby foods based on hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of diethylammonium (DEA) as a hydrophilic ion-pairing reagent (IP-HILIC-MS/MS). Sample treatment of the baby food included dilution with water and centrifugal ultrafiltration (CUF) with an additional washing step that notably improved the global performance of the process. Later dilution of the extract with acetonitrile allowed adequate separation in the HILIC system. With the proposed treatment, we obtained extraction recoveries higher than 80% and, additionally, no matrix effects were observed. The CUF-IP-HILIC-MS/MS method was validated according to the 2002/657/EC decision and was used for the quantification of nucleotides and nucleosides in sixteen samples of commercial baby foods.

  18. Direct determination of nuclear polarization produced by beam-foil interaction for the short-lived. beta. emitter /sup 12/B

    SciTech Connect

    Nojiri, Y.; Deutch, B.I.

    1983-07-18

    Nuclear polarization P of the short-lived ..beta.. emitter /sup 12/B was produced by the beam-foil interaction and directly determined via asymmetric ..beta.. decay. For a single tilted foil, at boron energy E/sub B/ = 1.0 MeV, Vertical BarPVertical Bar = 1.82(14)%. This was enhanced to Vertical BarPVertical Bar = 4.69(46)% by stacking four tilted foils. The dependence of P vs E/sub B/ was observed for a single tilted foil in the range of E/sub B/ = 0.6 to 1.3 MeV. The sign of P followed that of the tilt angle and was consistent with predictions from electron-density-gradient models.

  19. Resonance light scattering spectral method for the determination of serum albumin with the interaction of neutral red-sodium dodecyl sulfonate.

    PubMed

    Zhan, Guoqing; Zhang, Lixia; Li, Chunya

    2009-06-01

    Based on the enhancement of resonance light scattering (RLS) of serum albumin interaction with neutral red (NR) and sodium dodecyl sulfonate (SDS), a novel sensitive assay of serum albumins has been developed. Experimental conditions such as mixing sequence of reagents, pH, NR and SDS concentrations have been optimized. Linear relationships between the enhanced RLS intensity and the protein concentration were observed for bovine serum albumin (BSA) within the range of 0.01-5.0 microg mL(-1) and human serum albumin (HAS) of 0.01-7.0 microg mL(-1). The detection limits (S/N=3) are 6.0 ng mL(-1) for BSA and 5.0 ng mL(-1) for HAS, respectively. The method was successfully applied to the determination of HSA in human blood plasma samples with recovery from 97.3 to 104.3%.

  20. Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER Case-Control Study

    PubMed Central

    Wang, Sophia S.; Hartge, Patricia; Cozen, Wendy; Kelemen, Linda E.; Chanock, Stephen; Davis, Scott; Blair, Aaron; Schenk, Maryjean; Rothman, Nathaniel; Lan, Qing

    2007-01-01

    We previously reported a lower risk of non-Hodgkin lymphoma (NHL) associated with high consumption of vitamin B6 and methionine, dietary determinants of one-carbon metabolism. Evidence has linked genetic variants involved in one-carbon metabolism to NHL. We investigated 30 polymorphisms in 18 genes for their main effect on NHL among 1141 incident cases and 949 population-based controls and examined gene-nutrient interactions in a subgroup of 386 cases and 319 controls who provided detailed food-frequency information. Odds ratios (ORs) and 95% confidence intervals (CIs) were adjusted for age, sex, and race. We observed a decreased risk of NHL overall with BHMT Ex8+453A>T and increased risk with CBS Ex13+41C>T, FPGS Ex15-263T>C, and SHMT1 Ex12+138C>T and Ex12+236C>T. Furthermore, significant gene-nutrient interactions limited the protective association comparing high versus low vitamin B6 to FPGS Ex15-263T>C CC (OR = 0.22; 95% CI = 0.10-0.52), MTHFS IVS2-1411T>G TT/TG (OR = 0.54; 95% CI = 0.36-0.81), and MTR Ex26-20A>G AA (OR = 0.55; 95% CI = 0.35-0.86) genotypes, and the protective association of methionine to FTHFD Ex10-40G>T GG (OR = 0.63; 95% CI = 0.44-0.91), MTHFR Ex8-62A>C CC (OR = 0.13; 95% CI = 0.04-0.39), and MTRR Ex5+136T>C TT (OR = 0.67; 95% CI = 0.47-0.97) genotypes. Warranting replication, our finding of gene-nutrient interactions in one-carbon metabolism supports their etiologic involvement in lymphomagenesis. PMID:17119116

  1. Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation

    PubMed Central

    Picard, Marion A. L.; Boissier, Jérôme; Roquis, David; Grunau, Christoph; Allienne, Jean-François; Duval, David; Toulza, Eve; Arancibia, Nathalie; Caffrey, Conor R.; Long, Thavy; Nidelet, Sabine; Rohmer, Marine; Cosseau, Céline

    2016-01-01

    Background Among more than 20,000 species of hermaphroditic trematodes, Schistosomatidae are unusual since they have evolved gonochorism. In schistosomes, sex is determined by a female heterogametic system, but phenotypic sexual dimorphism appears only after infection of the vertebrate definitive host. The completion of gonad maturation occurs even later, after pairing. To date, the molecular mechanisms that trigger the sexual differentiation in these species remain unknown, and in vivo studies on the developing schistosomulum stages are lacking. To study the molecular basis of sex determination and sexual differentiation in schistosomes, we investigated the whole transcriptome of the human parasite Schistosoma mansoni in a stage- and sex-comparative manner. Methodology/ Principal Findings We performed a RNA-seq on males and females for five developmental stages: cercariae larvae, three in vivo schistosomulum stages and adults. We detected 7,168 genes differentially expressed between sexes in at least one of the developmental stages, and 4,065 of them were functionally annotated. Transcriptome data were completed with H3K27me3 histone modification analysis using ChIP-Seq before (in cercariae) and after (in adults) the phenotypic sexual dimorphism appearance. In this paper we present (i) candidate determinants of the sexual differentiation, (ii) sex-biased players of the interaction with the vertebrate host, and (iii) different dynamic of the H3K27me3 histone mark between sexes as an illustration of sex-biased epigenetic landscapes. Conclusions/ Significance Our work presents evidence that sexual differentiation in S. mansoni is accompanied by distinct male and female transcriptional landscapes of known players of the host-parasite crosstalk, genetic determinants and epigenetic regulators. Our results suggest that such combination could lead to the optimized sexual dimorphism of this parasitic species. As S. mansoni is pathogenic for humans, this study represents a

  2. Interaction between hexon and L4-100K determines virus rescue and growth of hexon-chimeric recombinant Ad5 vectors

    PubMed Central

    Yan, Jingyi; Dong, Jianing; Wu, Jiaxin; Zhu, Rui; Wang, Zhen; Wang, Baoming; Wang, Lizheng; Wang, Zixuan; Zhang, Haihong; Wu, Hui; Yu, Bin; Kong, Wei; Yu, Xianghui

    2016-01-01

    The immunogenicity of recombinant adenovirus serotype 5 (rAd5) vectors has been shown to be suppressed by neutralizing antibodies (NAbs) directed primarily against hexon hypervariable regions (HVRs). Preexisting immunity can be circumvented by replacing HVRs of rAd5 hexon with those derived from alternate adenovirus serotypes. However, chimeric modification of rAd5 hexon HVRs tends to cause low packaging efficiency or low proliferation of rAd5 vectors, but the related mechanism remains unclear. In this study, several Ad5-based vectors with precise replacement of HVRs with those derived from Ad37 and Ad43 were generated. We first observed that a HVR-exchanged rAd5 vector displayed a higher efficacy of the recombinant virus rescue and growth improvement compared with the rAd5 vector, although most hexon-chimeric rAd5 vectors constructed by us and other groups have proven to be nonviable or growth defective. We therefore evaluated the structural stability of the chimeric hexons and their interactions with the L4-100K chaperone. We showed that the viability of hexon-chimeric Ad5 vectors was not attributed to the structural stability of the chimeric hexon, but rather to the hexon maturation which was assisted by L4-100K. Our results suggested that the intricate interaction between hexon and L4-100K would determine the virus rescue and proliferation efficiency of hexon-chimeric rAd5 vectors. PMID:26934960

  3. Interaction between hexon and L4-100K determines virus rescue and growth of hexon-chimeric recombinant Ad5 vectors.

    PubMed

    Yan, Jingyi; Dong, Jianing; Wu, Jiaxin; Zhu, Rui; Wang, Zhen; Wang, Baoming; Wang, Lizheng; Wang, Zixuan; Zhang, Haihong; Wu, Hui; Yu, Bin; Kong, Wei; Yu, Xianghui

    2016-03-03

    The immunogenicity of recombinant adenovirus serotype 5 (rAd5) vectors has been shown to be suppressed by neutralizing antibodies (NAbs) directed primarily against hexon hypervariable regions (HVRs). Preexisting immunity can be circumvented by replacing HVRs of rAd5 hexon with those derived from alternate adenovirus serotypes. However, chimeric modification of rAd5 hexon HVRs tends to cause low packaging efficiency or low proliferation of rAd5 vectors, but the related mechanism remains unclear. In this study, several Ad5-based vectors with precise replacement of HVRs with those derived from Ad37 and Ad43 were generated. We first observed that a HVR-exchanged rAd5 vector displayed a higher efficacy of the recombinant virus rescue and growth improvement compared with the rAd5 vector, although most hexon-chimeric rAd5 vectors constructed by us and other groups have proven to be nonviable or growth defective. We therefore evaluated the structural stability of the chimeric hexons and their interactions with the L4-100K chaperone. We showed that the viability of hexon-chimeric Ad5 vectors was not attributed to the structural stability of the chimeric hexon, but rather to the hexon maturation which was assisted by L4-100K. Our results suggested that the intricate interaction between hexon and L4-100K would determine the virus rescue and proliferation efficiency of hexon-chimeric rAd5 vectors.

  4. Human Cannabinoid Receptor 2 Ligand-Interaction Motif: Transmembrane Helix 2 Cysteine, C2.59(89), as Determinant of Classical Cannabinoid Agonist Activity and Binding Pose.

    PubMed

    Zhou, Han; Peng, Yan; Halikhedkar, Aneetha; Fan, Pusheng; Janero, David R; Thakur, Ganesh A; Mercier, Richard W; Sun, Xin; Ma, Xiaoyu; Makriyannis, Alexandros

    2017-03-01

    TMH6/7. These data constitute initial evidence that TMH2 cysteine C2.59(89) is a component of the hCB2R binding pocket for classical cannabinoids. The results further demonstrate how interactions between classical cannabinoids and specific amino acids within the hCB2R* ligand-binding domain act as determinants of agonist pharmacological properties and the architecture of the agonist-hCB2R* conformational ensemble, allowing the receptor to adopt distinct activity states, such that interaction of classical cannabinoids with TMH6 cysteine C6.47(257) favors a binding pose more advantageous for agonist potency than does their interaction with TMH2 cysteine C2.59(89).

  5. Effect of metal ions on the reactions of the cumyloxyl radical with hydrogen atom donors. Fine control on hydrogen abstraction reactivity determined by Lewis acid-base interactions.

    PubMed

    Salamone, Michela; Mangiacapra, Livia; DiLabio, Gino A; Bietti, Massimo

    2013-01-09

    A time-resolved kinetic study on the effect of metal ions (M(n+)) on hydrogen abstraction reactions from C-H donor substrates by the cumyloxyl radical (CumO(•)) was carried out in acetonitrile. Metal salt addition was observed to increase the CumO(•) β-scission rate constant in the order Li(+) > Mg(2+) > Na(+). These effects were explained in terms of the stabilization of the β-scission transition state determined by Lewis acid-base interactions between M(n+) and the radical. When hydrogen abstraction from 1,4-cyclohexadiene was studied in the presence of LiClO(4) and Mg(ClO(4))(2), a slight increase in rate constant (k(H)) was observed indicating that interaction between M(n+) and CumO(•) can also influence, although to a limited extent, the hydrogen abstraction reactivity of alkoxyl radicals. With Lewis basic C-H donors such as THF and tertiary amines, a decrease in k(H) with increasing Lewis acidity of M(n+) was observed (k(H)(MeCN) > k(H)(Li(+)) > k(H)(Mg(2+))). This behavior was explained in terms of the stronger Lewis acid-base interaction of M(n+) with the substrate as compared to the radical. This interaction reduces the degree of overlap between the α-C-H σ* orbital and a heteroatom lone-pair, increasing the C-H BDE and destabilizing the carbon centered radical formed after abstraction. With tertiary amines, a >2-order of magnitude decrease in k(H) was measured after Mg(ClO(4))(2) addition up to a 1.5:1 amine/Mg(ClO(4))(2) ratio. At higher amine concentrations, very similar k(H) values were measured with and without Mg(ClO(4))(2). These results clearly show that with strong Lewis basic substrates variations in the nature and concentration of M(n+) can dramatically influence k(H), allowing for a fine control of the substrate hydrogen atom donor ability, thus providing a convenient method for C-H deactivation. The implications and generality of these findings are discussed.

  6. Molecular determinants of enterovirus 71 viral entry: cleft around GLN-172 on VP1 protein interacts with variable region on scavenge receptor B 2.

    PubMed

    Chen, Pan; Song, Zilin; Qi, Yonghe; Feng, Xiaofeng; Xu, Naiqing; Sun, Yinyan; Wu, Xing; Yao, Xin; Mao, Qunyin; Li, Xiuling; Dong, Wenjuan; Wan, Xiaobo; Huang, Niu; Shen, Xinliang; Liang, Zhenglun; Li, Wenhui

    2012-02-24

    Enterovirus 71 (EV71) is one of the major pathogens that cause hand, foot, and mouth disease outbreaks in young children in the Asia-Pacific region in recent years. Human scavenger receptor class B 2 (SCARB2) is the main cellular receptor for EV71 on target cells. The requirements of the EV71-SCARB2 interaction have not been fully characterized, and it has not been determined whether SCARB2 serves as an uncoating receptor for EV71. Here we compared the efficiency of the receptor from different species including human, horseshoe bat, mouse, and hamster and demonstrated that the residues between 144 and 151 are critical for SCARB2 binding to viral capsid protein VP1 of EV71 and seven residues from the human receptor could convert murine SCARB2, an otherwise inefficient receptor, to an efficient receptor for EV71 viral infection. We also identified that EV71 binds to SCARB2 via a canyon of VP1 around residue Gln-172. Soluble SCARB2 could convert the EV71 virions from 160 S to 135 S particles, indicating that SCARB2 is an uncoating receptor of the virus. The uncoating efficiency of SCARB2 significantly increased in an acidic environment (pH 5.6). These studies elucidated the viral capsid and receptor determinants of enterovirus 71 infection and revealed a possible target for antiviral interventions.

  7. Use of hydrologic budgets and hydrochemistry to determine ground-water and surface-water interactions for Rapid Creek, Western South Dakota

    USGS Publications Warehouse

    Anderson, Mark T.

    1995-01-01

    The study of ground-water and surface-water interactions often employs streamflow-gaging records and hydrologic budgets to determine ground-water seepage. Because ground-water seepage usually is computed as a residual in the hydrologic budget approach, all uncertainty of measurement and estimation of budget components is associated with the ground-water seepage. This uncertainty can exceed the estimate, especially when streamflow and its associated error of measurement, is large relative to other budget components. In a study of Rapid Creek in western South Dakota, the hydrologic budget approach with hydrochemistry was combined to determine ground-water seepage. The City of Rapid City obtains most of its municipal water from three infiltration galleries (Jackson Springs, Meadowbrook, and Girl Scout) constructed in the near-stream alluvium along Rapid Creek. The reach of Rapid Creek between Pactola Reservoir and Rapid City and, in particular the two subreaches containing the galleries, were studied intensively to identify the sources of water to each gallery. Jackson Springs Gallery was found to pump predominantly ground water with a minor component of surface water. Meadowbrook and Girl Scout Galleries induce infiltration of surface water from Rapid Creek but also have a significant component of ground water.

  8. Genome-wide fitness and genetic interactions determined by Tn-seq, a high-throughput massively parallel sequencing method for microorganisms.

    PubMed

    van Opijnen, Tim; Camilli, Andrew

    2010-11-01

    The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobials and vaccines. Here we present the method Tn-seq, with which it has become possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies in the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing of the flanking regions en masse. These changes are used to calculate each mutant's fitness. The method has been developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis; however, due to the wide activity of the Mariner transposon, Tn-seq can be applied to many different microbial species.

  9. Rapid determination of cocamidopropyl betaine impurities in cosmetic products by core-shell hydrophilic interaction liquid chromatography-tandem mass spectrometry.

    PubMed

    Wang, Perry G; Zhou, Wanlong

    2016-08-26

    Cocamidopropyl betaine (CAPB) is a common surfactant widely used in personal care products. Dimethylaminopropylamine (DMAPA) and lauramidopropyldimethylamine (LAPDMA) are two chemicals present as impurities in CAPB and have been reported as skin sensitizers. A rapid and sensitive ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method, using a core shell hydrophilic interaction liquid chromatography (HILIC) column, has been developed to quantify DMAPA and LAPDMA in cosmetic products. Corresponding stable isotopically labeled analogues of the above native compounds were used as internal standards to compensate for matrix effect and for loss of recovery. Each sample was first screened to determine whether the sample needed to be diluted to minimize matrix effects as well as to fit the calibration range. The concept of matrix effect factor (MEF) was introduced to quantitatively evaluate each sample with a unique matrix using the internal standards. Recoveries at three spiking levels of low, medium, and high concentrations ranged from 98.4 to 112% with RSDs less than 5%. This method has been validated and is the first UHPLC-MS/MS method, which uses core shell HILIC column and stable isotopically labeled internal standards to simultaneously determine these two CAPB impurities in cosmetic products.

  10. New multi-component solid forms of anti-cancer drug Erlotinib: role of auxiliary interactions in determining a preferred conformation.

    PubMed

    Sanphui, Palash; Rajput, Lalit; Gopi, Shanmukha Prasad; Desiraju, Gautam R

    2016-06-01

    Erlotinib is a BCS (biopharmaceutical classification system) class II drug used for the treatment of non-small cell lung cancer. There is an urgent need to obtain new solid forms of higher solubility to improve the bioavailability of the API (active pharmaceutical ingredient). In this context, cocrystals with urea, succinic acid, and glutaric acid and salts with maleic acid, adipic acid, and saccharin were prepared via wet granulation and solution crystallizations. Crystal structures of the free base (Z' = 2), cocrystals of erlotinib-urea (1:1), erlotinib-succinic acid monohydrate (1:1:1), erlotinib-glutaric acid monohydrate (1:1:1) and salts of erlotinib-adipic acid adipate (1:0.5:0.5) are determined and their hydrogen-bonding patterns are analyzed. Self recognition via the (amine) N-H...N (pyridine) hydrogen bond between the API molecules is replaced by several heterosynthons such as acid-pyridine, amide-pyridine and carboxylate-pyridinium in the new binary systems. Auxiliary interactions play an important role in determining the conformation of the API in the crystal. FT-IR spectroscopy is used to distinguish between the salts and cocrystals in the new multi-component systems. The new solid forms are characterized by powder X-ray diffraction (PXRD) and differential scanning calorimetry (DSC) to confirm their unique phase identity.

  11. The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering

    NASA Astrophysics Data System (ADS)

    Zhou, Ying-lin; Li, Yuan-zong

    2004-01-01

    For the first time, poly(ethylenimine) (PEI) was used to determine nucleic acids with a light scattering technique using a common spectrofluorometer. The interaction of PEI with DNA results in greatly enhanced intensity of light scattering at 300 nm, which is caused by the formation of the big particles between DNA and PEI. Based on this, a new quantitative method for nucleic acid determination in aqueous solutions has been developed. Under the optimum conditions, the enhanced intensity of light scattering is proportional to the concentration of nucleic acid in the range of 0.01-10.0 μg ml -1 for herring sperm DNA (hsDNA), 0.02-10.0 μg ml -1 for calf thymus DNA (ctDNA), 0.02-20.0 μg ml -1 for yeast RNA (yRNA). The detection limits are 5.3, 9.9, and 13.7 ng ml -1, respectively. Synthetic samples were determined satisfactorily. At the same time, the light scattering technique has been successfully used to obtain the information on the effects of pH and ionic strength on the formation and the stability of the DNA/PEI complex, which is important in some fields such as genetic engineering and gene transfer. Using ethidium bromide (EB) as a fluorescent probe, the binding of PEI with hsDNA was studied. Both the binding constant of EB with DNA and the number of binding sites per nucleotide decrease with increasing concentration of PEI, indicating noncompetitive inhibition of EB binding to DNA in the presence of PEI. And the association constant of PEI to DNA obtained is 1.2×10 5 M -1. IR-spectra show that PEI interacts with DNA through both the phosphate groups and the bases of DNA and the formation of DNA/PEI complex may cause the change of the conformation of the DNA secondary structure, which is also proved by UV-spectra.

  12. Salting-out assisted extraction method coupled with hydrophilic interaction liquid chromatography for determination of selected β-blockers and their metabolites in human urine.

    PubMed

    Magiera, Sylwia; Kolanowska, Anna; Baranowski, Jacek

    2016-06-01

    In this study, a new analytical method was developed and validated for the simultaneous analysis of β-blockers (metoprolol, propranolol, carvedilol) and their metabolites (5'-hydroxycarvedilol, O-desmethylcarvedilol, α-hydroxymetoprolol, O-desmethylmetoprolol, 5-hydroxypropranolol) in human urine. A salting-out assisted liquid-liquid extraction (SALLE) procedure was used for sample preparation. Several parameters affecting the extraction efficiency and method sensitivity including the type and volume of the extraction solvent, the type and quantity of the inorganic salt, extraction time and sample pH were investigated. Hydrophilic interaction liquid chromatography-ultraviolet detection (HILIC-UV) was used for the determination of all analytes. During method development, the effects of mobile phase components (type, pH, concentration of salt, organic modifier type and content, flow rate, column temperature) on the retention and separation of β-blockers and metabolites on the five different HILIC columns were examined. The method was linear for concentrations ranging from 0.1 to 8.0μg/mL, with determination coefficients higher than 0.993 for all analytes. The limits of quantification were in the range from 0.1 to 0.2μg/mL. Intra- and inter-day precision ranged from 0.1 to 8.9%, and accuracy was within±13% interval for all analytes. Under the optimized conditions, extraction efficiency was greater than 83.4% for determined compounds. The validated method was then applied to the measurement of β-blockers and their metabolites in human urine samples.

  13. Membrane location of apocytochrome c and cytochrome c determined from lipid-protein spin exchange interactions by continuous wave saturation electron spin resonance.

    PubMed Central

    Snel, M M; Marsh, D

    1994-01-01

    Apocytochrome c derived from horse heart cytochrome c was spin-labeled on the cysteine residue at position 14 or 17 in the N-terminal region of the primary sequence, and cytochrome c from yeast was spin-labeled on the single cysteine residue at sequence position 102 in the C-terminal region. The spin-labeled apocytochrome c and cytochrome c were bound to fluid bilayers composed of different negatively charged phospholipids that also contained phospholipid probes that were spin-labeled either in the headgroup or at different positions in the sn-2 acyl chain. The location of the spin-labeled cysteine residues on the lipid-bound proteins was determined relative to the spin-label positions in the different spin-labeled phospholipids by the influence of spin-spin interactions on the microwave saturation properties of the spin-label electron spin resonance spectra. The enhanced spin relaxation observed in the doubly labeled systems arises from Heisenberg spin exchange, which is determined by the accessibility of the spin-label group on the protein to that on the lipid. It is found that the labeled cysteine groups in horse heart apocytochrome c are located closest to the 14-C atom of the lipid acyl chain when the protein is bound to dimyristoyl- or dioleoyl-phosphatidylglycerol, and to that of the 5-C atom when the protein is bound to a dimyristoylphosphatidylglycerol/dimyristoylphosphatidylcholine (15:85 mol/mol mixture. On binding to dioleoylphosphatidylglycerol, the labeled cysteine residue in yeast cytochrome c is located closest to the phospholipid headgroups but possibly between the polar group region and the 5-C atom of the acyl chains. These data determine the extent to which the different regions of the proteins are able to penetrate negatively charged phospholipid bilayers. Images FIGURE 1 PMID:7948687

  14. Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination

    PubMed Central

    Grimes, Daniel T.; Keynton, Jennifer L.; Buenavista, Maria T.; Jin, Xingjian; Patel, Saloni H.; Kyosuke, Shinohara; Williams, Debbie J.; Hamada, Hiroshi; Hussain, Rohanah; Nauli, Surya M.; Norris, Dominic P.

    2016-01-01

    During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we characterize a Pkd1l1 mutant line in which Nodal is activated bilaterally, suggesting that PKD1L1 is not required for LPM Nodal pathway activation per se, but rather to restrict Nodal to the left side downstream of nodal flow. Epistasis analysis shows that Pkd1l1 acts as an upstream genetic repressor of Pkd2. This study therefore provides a genetic pathway for the early stages of L-R determination. Moreover, using a system in which cultured cells are supplied artificial flow, we demonstrate that PKD1L1 is sufficient to mediate a Ca2+ signaling response after flow stimulation. Finally, we show that an extracellular PKD domain within PKD1L1 is crucial for PKD1L1 function; as such, destabilizing the domain causes L-R defects in the mouse. Our demonstration that PKD1L1 protein can mediate a response to flow coheres with a mechanosensation model of flow sensation in which the force of fluid flow drives asymmetric gene expression in the embryo. PMID:27272319

  15. Synthesis, CMC determination, and intercalative binding interaction with nucleic acid of a surfactant-copper(II) complex with modified phenanthroline ligand (dpq).

    PubMed

    Nagaraj, Karuppiah; Ambika, Subramanian; Arunachalam, Sankaralingam

    2015-01-01

    A surfactant-copper(II) complex, [Cu(dpq)2DA](ClO4)2 (dpq = dipyrido[3,2-d:2'-3'-f]quinoxaline; DA-dodecylamine), was synthesized and characterized on the basis of elemental analyses, UV-vis, IR, and EPR spectra. The critical micelle concentration (CMC) value of this surfactant-copper(II) complex in aqueous solution was found out from conductance measurements. Specific conductivity data at different temperature served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (ΔG°(m), ΔH°(m) and ΔS°(m)). In addition, the complex has been examined by its ability to bind to nucleic acids (DNA and RNA) in tris-HCl buffer by UV-vis absorption, emission spectroscopy techniques, and viscosity measurements. The complex has been found to bind strongly to nucleic acids with apparent binding constants at DNA and RNA is 4.3 × 10(5), 9.0 × 10(5) M(-1), respectively. UV-vis studies of the interaction of the complex with DNA/RNA have revealed that the complex can bind to both DNA and RNA by the intercalative binding mode via ligand dpq into the base pairs of DNA and RNA which has been verified by viscosity measurements. The presence of long aliphatic chain in the surfactant complex increases this hydrophobic interaction. The binding constants have been calculated. The cytotoxic activity of this complex on human liver carcinoma cancer cells was determined by adopting 3-(4, 5-dimethylthiazol-2-yl)-2, 5- diphenyl tetrazolium bromide assay and specific staining techniques. The antimicrobial and antifungal screening tests of this complex have shown good results.

  16. Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination.

    PubMed

    Grimes, Daniel T; Keynton, Jennifer L; Buenavista, Maria T; Jin, Xingjian; Patel, Saloni H; Kyosuke, Shinohara; Vibert, Jennifer; Williams, Debbie J; Hamada, Hiroshi; Hussain, Rohanah; Nauli, Surya M; Norris, Dominic P

    2016-06-01

    During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This 'nodal flow' is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we characterize a Pkd1l1 mutant line in which Nodal is activated bilaterally, suggesting that PKD1L1 is not required for LPM Nodal pathway activation per se, but rather to restrict Nodal to the left side downstream of nodal flow. Epistasis analysis shows that Pkd1l1 acts as an upstream genetic repressor of Pkd2. This study therefore provides a genetic pathway for the early stages of L-R determination. Moreover, using a system in which cultured cells are supplied artificial flow, we demonstrate that PKD1L1 is sufficient to mediate a Ca2+ signaling response after flow stimulation. Finally, we show that an extracellular PKD domain within PKD1L1 is crucial for PKD1L1 function; as such, destabilizing the domain causes L-R defects in the mouse. Our demonstration that PKD1L1 protein can mediate a response to flow coheres with a mechanosensation model of flow sensation in which the force of fluid flow drives asymmetric gene expression in the embryo.

  17. Hydrophobic interactions as key determinants to the KCa3.1 channel closed configuration. An analysis of KCa3.1 mutants constitutively active in zero Ca2+.

    PubMed

    Garneau, Line; Klein, Hélène; Banderali, Umberto; Longpré-Lauzon, Ariane; Parent, Lucie; Sauvé, Rémy

    2009-01-02

    In this study we present evidence that residue Val282 in the S6 transmembrane segment of the calcium-activated KCa3.1 channel constitutes a key determinant of channel gating. A Gly scan of the S6 transmembrane segment first revealed that the substitutions A279G and V282G cause the channel to become constitutively active in zero Ca2+. Constitutive activity was not observed when residues extending from Cys276 to Ala286, other than Ala279 and Val282, were substituted to Gly. The accessibility of Cys engineered at Val275 deep in the channel cavity was next investigated for the ion-conducting V275C/V282G mutant and closed V275C channel in zero Ca2+ using Ag+ as probe. These experiments demonstrated that internal Ag+ ions have free access to the channel cavity independently of the channel conducting state, arguing against an activation gate located at the S6 segment C-terminal end. Experiments were also conducted where Val282 was substituted by residues differing in size and/or hydrophobicity. We found a strong correlation between constitutive activity in zero Ca2+ and the hydrophobic energy for side chain burial. Single channel recordings showed finally that constitutive activation in zero Ca2+ is better explained by a model where the channel is locked in a low conducting state with a high open probability rather than resulting from a change in the open/closed energy balance that would favor channel openings to a full conducting state in the absence of Ca2+. We conclude that hydrophobic interactions involving Val282 constitute key determinants to KCa3.1 gating by modulating the ion conducting state of the selectivity filter through an effect on the S6 transmembrane segment.

  18. Study on the interaction between nucleic acid and Eu 3+-oxolinic acid and the determination of nucleic acid using the resonance light scattering technique

    NASA Astrophysics Data System (ADS)

    Wu, Xia; Sun, Shuna; Yang, Jinghe; Wang, Minqin; Liu, Liyan; Guo, Changying

    2005-12-01

    At pH 9.75, the resonance light scattering (RLS) intensity of OA-Eu 3+ system is greatly enhanced by nucleic acid. Based on this phenomenon, a new quantitative method for nucleic acid in aqueous solution has been developed. Under the optimum condition, the enhanced RLS is proportional to the concentration of nucleic acid in the range of 1.0 × 10 -9 to 1.0 × 10 -6 g/ml for herring sperm DNA, 8.0 × 10 -10 to 1.0 × 10 -6 g/ml for calf thymus DNA and 1.0 × 10 -9 to 1.0 × 10 -6 g/ml for yeast RNA, and their detection limits are 0.020, 0.011 and 0.010 ng/ml, respectively. Synthetic samples and actual samples were satisfactorily determined. In addition, the interaction mechanism between nucleic acid and OA-Eu 3+ is also investigated.

  19. Determination of the intersublattice exchange interactions in GdCo12-xFexB6 (x = 0-3) intermetallic compounds by high field magnetization measurements

    NASA Astrophysics Data System (ADS)

    Diop, L. V. B.; Isnard, O.; Skourski, Y.; Ballon, G.

    2013-05-01

    High field magnetization measurements up to 60 T on free powder samples from GdCo12-xFexB6 (x = 0-3) compounds are reported. The data were used to evaluate the microscopic exchange interaction integral, JGd-3d, between Gd and 3d (Co,Fe) spins. The systems are ferrimagnets; they order magnetically between TC = 95 K for x = 3 and TC = 165 K for x = 0. The low temperature magnetization curves as well as the temperature dependence of intrinsic magnetic parameters are determined by magnetic measurements in pulsed magnetic field. The average magnetic moment ⟨μCo+Fe⟩ per mean transition metal atom (Co + Fe) is small and increases with increasing Fe concentration from 0.44 μΒ for x = 0 to 0.51 μΒ for x = 3 at T = 4 K. From high field magnetization curves, a value of JGd-3d/kB = -4.65 K is derived for x = 0, whereas mean field approximation yields a much larger 3d-3d exchange integral of JCo-Co/kB = 105 K. The obtained results reveal an increase of -JGd-3d/kB with Fe concentration. For x = 0.5, the intersublattice coefficient nGd-3d is found to keep an almost constant value of 5.87 ± 0.13 T*f.u.*μB-1 whatever the temperature in the 2 to 60 K range.

  20. Using geochemical investigations for determining the interaction between groundwater and saline water in arid areas: case of the Wadi Ouazzi basin (Morocco)

    NASA Astrophysics Data System (ADS)

    El Moukhayar, R.; Bahir, M.; Youbi, N.; Chkir, N.; Chamchati, H.; Caréra, P.

    2015-04-01

    The characteristics of the Essaouira basin water resources are a semi-arid climate, which is severely impacted by the climate (quantity and quality). Considering the importance of the Essaouira aquifer in the groundwater supply of the region, a study was conducted in order to understand groundwater evolution in this aquifer. The Essaouira aquifer is a coastal aquifer located on the Atlantic coastline of southern Morocco, corresponding to a sedimentary basin with an area of nearly 200 km2. The control of the fluid exchange and the influence of mixing zones between the groundwater and saline water was investigated by sampling from 20 wells, drillings and sources belonging to the Plio-Quaternary and Turonian aquifers. It is hypothesized that groundwater major ions chemistry can be employed to determine the interaction between the groundwater and saline water (coastal aquifers). Groundwater samples examined for electric conductivity and temperature showed that waters belonging to the Plio-Quaternary and Turonian aquifers present very variable electric conductivities, from 900 μs/cm to 3880 μs/cm. Despite this variability, they are from the same family and are characterized by sodium-chloride facies. However, a good correlation exists between the electrical conductivity and chloride and sodium contents. The lower electrical conductivities are situated in the North quarter immediately to the south of the Wadi Ouazzi.

  1. Determination of D-glucaric acid and/or D-glucaro-1,4-lacton in different apple varieties through hydrophilic interaction chromatography.

    PubMed

    Xie, Baogang; Liu, Yalan; Zou, Huiqin; Son, Yong; Wang, Huiyun; Wang, Haipeng; Shao, Jianghua

    2016-07-15

    d-Glucaric acid (GA) derivatives exhibit anti-cancerogenic properties in vivo in apples, but quantitative information about these derivatives is limited. Hydrophilic interaction-based HPLC with ultraviolet detection or mass spectrometry was developed to quantify GA and/or D-glucaro-1,4-lacton (1,4-GL) in apples. Although the formation of 1,4-GL from GA could be the prerequisite to exert biological effects in vivo, only a small portion of GA (<5%) was identified and converted to 1,4-GL in the rat stomach. The 1,4-GL content in apples ranged from 0.3 mg/g to 0.9 mg/g, and this amount can substantiate health claims associated with apples. The amount of 1,4-GL was 1.5 times higher in Gala and the ratio of 1,4-GL to GA was lower in Green Delicious apples than those in the other varieties. Our findings suggested that the variety and maturity of apples at harvest are factors that determine 1,4-GL content.

  2. LC-MS/MS determination and interaction of the main components from the traditional Chinese drug pair Danshen-Sanqi based on rat intestinal absorption.

    PubMed

    Huang, Juan; Zhang, Jing; Bai, Junqi; Xu, Wen; Wu, Dinghong; Qiu, Xiaohui

    2016-12-01

    The Chinese drug pair Danshen (Salvia miltiorrhiza)-Sanqi (Panax ginseng) has been widely used for centuries treating various cardiovascular disorders, among which salvianlic acid B (SAB), ginsenoside Rg1 (GRg1 ), ginsenoside Rb1 (GRb1 ) and notoginsenoside R1 (NGR1 ) were identified as the major components. The present study focused on the interaction between these components based on investigating their intestinal absorption using the Ussing chamber technique. The concentrations of SAB, GRg1 , GRb1 and NGR1 in the intestinal perfusate were determined by LC-MS/MS method, followed by Q (accumulative quantity) and Papp (apparent permeability). The results showed that all these four main components displayed very low permeabilities, which implied their poor absorption in the rat intestine. The intestinal absorption level of SAB displayed regioselectivity: duodenum < jejunum < ileum. However, there was no significant difference in the absorption of GRg1 and GRb1 in the different segments. The Q and Papp values of the four main components were obviously increased in jejunum when co-administrating Danshen extract with Sanqi extract. In conclusion, compatibility of Danshen and Sanqi could remarkably improve the intestinal absorption level of the main components in the pair. To some extent, this might explain the nature of the compatibility mechanisms of composite formulae in TCMs.

  3. Quantitative determination of buprenorphine, naloxone and their metabolites in rat plasma using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Joshi, Anand; Parris, Brian; Liu, Yongzhen; Heidbreder, Christian; Gerk, Phillip M; Halquist, Matthew

    2017-02-01

    A rapid and sensitive LC-MS/MS method was developed and validated for the simultaneous determination of buprenorphine and its three metabolites (buprenorphine glucuronide, norbuprenorphine and norbuprenorphine glucuronide) as well as naloxone and its metabolite naloxone glucuronide in the rat plasma. A hydrophilic interaction chromatography column and a mobile phase containing acetonitrile and ammonium formate buffer (pH 3.5) were used for the chromatographic separation. Mass spectrometric detection was achieved by an electrospray ionization source in the positive mode coupled to a triple quadrupole mass analyzer. The calibration curves for the six analytes displayed good linearity over the concentration range 1.0 or 5.0-1000 ng/mL. The intra and inter-day precision (CV) ranged from 2.68 to 16.4% and from 9.02 to 14.5%, respectively. The intra- and inter-day accuracy (bias) ranged from -14.2 to 15.2% and from -9.00 to 4.80%, respectively. The extraction recoveries for all the analytes ranged from 55 to 86.9%. The LC-MS/MS method was successfully applied to a pharmacokinetic study of buprenorphine-naloxone combination in rats.

  4. Rapid determination of amino acids in fruits of Ziziphus jujuba by hydrophilic interaction ultra-high-performance liquid chromatography coupled with triple-quadrupole mass spectrometry.

    PubMed

    Guo, Sheng; Duan, Jin-ao; Qian, Dawei; Tang, Yuping; Qian, Yefei; Wu, Dawei; Su, Shulan; Shang, Erxin

    2013-03-20

    In this study, a sensitive and rapid method for the simultaneous determination of free amino acids without derivatization using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry (HILIC-MS/MS) was developed. The method was performed on an ultra-high-performance liquid chromatography (UHPLC) separation system coupled with a triple-quadrupole mass spectrometry (TQ-MS) instrument. Sufficient separation of 23 underivatized amino acids was achieved on an Acquity BEH Amide column (2.1 mm × 100 mm, 1.7 μm) in a single run of 12 min. Then the method was applied for the analysis of the free amino acids in 46 batches of Ziziphus jujuba fruits which comprised 39 cultivars from 26 cultivation regions. Multivariate statistical analysis was also used to investigate the differences in free amino acid profiles among the samples. This study showed that HILIC-UHPLC-TQ-MS is an effective technique to analyze underivatized amino acids in the food samples.

  5. The leucine-rich repeat domain can determine effective interaction between RPS2 and other host factors in arabidopsis RPS2-mediated disease resistance.

    PubMed Central

    Banerjee, D; Zhang, X; Bent, A F

    2001-01-01

    Like many other plant disease resistance genes, Arabidopsis thaliana RPS2 encodes a product with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. This study explored the hypothesized interaction of RPS2 with other host factors that may be required for perception of Pseudomonas syringae pathogens that express avrRpt2 and/or for the subsequent induction of plant defense responses. Crosses between Arabidopsis ecotypes Col-0 (resistant) and Po-1 (susceptible) revealed segregation of more than one gene that controls resistance to P. syringae that express avrRpt2. Many F(2) and F(3) progeny exhibited intermediate resistance phenotypes. In addition to RPS2, at least one additional genetic interval associated with this defense response was identified and mapped using quantitative genetic methods. Further genetic and molecular genetic complementation experiments with cloned RPS2 alleles revealed that the Po-1 allele of RPS2 can function in a Col-0 genetic background, but not in a Po-1 background. The other resistance-determining genes of Po-1 can function, however, as they successfully conferred resistance in combination with the Col-0 allele of RPS2. Domain-swap experiments revealed that in RPS2, a polymorphism at six amino acids in the LRR region is responsible for this allele-specific ability to function with other host factors. PMID:11333251

  6. Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair.

    PubMed

    Rupp, W Dean

    2013-12-13

    The discovery of nucleotide excision repair in 1964 showed that DNA could be repaired by a mechanism that removed the damaged section of a strand and replaced it accurately by using the remaining intact strand as the template. This result showed that DNA could be actively metabolized in a process that had no precedent. In 1968, experiments describing postreplication repair, a process dependent on homologous recombination, were reported. The authors of these papers were either at Yale University or had prior Yale connections. Here we recount some of the events leading to these discoveries and consider the impact on further research at Yale and elsewhere.

  7. Hydrophilic interaction chromatography combined with dispersive liquid-liquid microextraction as a preconcentration tool for the simultaneous determination of the panel of underivatized neurotransmitters in human urine samples.

    PubMed

    Konieczna, Lucyna; Roszkowska, Anna; Niedźwiecki, Maciej; Bączek, Tomasz

    2016-01-29

    A simple and sensitive method using dispersive liquid-liquid microextraction (DLLME) followed by liquid chromatography coupled to mass spectrometry (LC-MS) with a hydrophilic interaction chromatography (HILIC) column was developed for the simultaneous determination of 13 compounds of different polarities, comprising monoamine neurotransmitters (dopamine, norepinephrine, epinephrine and serotonin) along with their respective precursors and metabolites, in human urine samples. The microextraction procedure was based on the fast injection of a mixture of ethanol (disperser solvent) and dichloromethane (extraction solvent) into a human urine sample, forming a cloudy solution in the Eppendorf tube. After centrifugation, the sedimented phase was collected and subsequently analyzed by LC-HILIC-MS in about 12min without a derivatization step. The separation was performed on an XBridge Amide™ BEH column 3.0×100mm, 3.5mm and the mobile phase consisted of phase A: 10mM ammonium formate buffer in water pH 3.0 and phase B: 10 mM ammonium formate buffer in acetonitrile, under gradient program elution. Tyrosine, tryptophan, 5-hydroxytryptophan, dopamine, epinephrine, norepinephrine, serotonin, 3-methoxytyramine, 5-hydroxyindole-3-acetic acid, 3,4-dihydroxy-l-phenylalanine and norvaline (internal standard) were detected in the positive ionization mode. While vanillylmandelic acid, homovanillic acid, 3,4-dihydroxyphenylacetic acid and 3,4-dihydroxybenzylamine (internal standard) were detected in the negative ionization mode. Parameters influencing DLLME and LC-HILIC-MS were investigated. Under the optimum conditions, the proposed method exhibited a low detection limit (5-10ngmL(-1)), and good linearity with R between 0.9991 and 0.9998. The recoveries in human urine samples were 99.0%±3.6%. for the 13 studied biogenic amines with intra- and inter-day RSDs of 0.24-9.55% and 0.31-10.0%, respectively. The developed DLLME-LC-MS method could be successfully applied for the

  8. Determinants of the human immunodeficiency virus type 1 p15NC-RNA interaction that affect enhanced cleavage by the viral protease.

    PubMed Central

    Sheng, N; Pettit, S C; Tritch, R J; Ozturk, D H; Rayner, M M; Swanstrom, R; Erickson-Viitanen, S

    1997-01-01

    During human immunodeficiency virus type 1 (HIV-1) virion assembly, cleavage of the Gag precursor by the viral protease results in the transient appearance of a nucleocapsid-p1-p6 intermediate product designated p15NC. Utilizing the p15NC precursor protein produced with an in vitro transcription-translation system or purified after expression in Escherichia coli, we have demonstrated that RNA is required for efficient cleavage of HIV p15NC. Gel mobility shift and nitrocellulose filter binding experiments indicate that purified p15NC protein specifically binds its corresponding mRNA with an estimated Kd of 1.5 nM. Binding was not affected by the presence or absence of zinc or EDTA. Moreover, mutagenesis of the cysteine residues within either of the two Cys-His arrays had no effect on RNA binding or on RNA-dependent cleavage by the viral protease. In contrast, decreased binding of RNA and diminished susceptibility to cleavage in vitro were observed with p15NC-containing mutations in one or more residues within the triplet of basic amino acids present in the region between the two zinc fingers. In addition, we found that 21- to 24-base DNA and RNA oligonucleotides of a particular sequence and secondary structure could substitute for p15 RNA in the enhancement of p15NC cleavage. Virus particles carrying a mutation in the triplet of NC basic residues (P3BE) show delayed cleavage of p15NC and a defect in core formation despite the eventual appearance of fully processed virion protein. These results define determinants of the p15NC-RNA interaction that lead to enhanced protease-mediated cleavage and demonstrate the importance of the triplet of basic residues in formation of the virus core. PMID:9223458

  9. Determinants of natural immunity against tuberculosis in an endemic setting: factors operating at the level of macrophage–Mycobacterium tuberculosis interaction

    PubMed Central

    Gaikwad, A N; Sinha, Sudhir

    2008-01-01

    We aimed to delineate factors operating at the interface of macrophage–mycobacterium interaction which could determine the fate of a ‘subclinical’ infection in healthy people of a tuberculosis-endemic region. Ten study subjects (blood donors) were classified as ‘high’ or ‘low’ responders based on the ability of their monocyte-derived macrophages to restrict or promote an infection with Mycobacterium tuberculosis. Bacterial multiplication between days 4 and 8 in high responder macrophages was significantly lower (P < 0·02) than low responders. All donor sera were positive for antibodies against cell-membrane antigens of M. tuberculosis and bacilli opsonized with heat-inactivated sera were coated with IgG. In low responder macrophages, multiplication of opsonized bacilli was significantly less (P < 0·04) than that of unopsonized bacilli. The levels of tumour necrosis factor (TNF)-α and interleukin (IL)-12 produced by infected high responder macrophages was significantly higher (P < 0·05) than low responders. However, infection with opsonized bacilli enhanced the production of IL-12 in low responders to its level in high responders. The antibody level against membrane antigens was also significantly higher (P < 0·05) in high responders, although the antigens recognized by two categories of sera were not remarkably different. Production of certain other cytokines (IL-1β, IL-4, IL-6 and IL-10) or reactive oxygen species (H2O2 and NO) by macrophages of high and low responders did not differ significantly. The study highlights the heterogeneity of Indian subjects with respect to their capability in handling subclinical infection with M. tuberculosis and the prominent role that TNF-α, opsonizing antibodies and, to a certain extent, IL-12 may play in containing it. PMID:18234054

  10. Determination of salivary cotinine through solid phase extraction using a bead-injection lab-on-valve approach hyphenated to hydrophilic interaction liquid chromatography.

    PubMed

    Ramdzan, Adlin N; Barreiros, Luísa; Almeida, M Inês G S; Kolev, Spas D; Segundo, Marcela A

    2016-01-15

    Cotinine, the first metabolite of nicotine, is often used as a biomarker in the monitoring of environmental tobacco smoke (ETS) exposure due to its long half-life. This paper reports on the development of an at-line automatic micro-solid phase extraction (μSPE) method for the determination of salivary cotinine followed by its analysis via hydrophilic interaction liquid chromatography (HILIC). The SPE methodology is based on the bead injection (BI) concept in a mesofluidic lab-on-valve (LOV) flow system to automatically perform all SPE steps. Three commercially available reversed-phase sorbents were tested, namely, Oasis HLB, Lichrolut EN and Focus, and the spherically shaped sorbents (i.e., Oasis HLB and Focus) provided better packing within the SPE column and hence higher column efficiency. An HILIC column was chosen based on its potential for achieving higher sensitivity and better retention of polar compounds such as cotinine. The method uses an isocratic program with acetonitrile:100mM ammonium acetate buffer, pH 5.8 in 95:5 v/v ratio as the mobile phase at a flow rate of 1.0 mL min(-1). Using this approach, the linear calibration range was from 10 to 1000 ng which corresponded to 5-500 μg L(-1). The corresponding μSPE-BI-LOV system was proven to be reliable in the handing and analysis of viscous biological samples such as saliva, achieving a sampling rate of 6h(-1) and a limit of detection and quantification of 1.5 and 3μgL(-1), respectively.

  11. Determination of vanadium as 4-(2-pyridylazo)resorcinol-hydrogen peroxide ternary complexes by ion-interaction reversed-phase liquid chromatography.

    PubMed

    Vachirapatama, Narumol; Dicinoski, Greg W; Townsend, Ashley T; Haddad, Paul R

    2002-05-17

    The separation and determination of the vanadium(V) ternary complex formed with 4-(2-pyridylazo)resorcinol (PAR) and hydrogen peroxide using ion-interaction reversed-phase high-performance liquid chromatography on a C18 column has been investigated. The optimal mobile phase was a methanol-water solution (32:68, v/v) containing 3 mM tetrabutylammonium bromide, 5 mM acetic acid and 5 mM citrate buffer at pH 7, with absorbance detection at 540 nm. The stoichiometry of the ternary complex of vanadium at pH 6 in 10 mM acetate buffer using the mole ratio and Job's method by HPLC indicated that the mole ratio of V(V):PAR:H2O2 was 1:1:1. The optimal conditions for precolumn formation of the ternary complex were 10 mM acetate, 7 mM H2O2, 0.3 mM PAR, and pH 6. The method gave relative standard deviations of retention time, peak area and peak height for the ternary complex of 0.187, 0.45 and 0.57%, respectively. The detection limit (at a signal-to-noise ratio of 3) for V(V) was 0.09 ng/ml in the digested sample using a 100-microl injection loop (or 0.09 microg/g in the solid fertiliser sample). The method was applied to the analysis of fertilisers (phosphate rocks and nitrogen, phosphorus and potassium fertiliser). The results for vanadium obtained by the HPLC method agreed well with those from magnetic sector inductively coupled plasma MS analysis.

  12. Comparison of hydrophilic interaction and reversed phase liquid chromatography coupled with tandem mass spectrometry for the determination of eight artificial sweeteners and common steviol glycosides in popular beverages.

    PubMed

    Kubica, Paweł; Namieśnik, Jacek; Wasik, Andrzej

    2016-08-05

    Hydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry (MS/MS) was used to separate artificial and natural sweeteners approved for use in European Union (EU). Among three tested HILIC columns (BlueOrchid PAL-HILIC, Ascentis Express Si and Acclaim™ Trinity™ P2) the last one was selected for the development of HILIC method due to the best results obtained with it. Early eluting and coeluting compounds in HILIC (acesulfame-K, saccharin, cyclamate, sucralose and aspartame) were successfully separated by the HILIC-based approach for the first time. The developed HILIC method allows for determination of all high potency sweeteners in one analytical run. The calibration curves for all analytes had good linearity within the tested ranges. The limits of detection and quantitation were in the range 0.81-3.30ng/mL and 2.32-9.89ng/mL, respectively. The obtained recoveries used for trueness and precision estimation were from 98.6% to 106.2% with standard deviation less than 4.1%. Sample preparation was reduced to a necessary minimum and contained only proper dilution and centrifugation. More than twenty samples of beverages were analyzed with the developed HILIC method. Finally, the chromatographic parameters of peaks (reduced retention time, width at baseline, width at 50% of peak height, tailing factor and efficiency) obtained in HILIC mode and in RPLC mode were compared. Developed HILIC method along with RPLC method can be applied for rapid evaluation of sweeteners' content, quality and safety control.

  13. Determination of phospholipids in milk samples by means of hydrophilic interaction liquid chromatography coupled to evaporative light scattering and mass spectrometry detection.

    PubMed

    Donato, Paola; Cacciola, Francesco; Cichello, Filomena; Russo, Marina; Dugo, Paola; Mondello, Luigi

    2011-09-16

    The combined use of the state-of-the-art hybrid mass spectrometers together with high efficient liquid chromatography could surely be a useful tool for such a challenging task, as phospholipids (PLs) analysis. In this research, we used hydrophilic interaction liquid chromatography (150 mm×2.1 mm I.D., 2.7 μm d.p. partially porous column) to achieve the separation of major PLs classes in cow's and donkey's milk samples. Solid-phase extraction (SPE) was performed in order to pre-concentrate minor PLs from non polar lipids (triacylglycerols) and the recovery for the extraction method was assayed on a milk sample, fortified with 5 μg/mL of SM pure standard, and analyzed in triplicate. A value of 89.99% was calculated, with a coefficient of variation (CV%) of 1.93. A 70-min long stepwise gradient of water/acetonitrile afforded baseline separation of PLs classes, at 50 μL/min flow rate. Accurate detection by an ion trap-time of flight (IT-TOF) mass spectrometer (in both positive and negative ionization mode) allowed to fully characterize the distinctive phospholipid profile and fatty acid composition of cow's and donkey's milk, the latter being analyzed for the first time. Evaporative light scattering detection was further employed to attain the quantitative evaluation of major PLs classes identified, by the external calibration method using reference material solutions in the 5-200 μg/mL concentration range. Major difference between the two analyzed samples consisted in the total PLs amount, which in cow's milk was determined as over 20-fold higher than the donkey's.

  14. Capillary electrophoresis coupled with end-column electrochemiluminescence for the determination of ephedrine in human urine, and a study of its interactions with three proteins.

    PubMed

    Yang, Ran; Zeng, Hua-Jin; Li, Jian-Jun; Zhang, Ying; Li, Shi-Jun; Qu, Ling-Bo

    2011-01-01

    A tris(2,2-bipyridyl)ruthenium(II) (Ru(bpy)₃²⁺)-based electrochemiluminescence (ECL) detection coupled with capillary electrophoresis (CE) method has been established for the sensitive determination of ephedrine for the first time. Under the optimized conditions [ECL detection at 1.15 V, 25 mmol/L phosphate buffer solution (PBS), pH 8.0, as running buffer, separation voltage 12.5 kV, 5 mmol/L Ru(bpy)₃²⁺ with 60 mmol/L PBS, pH 8.5, in the detection cell] linear correlation (r = 0.9987) between ECL intensity and ephedrine concentration was obtained in the range 6.0 × 10⁻⁸-6.0 × 10⁻⁶ g/mL. The detection limit was 4.5 × 10⁻⁹ g/mL (S:N = 3). The developed method was successfully applied to the analysis of ephedrine in human urine and the investigation of its interactions with three proteins, including bovine serum albumin (BSA), cytochrome C (Cyt-C) and myoglobin (Mb). The number of binding sites and the binding constants between ephedrine and BSA, Cyt-C and Mb were 8.52, 12.60, 10.66 and 1.55 × 10⁴  mol/L, 6.58 × 10³  mol/L and 1.59 × 10⁴  mol/L, respectively.

  15. "I'm Prepared for Anything Now": Student Teacher and Cooperating Teacher Interaction as a Critical Factor in Determining the Preparation of "Quality" Elementary Reading Teachers

    ERIC Educational Resources Information Center

    Lesley, Mellinee K.; Hamman, Doug; Olivarez, Arturo; Button, Kathryn; Griffith, Robin

    2009-01-01

    This research is an examination of the interactions between 19 pairs of student teachers and cooperating teachers engaged in guided reading instruction in Grades 1 through 3. As the basis for the study, the authors analyzed interaction patterns through conducting content analysis (Van Sluys, Lewison, & Seely Flint, 2006) and discourse analysis…

  16. Enhancing User Experience through Emotional Interaction: Determining Users' Interests in Online Art Collections Using AMARA (Affective Museum of Art Resource Agent)

    ERIC Educational Resources Information Center

    Park, S. Joon

    2013-01-01

    The need for emotional interaction has already influenced various disciplines and industries, and online museums represent a domain where providing emotional interactions could have a significant impact. Today, online museums lack the appropriate affective and hedonic values necessary to engage art enthusiasts on an emotional level. To address…

  17. Structural determinants for binding of sorting nexin 17 (SNX17) to the cytoplasmic adaptor protein Krev interaction trapped 1 (KRIT1).

    PubMed

    Stiegler, Amy L; Zhang, Rong; Liu, Weizhi; Boggon, Titus J

    2014-09-05

    Sorting nexin 17 (SNX17) is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. SNX17 localizes to early endosomes where it directly binds NPX(Y/F) motifs in the cytoplasmic tails of its target receptors to mediate their rates of endocytic internalization, recycling, and/or degradation. SNX17 has also been implicated in mediating cell signaling and can interact with cytoplasmic proteins. KRIT1 (Krev interaction trapped 1), a cytoplasmic adaptor protein associated with cerebral cavernous malformations, has previously been shown to interact with SNX17. Here, we demonstrate that SNX17 indeed binds directly to KRIT1 and map the binding to the second Asn-Pro-Xaa-Tyr/Phe (NPX(Y/F)) motif in KRIT1. We further characterize the interaction as being mediated by the FERM domain of SNX17. We present the co-crystal structure of SNX17-FERM with the KRIT1-NPXF2 peptide to 3.0 Å resolution and demonstrate that the interaction is highly similar in structure and binding affinity to that between SNX17 and P-selectin. We verify the molecular details of the interaction by site-directed mutagenesis and pulldown assay and thereby confirm that the major binding site for SNX17 is confined to the NPXF2 motif in KRIT1. Taken together, our results verify a direct interaction between SNX17 and KRIT1 and classify KRIT1 as a SNX17 binding partner.

  18. Determination of nicotine and nicotine metabolites in urine by hydrophilic interaction chromatography-tandem mass spectrometry: Potential use of smokeless tobacco products by ice hockey players.

    PubMed

    Marclay, François; Saugy, Martial

    2010-11-26

    Consumption of nicotine in the form of smokeless tobacco (snus, snuff, chewing tobacco) or nicotine-containing medication (gum, patch) may benefit sport practice. Indeed, use of snus seems to be a growing trend and investigating nicotine consumption amongst professional athletes is of major interest to sport authorities. Thus, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection and quantification of nicotine and its principal metabolites cotinine, trans-3-hydroxycotinine, nicotine-N'-oxide and cotinine-N-oxide in urine was developed. Sample preparation was performed by liquid-liquid extraction followed by hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS/MS) operated in electrospray positive ionization (ESI) mode with selective reaction monitoring (SRM) data acquisition. The method was validated and calibration curves were linear over the selected concentration ranges of 10-10,000 ng/mL for nicotine, cotinine, trans-3-hydroxycotinine and 10-5000 ng/mL for nicotine-N'-oxide and cotinine-N-oxide, with calculated coefficients of determination (R(2)) greater than 0.95. The total extraction efficiency (%) was concentration dependent and ranged between 70.4 and 100.4%. The lower limit of quantification (LLOQ) for all analytes was 10 ng/mL. Repeatability and intermediate precision were ≤9.4 and ≤9.9%, respectively. In order to measure the prevalence of nicotine exposure during the 2009 Ice Hockey World Championships, 72 samples were collected and analyzed after the minimum of 3 months storage period and complete removal of identification means as required by the 2009 International Standards for Laboratories (ISL). Nicotine and/or metabolites were detected in every urine sample, while concentration measurements indicated an exposure within the last 3 days for eight specimens out of ten. Concentrations of nicotine, cotinine, trans-3-hydroxycotinine, nicotine-N'-oxide and cotinine-N-oxide were found to range

  19. A 96-well single-pot liquid-liquid extraction, hydrophilic interaction liquid chromatography-mass spectrometry method for the determination of muraglitazar in human plasma.

    PubMed

    Xue, Y-J; Liu, Jane; Unger, Steve

    2006-06-07

    A single-pot liquid-liquid extraction (LLE) with hydrophilic interaction liquid chromatography/tandem mass spectrometry (HILIC/MS/MS) method has been developed and validated for the determination of muraglitazar, a hydrophobic diabetes drug, in human plasma. To 0.050 ml of each plasma sample in a 96-well plate, the internal standard solution in acetonitrile and toluene were added to extract the compound of interest. The plate was vortexed, followed by centrifugation. The organic layer was then directly injected into an LC/MS/MS system. Chromatographic separation was achieved isocratically on a Thermohypersil_Keystone, Hypersil silica column (3 mmx50 mm, 3 microm). The mobile phase contained 85% of methyl t-butyl ether and 15% of 90/10 (v/v) acetonitrile/water with 0.3% trifluoroacetic acid. Post-column mobile phase of 50/50 (v/v) acetonitrile/water containing 0.1% formic acid was added. Detection was by positive ion electrospray tandem mass spectrometry on a Sciex API 4000. The standard curve, ranged from 1 to 1000 ng/ml, was fitted to a 1/x weighted quadratic regression model. This single-pot LLE approach effectively eliminated time-consuming organic layer transfer, dry-down, and sample reconstitution steps, which are essential for a conventional liquid-liquid extraction procedure. The modified mobile phase was more compatible with the direct injection of the commonly used extraction solvents in LLE. Furthermore, the modified mobile phase improved the retention of muraglitazar, a hydrophobic compound, on the normal phase silica column. The validation results demonstrated that this method was rugged and suitable for analyzing muraglitazar in human plasma. In comparison with a revised-phase LC/MS/MS method, this single-pot LLE, HILIC/MS/MS method improved the detection sensitivity by more than four-fold based upon the LLOQ signal to noise ratio. This approach may be applied to other hydrophobic compounds with proper modification of the mobile phase compositions.

  20. Conserved charged amino acids are key determinants for fatty acid binding proteins (FABPs)-membrane interactions. A multi-methodological computational approach.

    PubMed

    Zamarreño, Fernando; Giorgetti, Alejandro; Amundarain, María Julia; Viso, Juan Francisco; Córsico, Betina; Costabel, Marcelo D

    2017-03-16

    Based on the analysis of the mechanism of ligand transfer to membranes employing in vitro methods, Fatty Acid Binding Protein (FABP) family has been divided in two subgroups: collisional and diffusional FABPs. Although the collisional mechanism has been well characterized employing in vitro methods, the structural features responsible for the difference between collisional and diffusional mechanisms remain uncertain. In this work, we have identified the amino acids putatively responsible for the interaction with membranes of both, collisional and diffusional, subgroups of FABPs. Moreover, we show how specific changes in FABPs' structure could change the mechanism of interaction with membranes. We have computed protein-membrane interaction energies for members of each subgroup of the family, and performed Molecular Dynamics simulations that have shown different configurations for the initial interaction between FABPs and membranes. In order to generalize our hypothesis, we extended the electrostatic and bioinformatics analysis over FABPs of different mammalian genus. Also, our methodological approach could be used for other systems involving protein-membrane interactions.

  1. Determination of temperate bird-flower interactions as entangled mutualistic and antagonistic sub-networks: characterization at the network and species levels.

    PubMed

    Yoshikawa, Tetsuro; Isagi, Yuji

    2014-05-01

    Most network studies on biological interactions consider only a single interaction type. However, individual species are simultaneously positioned in various types of interactions. The ways in which different network types are merged and entangled, and the variations in network structures between different sympatric networks, require full elucidation. Incorporating interaction types and disentangling complex networks is crucial, because the integration of various network architectures has the potential to alter the stability and co-evolutionary dynamics of the whole network. To reveal how different types of interaction networks are entangled, we focused on the interaction between birds and flowers of temperate plants in Japan, where flower-feeding birds are mainly generalist passerines, acting as pollinators and predators of flowers. Using long-term monitoring data, we investigated the flower-feeding episodes of birds. We constructed the whole network (WN) between birds and plants, separating the network into mutualistic and antagonistic sub-networks (MS and AS, respectively). We investigated structural properties of the three quantified networks and species-level characteristics of the main bird species. For bird species, we evaluated dietary similarity, dietary specialization and shifts of feeding behaviour relative to plant traits. Our results indicate that WN comprises entangled MS and AS, sharing considerable proportions of bird and plant assemblages. We observed distinctive differences in the network structural properties between the two sub-networks. In comparison with AS, MS had lower numbers of bird and plant species, showed lower specialization and modularity and exhibited higher nestedness. At the species level, the Japanese white-eye acted as pollinator, while the brown-eared bulbul acted as both pollinator and predator for large numbers of flowers, based on its behavioural plasticity. Overall, the pattern of avian feeding behaviour was influenced by

  2. Root distribution and interactions between allelopathic rice and c4 grass weed species as determined by 13c isotope discrimination analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivars which carry allelopathic traits (traits that enable them to suppress weeds) could improve the economical management and sustainability of rice production. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but ...

  3. Interaction of flavan-3-ol derivatives and different caseins is determined by more than proline content and number of proline repeats.

    PubMed

    Bohin, Maxime C; Vincken, Jean-Paul; Westphal, Adrie H; Tripp, Annelise M; Dekker, Peter; van der Hijden, Harry T W M; Gruppen, Harry

    2014-09-01

    Interactions of Type A and B flavan-3-ol dimers (procyanidins) and several monomeric flavan-3-ols, with α-casein and β-casein, were investigated. Binding affinities measured were related to the ligands structure, including several properties (e.g. intrinsic flexibility (number of rotatable bonds) and hydrophobicity), and to the amino-acid composition of the caseins. A monomeric flavan-3-ol esterified with gallic acid (EGCG) had a five to ten times higher affinity to caseins compared to the non-galloylated dimeric flavan-3-ols. In this case, the larger number of rotatable bonds in EGCG might be accountable for this difference. Comparing flavan-3-ol dimers, intrinsic flexibility did not consistently promote interactions, as procyanidin A1 displayed a higher affinity to α-casein than the supposedly more flexible B-type dimers investigated. Despite its higher content of proline, compared to α-casein, β-casein did not always have a higher affinity for the ligands investigated (e.g. no interaction with procyanidin A1 detected). These results suggest that more factors than proline content and the number of proline repeats govern phenolic-casein interactions.

  4. Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly.

    PubMed

    Cho, Suhyung; Hoang, Amy; Sinha, Rahul; Zhong, Xiang-Yang; Fu, Xiang-Dong; Krainer, Adrian R; Ghosh, Gourisankar

    2011-05-17

    It has been widely accepted that the early spliceosome assembly begins with U1 small nuclear ribonucleoprotein (U1 snRNP) binding to the 5' splice site (5'SS), which is assisted by the Ser/Arg (SR)-rich proteins in mammalian cells. In this process, the RS domain of SR proteins is thought to directly interact with the RS motif of U1-70K, which is subject to regulation by RS domain phosphorylation. Here we report that the early spliceosome assembly event is mediated by the RNA recognition domains (RRM) of serine/arginine-rich splicing factor 1 (SRSF1), which bridges the RRM of U1-70K to pre-mRNA by using the surface opposite to the RNA binding site. Specific mutation in the RRM of SRSF1 that disrupted the RRM-RRM interaction also inhibits the formation of spliceosomal E complex and splicing. We further demonstrate that the hypo-phosphorylated RS domain of SRSF1 interacts with its own RRM, thus competing with U1-70K binding, whereas the hyper-phosphorylated RS domain permits the formation of a ternary complex containing ESE, an SR protein, and U1 snRNP. Therefore, phosphorylation of the RS domain in SRSF1 appears to induce a key molecular switch from intra- to intermolecular interactions, suggesting a plausible mechanism for the documented requirement for the phosphorylation/dephosphorylation cycle during pre-mRNA splicing.

  5. Determination of cell metabolite VEGF₁₆₅ and dynamic analysis of protein-DNA interactions by combination of microfluidic technique and luminescent switch-on probe.

    PubMed

    Lin, Xuexia; Leung, Ka-Ho; Lin, Ling; Lin, Luyao; Lin, Sheng; Leung, Chung-Hang; Ma, Dik-Lung; Lin, Jin-Ming

    2016-05-15

    In this paper, we rationally design a novel G-quadruplex-selective luminescent iridium (III) complex for rapid detection of oligonucleotide and VEGF165 in microfluidics. This new probe is applied as a convenient biosensor for label-free quantitative analysis of VEGF165 protein from cell metabolism, as well as for studying the kinetics of the aptamer-protein interaction combination with a microfluidic platform. As a result, we have successfully established a quantitative analysis of VEGF165 from cell metabolism. Furthermore, based on the principles of hydrodynamic focusing and diffusive mixing, different transient states during kinetics process were monitored and recorded. Thus, the combination of microfluidic technique and G-quadruplex luminescent probe will be potentially applied in the studies of intramolecular interactions and molecule recognition in the future.

  6. On-line determination by small angle X-ray scattering of the shape of hen egg white lysozyme immediately following elution from a hydrophobic interaction chromatography column.

    PubMed

    Kulsing, Chadin; Komaromy, Andras Z; Boysen, Reinhard I; Hearn, Milton T W

    2016-10-21

    This study documents the use of an integrated approach, involving on-line hydrophobic interaction chromatography interfaced with Small Angle X-ray Scattering (HIC-SAXS) measurements, to monitor the conformational status of proteins immediately upon elution from a chromatographic column operated at different temperatures. Moreover, this approach provides an additional avenue to interrogate the changes in protein shape that may occur across the eluted chromatographic peak. To this end, radii of gyration were extrapolated from the Guinier approximation with the HIC-SAXS data, whilst pair distribution functions and bead model simulations were generated by using the indirect transform program GNOM and ab initio reconstruction with GASBOR to provide further insight into protein conformational changes that occur during hydrophobic interaction chromatography.

  7. The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions

    PubMed Central

    Nanou, Aikaterini; Toumpeki, Chrisavgi; Lavigne, Matthieu D.; Lazou, Vassiliki; Demmers, Jeroen; Paparountas, Triantafillos; Thanos, Dimitris; Katsantoni, Eleni

    2017-01-01

    STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here, LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a GAS motif, and such binding induced activation or repression. Strong STAT5 binding was seen more frequently in intergenic regions, which might function as distal enhancer elements. Groups of genes bound weaker by STAT5a and stronger by LSD1/HDAC3 showed an absence of the GAS motif, and were differentially regulated based on their genomic binding localization and binding affinities. These genes exhibited increased binding frequency in promoters, and in conjunction with the absence of GAS sites, the data indicate a requirement for stabilization by additional factors, which might recruit LSD1/HDAC3. Our study describes an interaction network of STAT5a/LSD1/HDAC3 and a dual function of LSD1/HDAC3 on STAT5-dependent transcription, defined by protein–protein interactions, genomic binding localization/affinity and motifs. PMID:27651463

  8. Interaction between the first and last nucleotides of pre-mRNA introns is a determinant of 3' splice site selection in S. cerevisiae.

    PubMed Central

    Chanfreau, G; Legrain, P; Dujon, B; Jacquier, A

    1994-01-01

    The splicing of group II and nuclear pre-mRNAs introns occurs via a similar splicing pathway and some of the RNA-RNA interactions involved in these splicing reactions show structural similarities. Recently, genetic analyses performed in a group II intron and the yeast nuclear actin gene suggested that non Watson-Crick interactions between intron boundaries are important for the second splicing step efficiency in both classes of introns. We here show that, in the yeast nuclear rp51A intron, a G to A mutation at the first position activates cryptic 3' splice sites with the sequences UAC/ or UAA/. Moreover, the natural 3' splice site could be reactivated by a G to C substitution of the last intron nucleotide. These results demonstrate that the interaction between the first and last intron nucleotides is a conserved feature of nuclear pre-mRNA splicing in yeast and is involved in the mechanism of 3' splice site selection. Images PMID:8029003

  9. Non-linear Tidal Interactions and Their Role in Determining the Mean State and Variability of the Ionosphere-Thermosphere (IT) System

    NASA Astrophysics Data System (ADS)

    Jones, McArthur, Jr.

    Atmospheric tides are vertically-propagating waves generated in the lower and middle atmosphere that are widely known to affect the dynamics and electrodynamics of the ionosphere-thermosphere (IT) system. The tidal spectrum evolves with height due to wave-mean flow, wave-wave, and wave-plasma interactions, leading to the tidal spectrum observed by ground- and space-based observing platforms in the IT. Some of these observations and prior theoretical work suggest that non-linear interactions may produce important effects. However, one can only speculate about how non-linear tidal interactions and their various generation mechanisms might result in mean state, spatial, and temporal variations in the IT system based on prior work. Through numerical experiments performed with the National Center for Atmospheric Research Thermosphere General Circulation Models, this work seeks to quantify and understand how non-linear tidal interactions affect the IT system. The main results to emerge from this study are as follows: (1) Interaction between the zonally-symmetric solar-driven circulation and the longitude-dependent ionospheric magneto-plasma produce non-migrating atmospheric tides that reconcile existing data-model disparities, mainly under solar maximum conditions; (2) Dissipating tides of lower atmospheric origin act to alter the pressure gradient force via the eddy heat transport causing zonal-mean wind differences of up to 30 m/s in the dynamo region; (3) Variations of up to 30 K in zonal-mean temperatures of the IT between solar minimum and maximum result from a combination of net eddy heat transport effects and tidal modulation of net nitric oxide cooling; (4) The net transport of atomic oxygen produced by dissipating tides is shown to significantly contribute to atomic oxygen changes in the IT; (5) Measurable solar cycle variations in electron density in the F-region result from tidally driven net changes in the major constituents of the thermosphere. The major

  10. Interactions between Multiple Genetic Determinants in the 5′ UTR and VP1 Capsid Control Pathogenesis of Chronic Post-Viral Myopathy caused by Coxsackievirus B1

    PubMed Central

    Sandager, Maribeth M.; Nugent, Jaime L.; Schulz, Wade L.; Messner, Ronald P.; Tam, Patricia E.

    2008-01-01

    Mice infected with coxsackievirus B1 Tucson (CVB1T) develop chronic, post-viral myopathy (PVM) with clinical manifestations of hind limb muscle weakness and myositis. The objective of the current study was to establish the genetic basis of myopathogenicity in CVB1T. Using a reverse genetics approach, full attenuation of PVM could only be achieved by simultaneously mutating four sites located at C706U in the 5′ untranslated region (5′ UTR) and at Y87F, V136A, and T276A in the VP1 capsid. Engineering these four myopathic determinants into an amyopathic CVB1T variant restored the ability to cause PVM. Moreover, these same four determinants controlled PVM expression in a second strain of mice, indicating that the underlying mechanism is operational in mice of different genetic backgrounds. Modeling studies predict that C706U alters both local and long-range pairing in the 5′ UTR, and that VP1 determinants are located on the capsid surface. However, these differences did not affect viral titers, temperature stability, pH stability, or the antibody response to virus. These studies demonstrate that PVM develops from a complex interplay between viral determinants in the 5′ UTR and VP1 capsid and have uncovered intriguing similarities between genetic determinants that cause PVM and those involved in pathogenesis of other enteroviruses. PMID:18029287

  11. Results of test MA22 in the NASA/LaRC 31-inch CFHT on an 0.010-scale model (32-0) of the space shuttle configuration 3 to determine RCS jet flow field interaction, volume 1. [wind tunnel tests for interactions of aerodynamic heating on jet flow

    NASA Technical Reports Server (NTRS)

    Kanipe, D. B.

    1976-01-01

    A wind tunnel test was conducted in the Langley Research Center 31-inch Continuous Flow Hypersonic Wind Tunnel from May 6, 1975 through June 3, 1975. The primary objectives of this test were the following: (1) to study the ability of the wind tunnel to repeat, on a run-to-run basis, data taken for identical configurations to determine if errors in repeatability could have a significant effect on jet interaction data, (2) to determine the effect of aerodynamic heating of the scale model on jet interaction, (3) to investigate the effects of elevon and body flap deflections on jet interaction, (4) to determine if the effects from jets fired separately along different axes can be added to equal the effects of the jets fired simultaneously (super position effects), (5) to study multiple jet effects, and (6) to investigate area ratio effects, i.e., the effect on jet interaction measurements of using wind tunnel nozzles with different area ratios in the same location. The model used in the test was a .010-scale model of the Space Shuttle Orbiter Configuration 3. The test was conducted at Mach 10.3 and a dynamic pressure of 150 psf. RCS chamber pressure was varied to simulate free flight dynamic pressures of 5, 7.5, 10, and 20 psf.

  12. Donor-Acceptor Interaction Determines the Mechanism of Photoinduced Electron Injection from Graphene Quantum Dots into TiO2: π-Stacking Supersedes Covalent Bonding.

    PubMed

    Long, Run; Casanova, David; Fang, Wei-Hai; Prezhdo, Oleg V

    2017-02-22

    Interfacial electron transfer (ET) constitutes the key step in conversion of solar energy into electricity and fuels. Required for fast and efficient charge separation, strong donor-acceptor interaction is typically achieved through covalent chemical bonding and leads to fast, adiabatic ET. Focusing on interfaces of pyrene, coronene, and a graphene quantum dot (GQD) with TiO2, we demonstrate the opposite situation: covalent bonding leads to weak coupling and nonadiabatic (NA) ET, while through-space π-electron interaction produces adiabatic ET. Using real-time time-dependent density functional theory combined with NA molecular dynamics, we simulate photoinduced ET into TiO2 from flat and vertically placed molecules and GQD containing commonly used carboxylic acid linkers. Both arrangements can be achieved experimentally with GQDs and other two-dimensional materials, such as MoS2. The weak through-bond donor-acceptor coupling is attributed to the π-electron withdrawing properties of the carboxylic acid group. The calculated ET time scales are in excellent agreement with pump-probe optical experiments. The simulations show that the ET proceeds faster than energy relaxation. The electron couples to a broad spectrum of vibrational modes, ranging from 100 cm(-1) large-scale motions to 1600 cm(-1) C-C stretches. Compared to graphene/TiO2 heterojunctions, the molecule/TiO2 and GQD/TiO2 systems exhibit energy gaps, allowing for longer-lived excited states and hot electron injection, facilitating charge separation and higher voltage. The reported state-of-the-art simulations generate a detailed time-domain, atomistic description of the interfacial charge and energy transfer and relaxation processes, and demonstrate that the fundamental principles leading to efficient charge separation in nanoscale materials depend strongly and often unexpectedly on the type of donor-acceptor interaction. Understanding these principles is critical to the development of highly efficient

  13. Preparation and Determination of Drug-Polymer Interaction and In-vitro Release of Mefenamic Acid Microspheres Made of CelluloseAcetate Phthalate and/or Ethylcellulose Polymers

    PubMed Central

    Jelvehgari, Mitra; Hassanzadeh, Davoud; Kiafar, Farhad; Delf Loveym, Badir; Amiri, Sara

    2011-01-01

    The objective of this study was to formulate and evaluate the drug-polymer interaction of mefenamic acid (MA) using two polymers with different characteristics as ethylcellulose (EC) and/or cellulose acetate phthalate (CAP). Microspheres were prepared by the modified emulsion solvent evaporation (MESE). The effect of drug-polymer interaction was studied for each of microspheres. Important parameters in the evaluation of a microencapsulation technique are encapsulation efficiency, yield production, particle size, surface characteristics of microspheres, scanning electronic microscopy (SEM), powder X-ray diffraction analysis (XRD), and differential scanning calorimetry (DSC). The in-vitro release studies are performed in Tris buffer (pH 9) with Sodium lauryl sulfate (SLS). Microspheres containing CAP and EC showed 68-97% and 63-76% of entrapment efficiency, respectively. The thermogram X-ray and DSC showed stable character of MA in the microspheres and revealed an absence of drug polymer interaction. The prepared microspheres were spherical in shape and had a size range of 235-436 μm for CAP-microspheres and 358-442 μm for EC-microspheres. The results suggest that MA was successfully and efficiently encapsulated; the release rates of matrix microspheres are related to the type of polymer, only when polymers (EC and CAP combine with 1 : 1 ratio) were used to get prolonged drug release with reducing the polymers content in the microspheres. Data obtained from in-vitro release for microspheres and commercial capsule were fitted to various kinetic models and the high correlation was obtained in the peppas model. Mefenamic acid, Ethylcellulose, Cellulose acetate phthalate, Microparticles, Modified emulsion-solvent evaporation. PMID:24250377

  14. A combined model for predicting CYP3A4 clinical net drug-drug interaction based on CYP3A4 inhibition, inactivation, and induction determined in vitro.

    PubMed

    Fahmi, Odette A; Maurer, Tristan S; Kish, Mary; Cardenas, Edwin; Boldt, Sherri; Nettleton, David

    2008-08-01

    Although approaches to the prediction of drug-drug interactions (DDIs) arising via time-dependent inactivation have recently been developed, such approaches do not account for simple competitive inhibition or induction. Accordingly, these approaches do not provide accurate predictions of DDIs arising from simple competitive inhibition (e.g., ketoconazole) or induction of cytochromes P450 (e.g., phenytoin). In addition, methods that focus upon a single interaction mechanism are likely to yield misleading predictions in the face of mixed mechanisms (e.g., ritonavir). As such, we have developed a more comprehensive mathematical model that accounts for the simultaneous influences of competitive inhibition, time-dependent inactivation, and induction of CYP3A in both the liver and intestine to provide a net drug-drug interaction prediction in terms of area under the concentration-time curve ratio. This model provides a framework by which readily obtained in vitro values for competitive inhibition, time-dependent inactivation and induction for the precipitant compound as well as literature values for f(m) and F(G) for the object drug can be used to provide quantitative predictions of DDIs. Using this model, DDIs arising via inactivation (e.g., erythromycin) continue to be well predicted, whereas those arising via competitive inhibition (e.g., ketoconazole), induction (e.g., phenytoin), and mixed mechanisms (e.g., ritonavir) are also predicted within the ranges reported in the clinic. This comprehensive model quantitatively predicts clinical observations with reasonable accuracy and can be a valuable tool to evaluate candidate drugs and rationalize clinical DDIs.

  15. Determination of the S-ZnO structural interaction in thiol-capped ZnO nanoparticles: a sulfur K-edge XAS study

    NASA Astrophysics Data System (ADS)

    Guglieri, Clara; Aquilanti, Giuliana; Díaz-Moreno, Sofía; Chaboy, J.

    2017-02-01

    ZnO nanoparticles capped with thiol molecules display room temperature ferromagnetism which has been associated with the structural details of the interface formed between the organic molecule and the ZnO core. Although the local order around sulfur atoms at the ZnS/ZnO interface has been related to the occurrence of the ferromagnetic like behavior, no direct structural determination has been obtained yet. We report here a detailed x-ray absorption spectroscopy study performed at the sulfur K-edge to determine the local structure around the sulfur atoms in these systems and how it is modified by varying the length of the organic molecule.

  16. Determination of the S-ZnO structural interaction in thiol-capped ZnO nanoparticles: a sulfur K-edge XAS study.

    PubMed

    Guglieri, Clara; Aquilanti, Giuliana; Díaz-Moreno, Sofía; Chaboy, J

    2017-02-03

    ZnO nanoparticles capped with thiol molecules display room temperature ferromagnetism which has been associated with the structural details of the interface formed between the organic molecule and the ZnO core. Although the local order around sulfur atoms at the ZnS/ZnO interface has been related to the occurrence of the ferromagnetic like behavior, no direct structural determination has been obtained yet. We report here a detailed x-ray absorption spectroscopy study performed at the sulfur K-edge to determine the local structure around the sulfur atoms in these systems and how it is modified by varying the length of the organic molecule.

  17. Well width dependence of electron-phonon interaction in ZnSe/ZnS xSe 1- x superlattices determined by micro-raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Spagnolo, V.; Scamarcio, G.; Corvasce, C.; Lugará, M.; Suemune, I.

    1994-07-01

    We report a study of multiphonon resonant Raman scattering in a series of symmetric (ZnSe) d(ZnS 1- xSe x) d superlattices (SL), 20Å ≤ d ≤ 150Å. In addition to confined optical phonons, the energies of interface (IF) modes with in-plane wavevectors have been assessed by means of micro-probe Raman measurements in backscattering from the SL edge. The comparison between one- and two-phonon spectra shows that the electron-phonon interaction is dominated by ZnSe-like IF phonons for d < 50Å, whereas LO 2 phonons prevail for larger well.

  18. Exploiting interactions between structure size and indentation size effects to determine the characteristic dimension of nano-structured materials by indentation

    NASA Astrophysics Data System (ADS)

    Hou, Xiaodong; Jennett, Nigel M.; Parlinska-Wojtan, Magdalena

    2013-07-01

    It was shown that yield (or flow) stress is determined by a critical dimension and the reciprocal sum of component critical dimensions (such as indentation size, structure size and dislocation density) combine into a single critical dimension as predicted by slip distance theory (Hou et al 2012 Acta. Mater. 60 4128). This suggests that ‘length determines strength’ and all lengths contribute at all times to the critical value. We have already shown that Cu hardness increases when grain size falls below six times the indentation contact radius (Hou et al 2008 J. Phys. D: Appl. Phys. 41 074006). In this paper, we test the inverse case (indent size greater than grain size), by indenting two different metallic glasses (NiAl and ZrTiAlCuBe). We show that the indentation size effect (ISE) does indeed become observable even when the indent size is larger than the grain size by up to an order of magnitude. The indentation depth (size) at onset of the ISE is proportional to the characteristic structure size of these nano-structured materials and suggests a novel use of ISE as a determinant of structure size. These findings have implications for the design of hardness reference blocks and the use of hardness mapping to determine materials property variations.

  19. Determining an Effective Interactive Multimedia Arabic Language Courseware for Malaysian Primary School Children: An Alternative Paradigm for Learning in the Classroom

    ERIC Educational Resources Information Center

    Faryadi, Qais; Bakar, Zainab Abu; Maidinsah, Hamidah

    2007-01-01

    The prime purpose of this experimental research was to determine whether learning Arabic as a foreign language can be effectively enhanced through traditional methodology. As such, this research carefully investigated and critically analyzed the effectiveness of the traditional paradigm in teaching Arabic as a foreign language to 3rd grade primary…

  20. Staphylococcal protein A simultaneously interacts with framework region 1, complementarity-determining region 2, and framework region 3 on human VH3-encoded Igs.

    PubMed

    Potter, K N; Li, Y; Capra, J D

    1996-10-01

    Staphylococcal protein A (SPA) is a B cell superantigen that binds to human VH3-encoded Igs independently of the D- and JH-encoded regions and light chain sequences. The SPA-binding structure formed by VH3-encoded Igs remains controversial. We localized the regions in a VH3-encoded Ab required for SPA binding by producing mutant Abs in the baculovirus expression system in which regions of a human-derived Ab known to bind SPA were exchanged with those from a mouse Ab of the J558 family, a family not associated with SPA binding. The pattern of SPA binding indicates not only that residues in FR1, CDR2, and FR3 are involved but also that the three regions are required to interact simultaneously with SPA for binding to occur. When any one of the three regions was replaced with the corresponding region from the nonbinding Ab, SPA binding was severely disrupted. These data indicate that SPA requires simultaneous interaction with three distinct regions of a VH3 structure, which together in three-dimensional space form an extended solvent-exposed surface. These studies more precisely define the genetic requirements for VH3-encoded Ig binding to SPA.

  1. Collagen remodeling by phagocytosis is determined by collagen substrate topology and calcium-dependent interactions of gelsolin with nonmuscle myosin IIA in cell adhesions

    PubMed Central

    Arora, P. D.; Wang, Y.; Bresnick, A.; Dawson, J.; Janmey, P. A.; McCulloch, C. A.

    2013-01-01

    We examine how collagen substrate topography, free intracellular calcium ion concentration ([Ca2+]i, and the association of gelsolin with nonmuscle myosin IIA (NMMIIA) at collagen adhesions are regulated to enable collagen phagocytosis. Fibroblasts plated on planar, collagen-coated substrates show minimal increase of [Ca2+]i, minimal colocalization of gelsolin and NMMIIA in focal adhesions, and minimal intracellular collagen degradation. In fibroblasts plated on collagen-coated latex beads there are large increases of [Ca2+]i, time- and Ca2+-dependent enrichment of NMMIIA and gelsolin at collagen adhesions, and abundant intracellular collagen degradation. NMMIIA knockdown retards gelsolin recruitment to adhesions and blocks collagen phagocytosis. Gelsolin exhibits tight, Ca2+-dependent binding to full-length NMMIIA. Gelsolin domains G4–G6 selectively require Ca2+ to interact with NMMIIA, which is restricted to residues 1339–1899 of NMMIIA. We conclude that cell adhesion to collagen presented on beads activates Ca2+ entry and promotes the formation of phagosomes enriched with NMMIIA and gelsolin. The Ca2+ -dependent interaction of gelsolin and NMMIIA in turn enables actin remodeling and enhances collagen degradation by phagocytosis. PMID:23325791

  2. Determination of molecular groups involved in the interaction of annexin A5 with lipid membrane models at the air-water interface.

    PubMed

    Fezoua-Boubegtiten, Zahia; Desbat, Bernard; Brisson, Alain; Lecomte, Sophie

    2010-06-01

    Annexin A5 (AnxA5) is a member of a family of homologous proteins sharing the ability to bind to negatively charged phospholipid membranes in a Ca(2+)-dependent manner. In this paper, we used polarization-modulated infrared reflection absorption spectroscopy (PMIRRAS), Brewster angle microscopy (BAM), and ellipsometry to investigate changes both in the structure of AnxA5 and phospholipid head groups associated with membrane binding. We found that the secondary structure of AnxA5 in the AnxA5/Ca(2+)/lipid ternary complex is conserved, mainly in alpha-helices and the average orientation of the alpha-helices of the protein is slightly tilted with respect to the normal to the phospholipid monolayer. Upon interaction between AnxA5 and phospholipids, a shift of the nu(as) PO(2)(-) band is observed by PMIRRAS. This reveals that the phosphate group is the main group involved in the binding of AnxA5 to phospholipids via Ca(2+) ions, even when some carboxylate groups are accessible (PS). PMIRRAS spectra also indicate a change of carboxylate orientation in the aspartate and glutamate residues implicated in the association of the AnxA5, which could be linked to the 2D crystallization of protein under the phospholipid monolayer. Finally, we demonstrated that the interaction of AnxA5 with pure carboxylate groups of an oleic acid monolayer is possible, but the orientation of the protein under the lipid is completely different.

  3. An interaction domain in human SAMD9 is essential for myxoma virus host-range determinant M062 antagonism of host anti-viral function.

    PubMed

    Nounamo, Bernice; Li, Yibo; O'Byrne, Peter; Kearney, Aoife M; Khan, Amir; Liu, Jia

    2017-03-01

    In humans, deleterious mutations in the sterile α motif domain protein 9 (SAMD9) gene are associated with cancer, inflammation, weakening of the immune response, and developmental arrest. However, the biological function of SAMD9 and its sequence-structure relationships remain to be characterized. Previously, we found that an essential host range factor, M062 protein from myxoma virus (MYXV), antagonized the function of human SAMD9. In this study, we examine the interaction between M062 and human SAMD9 to identify regions that are critical to SAMD9 function. We also characterize the in vitro kinetics of the interaction. In an infection assay, exogenous expression of SAMD9 N-terminus leads to a potent inhibition of wild-type MYXV infection. We reason that this effect is due to the sequestration of viral M062 by the exogenously expressed N-terminal SAMD9 region. Our studies reveal the first molecular insight into viral M062-dependent mechanisms that suppress human SAMD9-associated antiviral function.

  4. Glucose-β-CD interaction assisted ACN field-amplified sample stacking in CZE for determination of trace amlodipine in beagle dog plasma.

    PubMed

    Li, Ji; Li, You; Zhang, Wenting; Chen, Zhao; Fan, Guorong

    2013-06-01

    A simple, sensitive and low-cost method using CE coupled with glucose-β-CD interaction assisted ACN stacking technique has been developed for quantification of trace amlodipine in dog plasma. The plasma samples were extracted with methyl tert-butyl ether. The separation was performed at 25°C in a 31.2 cm × 75 μm fused-silica capillary with an applied voltage of 15 kV. The BGE was composed of 6.25 mM borate/25 mM phosphate (pH 2.5) and 5 mg/mL glucose-β-CD. The detection wavelength was 200 nm. Because CD could diminish the interaction between drugs and matrix, and derivation groups of CD play an important role in separation performance, the effects of β-CD, and its derivatives on the separation were studied at several concentrations (0, 2.5, 5.0, 10.0 mg/mL). In this study, organic solvent field-amplified sample stacking technique in combination with glucose-β-CD enhanced the sensitivity about 60-70 folds and glucose-β-CD could effectively improve the peak shape. All the validation data, such as accuracy, precision extraction recovery, and stability, were within the required limits. The calibration curve was linear for amlodipine from 1 to 200 ng/mL. The method developed was successfully applied to the pharmacokinetic studies of amlodipine besylate in beagle dogs.

  5. Determination of the spin triplet p Λ scattering length from the final state interaction in the p ⃗p →p K+Λ reaction

    NASA Astrophysics Data System (ADS)

    Hauenstein, F.; Borodina, E.; Clement, H.; Doroshkevich, E.; Dzhygadlo, R.; Ehrhardt, K.; Eyrich, W.; Gast, W.; Gillitzer, A.; Grzonka, D.; Haidenbauer, J.; Hanhart, C.; Jowzaee, S.; Kilian, K.; Klaja, P.; Kober, L.; Krapp, M.; Mertens, M.; Moskal, P.; Ritman, J.; Roderburg, E.; Röder, M.; Schroeder, W.; Sefzick, T.; Wintz, P.; Wüstner, P.; COSY-TOF Collaboration

    2017-03-01

    The p ⃗p →p K+Λ reaction has been measured with the COSY-TOF detector at a beam momentum of 2.7 GeV /c . The polarized proton beam enables the measurement of the beam analyzing power by the asymmetry of the produced kaon (ANK). This observable allows the p Λ spin triplet scattering length to be extracted for the first time model independently from the final state interaction in the reaction. The obtained value is at=(-2 .55-1.39+0.72stat .±0 .6syst .±0 .3theo .) fm . This value is compatible with theoretical predictions and results from model-dependent analyses.

  6. Ranking solvent interactions and dielectric constants with [Pt(mesBIAN)(tda)]: A cautionary tale for polarity determinations in ionic liquids.

    PubMed

    Baker, Gary A; Rachford, Aaron A; Castellano, Felix N; Baker, Sheila N

    2013-04-02

    The solvatochromic properties of [Pt(mesBIAN)(tda)] are studied in traditional molecular solvents and ionic liquids and duly compared along established empirical solvent parameter scales. The charge-transfer absorption band of [Pt(mesBIAN)(tda)] is determined to be primarily dependent upon solvent acidity and dipolarity. Notably, ionic liquids do not obey the same well-behaved trend as molecular solvents, highlighting the complexity and domain (nano)segregation inherent to ionic liquids.

  7. IFPA Meeting 2013 Workshop Report III: maternal placental immunological interactions, novel determinants of trophoblast cell fate, dual ex vivo perfusion of the human placenta.

    PubMed

    Abumaree, M H; Brownbill, P; Burton, G; Castillo, C; Chamley, L; Croy, B A; Drewlo, S; Dunk, C; Girard, S; Hansson, S; Jones, S; Jurisicova, A; Lewis, R; Letarte, M; Parast, M; Pehrson, C; Rappolee, D; Schneider, H; Tannetta, D; Varmuza, S; Wadsack, C; Wallace, A E; Zenerino, C; Lash, G E

    2014-02-01

    Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialised topics. At IFPA meeting 2013 there were twelve themed workshops, three of which are summarized in this report. These workshops related to various aspects of placental biology but collectively covered areas of placental function, cell turnover and immunology: 1) immunology; 2) novel determinants of placental cell fate; 3) dual perfusion of human placental tissue.

  8. A Single-Center, Open-Label, 3-Way Crossover Trial to Determine the Pharmacokinetic and Pharmacodynamic Interaction Between Nebivolol and Valsartan in Healthy Volunteers at Steady State

    PubMed Central

    Chen, Chun Lin; Desai-Krieger, Daksha; Ortiz, Stephan; Kerolous, Majid; Wright, Harold M.; Ghahramani, Parviz

    2015-01-01

    Combining different classes of antihypertensives is more effective for reducing blood pressure (BP) than increasing the dose of monotherapies. The aims of this phase I study were to investigate pharmacokinetic and pharmacodynamic interactions between nebivolol, a vasodilatory β1-selective blocker, and valsartan, an angiotensin II receptor blocker, and to assess safety and tolerability of the combination. This was a single-center, randomized, open-label, multiple-dose, 3-way crossover trial in 30 healthy adults aged 18–45 years. Participants were randomized into 1 of 6 treatment sequences (1:1:1:1:1:1) consisting of three 7-day treatment periods followed by a 7-day washout. Once-daily oral treatments comprised nebivolol (20 mg), valsartan (320 mg), and nebivolol–valsartan combination (20/320 mg). Outcomes included AUC0-τ,ss, Cmax,ss, Tmax,ss, changes in BP, pulse rate, plasma angiotensin II, plasma renin activity, 24-hour urinary aldosterone, and adverse events. Steady-state pharmacokinetic interactions were observed but deemed not clinically significant. Systolic and diastolic BP reduction was significantly greater with nebivolol–valsartan combination than with either monotherapy. The mean pulse rate associated with nebivolol and nebivolol–valsartan treatments was consistently lower than that associated with valsartan monotherapy. A sharp increase in mean day 7 plasma renin activity and plasma angiotensin II that occurred in valsartan-treated participants was significantly attenuated with concomitant nebivolol administration. Mean 24-hour urine aldosterone at day 7 was substantially decreased after combined treatment, as compared with either monotherapy. All treatments were safe and well tolerated. In conclusion, nebivolol and valsartan coadministration led to greater reductions in BP compared with either monotherapy; nebivolol and valsartan lower BP through complementary mechanisms. PMID:25853236

  9. Interactions between Inhibitory Interneurons and Excitatory Associational Circuitry in Determining Spatio-Temporal Dynamics of Hippocampal Dentate Granule Cells: A Large-Scale Computational Study

    PubMed Central

    Hendrickson, Phillip J.; Yu, Gene J.; Song, Dong; Berger, Theodore W.

    2015-01-01

    This paper reports on findings from a million-cell granule cell model of the rat dentate gyrus that was used to explore the contributions of local interneuronal and associational circuits to network-level activity. The model contains experimentally derived morphological parameters for granule cells, which each contain approximately 200 compartments, and biophysical parameters for granule cells, basket cells, and mossy cells that were based both on electrophysiological data and previously published models. Synaptic input to cells in the model consisted of glutamatergic AMPA-like EPSPs and GABAergic-like IPSPs from excitatory and inhibitory neurons, respectively. The main source of input to the model was from layer II entorhinal cortical neurons. Network connectivity was constrained by the topography of the system, and was derived from axonal transport studies, which provided details about the spatial spread of axonal terminal fields, as well as how subregions of the medial and lateral entorhinal cortices project to subregions of the dentate gyrus. Results of this study show that strong feedback inhibition from the basket cell population can cause high-frequency rhythmicity in granule cells, while the strength of feedforward inhibition serves to scale the total amount of granule cell activity. Results furthermore show that the topography of local interneuronal circuits can have just as strong an impact on the development of spatio-temporal clusters in the granule cell population as the perforant path topography does, both sharpening existing clusters and introducing new ones with a greater spatial extent. Finally, results show that the interactions between the inhibitory and associational loops can cause high frequency oscillations that are modulated by a low-frequency oscillatory signal. These results serve to further illustrate the importance of topographical constraints on a global signal processing feature of a neural network, while also illustrating how rich

  10. Enantiospecific determination of DL-methylphenidate and DL-ethylphenidate in plasma by liquid chromatography-tandem mass spectrometry: application to human ethanol interactions.

    PubMed

    Zhu, Hao-Jie; Patrick, Kennerly S; Markowitz, John S

    2011-04-01

    In humans, concomitant DL-methylphenidate (DL-MPH) and ethanol results in the carboxylesterase 1 (hCES1) mediated biotransformation of MPH to the transesterification metabolite DL-ethylphenidate (DL-EPH). The separate enantiomers of MPH and EPH are found at low ng/ml to pg/ml plasma concentrations. Substantial pharmacological differences exist between D- and L-isomers of MPH and EPH, both in terms of pharmacological potencies and receptor selectivity, as well as in pharmacokinetic properties. Accordingly, a sensitive, accurate and precise enantiospecific analytical method is required in order to fully explore pharmacokinetic-pharmacodynamic correlations regarding the MPH-ethanol interaction. The present study describes a novel liquid chromatographic-tandem mass spectrometric method for simultaneous analysis of D- and L-MPH as well as D- and L-EPH concentrations from human plasma. This assay provides baseline resolution of the individual MPH and EPH isomers utilizing a vancomycin-based chiral column. The lower limit of quantification was 0.025 ng/ml for each isomer when extracting 0.5 ml plasma aliquots. Calibration curves were linear over the range from 0.025 ng/ml to 25 ng/ml for all analytes (r(2)>0.995). Assay accuracy and precision were excellent and stability studies and assessment of potential matrix effects contributed to the validation of the method. Application of the method to human plasma samples collected after the administration of dl-MPH with or without ethanol is included, and the implications of this pharmacokinetic drug interaction discussed.

  11. Enantiospecific determination of dl-methylphenidate and dl-ethylphenidate in plasma by liquid chromatography-tandem mass spectrometry: Application to human ethanol interactions

    PubMed Central

    Zhu, Hao-Jie; Patrick, Kennerly S.; Markowitz, S.

    2011-01-01

    In humans, concomitant dl-methylphenidate (dl-MPH) and ethanol results in the carboxylesterase 1 (hCES1) mediated biotransformation of MPH to the transesterification metabolite dl-ethylphenidate (dl-EPH). The separate enantiomers of MPH and EPH are found at low ng/ml to pg/ml plasma concentrations. Substantial pharmacological differences exist between d- and l-isomers of MPH and EPH, both in terms of pharmacological potencies and receptor selectivity, as well as in pharmacokinetic properties. Accordingly, a sensitive, accurate and precise enantiospecific analytical method is required in order to fully explore pharmacokinetic – pharmacodynamic correlations regarding the MPH – ethanol interaction. The present study describes a novel liquid chromatographic-tandem mass spectrometric method for simultaneously analysis of d- and l-MPH as well as d- and l-EPH concentration from human plasma. This assay provides baseline resolution of the individual MPH and EPH isomers utilizing a vancomycin-based chiral column. The lower limit of quantification was 0.025 ng/ml for each isomer when extracting 0.5 ml plasma aliquots. Calibration curves were linear over the range from 0.025 ng/ml to 25 ng/ml for all analytes (r2 > 0.995). Assay accuracy and precision were excellent and stability studies and assessment of potential matrix effects contributed to the validation of the method. Application of the method to human plasma samples collected after the administration of dl-MPH with or without ethanol was included, and the implications of this pharmacokinetic drug interaction were discussed. PMID:21402502

  12. Equilibrium binding assays reveal the elevated stoichiometry and salt dependence of the interaction between full-length human sex-determining region on the Y chromosome (SRY) and DNA.

    PubMed

    Baud, Stephanie; Margeat, Emmanuel; Lumbroso, Serge; Paris, Françoise; Sultan, Charles; Royer, Catherine; Poujol, Nicolas

    2002-05-24

    In an effort to better define the molecular mechanism of the functional specificity of human sex-determining region on the Y chromosome (SRY), we have carried out equilibrium binding assays to study the interaction of the full-length bacterial-expressed protein with a DNA response element derived from the CD3epsilon gene enhancer. These assays are based on the observation of the fluorescence anisotropy of a fluorescein moiety covalently bound to the target oligonucleotide. The low anisotropy value due to the fast tumbling of the free oligonucleotide in solution increases substantially upon binding the protein to the labeled target DNA. Our results indicate that the full-length human wild-type SRY (SRY(WT)) forms a complex of high stoichiometry with its target DNA. Moreover, we have demonstrated a strong salt dependence of both the affinity and specificity of the interaction. We have also addressed the DNA bending properties of full-length human SRY(WT) in solution by fluorescence resonance energy transfer and revealed that maximal bending is achieved with a protein to DNA ratio significantly higher than the classical 1:1. Oligomerization thus appears, at least in vitro, to be tightly coupled to SRY-DNA interactions. Alteration of protein-protein interactions observed for the mutant protein SRY(Y129N), identified in a patient presenting with 46,XY sex reversal, suggests that oligomerization may play an important role in vivo as well.

  13. PIC: Protein Interactions Calculator

    PubMed Central

    Tina, K. G.; Bhadra, R.; Srinivasan, N.

    2007-01-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic–aromatic interactions, aromatic–sulphur interactions and cation–π interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside. PMID:17584791

  14. PIC: Protein Interactions Calculator.

    PubMed

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

  15. Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

    NASA Astrophysics Data System (ADS)

    Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

    From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

  16. Strategy for the Prediction of Steady-State Exposure of Digoxin to Determine Drug-Drug Interaction Potential of Digoxin With Other Drugs in Digitalization Therapy.

    PubMed

    Srinivas, Nuggehally R

    2016-01-20

    Digoxin, a narrow therapeutic index drug, is widely used in congestive heart failure. However, the digitalization therapy involves dose titration and can exhibit drug-drug interaction. Ctrough versus area under the plasma concentration versus time curve in a dosing interval of 24 hours (AUC0-24h) and Cmax versus AUC0-24h for digoxin were established by linear regression. The predictions of digoxin AUC0-24h values were performed using published Ctrough or Cmax with appropriate regression lines. The fold difference, defined as the quotient of the observed/predicted AUC0-24h values, was evaluated. The mean square error and root mean square error, correlation coefficient (r), and goodness of the fold prediction were used to evaluate the models. Both Ctrough versus AUC0-24h (r = 0.9215) and Cmax versus AUC0-24h models for digoxin (r = 0.7781) showed strong correlations. Approximately 93.8% of the predicted digoxin AUC0-24h values were within 0.76-fold to 1.25-fold difference for Ctrough model. In sharp contrast, the Cmax model showed larger variability with only 51.6% of AUC0-24h predictions within 0.76-1.25-fold difference. The r value for observed versus predicted AUC0-24h for Ctrough (r = 0.9551; n = 177; P < 0.001) was superior to the Cmax (r = 0.6134; n = 275; P < 0.001) model. The mean square error and root mean square error (%) for the Ctrough model were 11.95% and 16.2% as compared to 67.17% and 42.3% obtained for the Cmax model. Simple linear regression models for Ctrough/Cmax versus AUC0-24h were derived for digoxin. On the basis of statistical evaluation, Ctrough was superior to Cmax model for the prediction of digoxin AUC0-24h and can be potentially used in a prospective setting for predicting drug-drug interaction or lack of it.

  17. Determination of binding capacity and adsorption enthalpy between Human Glutamate Receptor (GluR1) peptide fragments and kynurenic acid by surface plasmon resonance experiments. Part 2: Interaction of GluR1270-300 with KYNA.

    PubMed

    Csapó, E; Bogár, F; Juhász, Á; Sebők, D; Szolomájer, J; Tóth, G K; Majláth, Z; Vécsei, L; Dékány, I

    2015-09-01

    In the course of our previous work, the interactions of two peptide fragments (GluR1201-230 and GluR1231-259) of human glutamate receptor (GluR1201-300) polypeptide with kynurenic acid (KYNA) were investigated by surface plasmon resonance (SPR) spectroscopy. Besides quantitation of the interactions, the enthalpies of binding of KYNA on certain peptide fragment-modified gold surfaces were also reported. In the present work, a third peptide fragment (GluR1270-300) of the glutamate receptor was synthesized and its interaction with KYNA was investigated by an SPR technique. This 31-membered peptide was chemically bonded onto a gold-coated SPR chip via a cysteine residue. The peptide-functionalized biosensor chip was analyzed by atomic force microscopy (AFM) and theoretical calculations were performed on the structure and dimensions of the peptide on the gold surface. In order to determine the isosteric heat of adsorption of the binding of KYNA on the peptide-functionalized gold thin film, SPR experiments were carried out between +10°C and +40°C. The results on the GluR1270-300-KYNA system were compared with the previously published binding parameters of the interactions of GluR1201-230 and GluR1231-259 with KYNA. The binding abilities of KYNA with all three peptide fragments immobilized on the gold surface were estimated by a molecular docking procedure and the binding free energies of these AMPA receptor subunits with KYNA were determined.

  18. Omega-3 fatty acid deficiency in major depressive disorder is caused by the interaction between diet and a genetically determined abnormality in phospholipid metabolism.

    PubMed

    Ross, Brian M

    2007-01-01

    Omega-3 fatty acids are a type of polyunsaturated fatty acid (PUFA). A growing body of evidence suggests that this form PUFA is a useful and well tolerated treatment for major depressive disorder, a common and serious mental illness. The efficacy of omega-3 PUFA is routinely explained as being due to a deficiency caused by inadequate dietary intake of this class of fatty acid. The hypothesis considered states that low omega-3 PUFA abundance in patients with major depressive and related disorders is due to an underlying genetically determined abnormality. The hypothesis can explain why although a specific and consistent deficit in omega-3, but not omega-6, PUFA occurs in major depressive and related disorders, the literature does not consistently support the notion that this is due to deficient dietary intake. Specifically it is hypothesized that having genetically determined low activity of fatty acid CoA ligase 4 and/or Type IV phospholipase A(2) combined with the low dietary availability of omega-3 PUFA results in reduced cellular uptake of omega-3 PUFA and constitutes a risk factor for depression. The hypothesis also has important consequences for the pharmacological treatment of depression in that it predicts that administering agents which enhance phospholipid synthesis, particularly those containing ethanolamine such as CDP-ethanolamine, should be effective antidepressants especially when co-administered with omega-3 PUFA.

  19. Analysis of the multiple roles of gld-1 in germline development: Interactions with the sex determination cascade and the glp-1 signaling pathway

    SciTech Connect

    Francis, R.; Schedl, T.; Maine, E.

    1995-02-01

    The Caenorhabditis elegans gene gld-1 is essential for oocyte development; in gld-1 (null) hermaphrodites, a tumor forms where oogenesis would normally occur. We use genetic epistasis analysis to demonstrate that tumor formation is dependent on the sexual fate of the germline. When the germline sex determination pathway is set in the female mode (terminal fem/fog genes inactive), gld-1 (null) germ cells exit meiotic prophase and proliferate to form a tumor, but when the pathway is et in the male mode, they develop into sperm. We conclude that the gld-1 (null) phenotype is cell-type specific and that gld-1(+) acts at the end of the cascade to direct oogenesis. We also use cell ablation and epistasis analysis to examine the dependence of tumor formation on the glp-1 signaling pathway. Although glp-1 activity promotes tumor growth, it is not essential for tumor formation by gld-1 (null) germ cells. These data also reveal that gld-1(+) plays a nonessential (and sex nonspecific) role in regulating germ cell proliferation before their entry into meiosis. Thus gld-1(+) may negatively regulate proliferation at two distinct points in germ cell development: before entry into meiotic prophase in both sexes (nonessential premeiotic gld-1 function) and during meiotic prophase when the sex determination pathway is set in the female mode (essential meiotic gld-1 function). 46 refs., 9 figs., 4 tabs.

  20. Development of a chemical kinetic measurement apparatus and the determination of the reaction rate constants for lithium-lead/water interaction

    SciTech Connect

    Biney, P.O.

    1993-04-01

    An experimental set-up for accurate measurement of hydrogen generation rate in Lithium-Lead (Li[sub 17]Pb[sub 83]) Steam or water interactions has been designed. The most important features of the design include a pneumatic actuated quick opening and closing high temperature all stainless steel valve used to control the reaction time and the placement of most measuring devices below a water line to minimize leakage of the hydrogen collected. A PC based data acquisition and control system provides remote process sequencing, acquisition and control of all major components of the set-up. Initial tests indicate that the first design objective of maintaining leakproof gas collection chamber has been achieved. Initial pressure tests indicated that the pressure drop over a time span of 30 minutes was within the tolerance of the pressure transducer used to measure the pressure (within 0.690 kPa) at a nominal system pressure of 685 kPa. The experimental system hardware, data acquisition and control programs and data analysis program have been completed, tested and are currently functional.

  1. Studying wind energy/bird interactions: a guidance document. Metrics and methods for determining or monitoring potential impacts on birds at existing and proposed wind energy sites

    USGS Publications Warehouse

    Anderson, R.; Morrison, M.; Sinclair, K.; Strickland, D.; Davis, H.; Kendall, W.

    1999-01-01

    In the 1980s little was known about the potential environmental effects associated with large scale wind energy development. Although wind turbines have been used in farming and remote location applications throughout this country for centuries, impacts on birds resulting from these dispersed turbines had not been reported. Thus early wind energy developments were planned, permitted, constructed, and operated with little consideration for the potential effects on birds. In the ensuing years wind plant impacts on birds became a source of concern among a number of stakeholder groups. Based on the studies that have been done to date, significant levels of bird fatalities have been identified at only one major commercial wind energy development in the United States. Research on wind energy/bird interactions has spanned such a wide variety of protocols and vastly different levels of study effort that it is difficult to make comparisons among study findings. As a result there continues to be interest, confusion, and concern over wind energy development's potential impacts on birds. Some hypothesize that technology changes, such as less dense wind farms with larger, slower-moving turbines, will decrease the number of bird fatalities from wind turbines. Others hypothesize that, because the tip speed may be the same or faster, new turbines will not result in decreased bird fatalities but may actually increase bird impacts. Statistically significant data sets from scientifically rigorous studies will be required before either hypothesis can be tested.

  2. Simultaneous determination of trimethylamine and trimethylamine N-oxide in mouse plasma samples by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry.

    PubMed

    Mi, Si; Zhao, Yuan-Yuan; Jacobs, René L; Curtis, Jonathan M

    2017-02-01

    A method was developed that applies hydrophilic interaction liquid chromatography with tandem mass spectrometry in the multiple reaction monitoring mode to separate and accurately quantify trimethylamine and trimethylamine N-oxide in a single chromatographic run. This was achieved by converting trimethylamine to ethyl betaine, which is less volatile and hence results in greatly improved quantitation. Ethyl betaine also gives a similar response to trimethylamine N-oxide using positive-ion electrospray ionization mass spectrometry. It is readily separated from trimethylamine N-oxide by hydrophilic liquid chromatography in a 5 min run and with improved peak shape compared to underivatized trimethylamine. Validation of the method yielded a limit of detection (S/N ≥ 3) of 0.5 ng/mL for trimethylamine and 0.25 ng/mL for trimethylamine N-oxide. Method accuracies of 91.4-105.3% with precisions of 0.4-5.5% were obtained for standard mixtures over the range of 2.5-500 ng/mL. Recoveries measured for the extraction of trimethylamine and trimethylamine N-oxide spikes into mouse plasma were both >90%. The method, which simultaneously measures trimethylamine and trimethylamine N-oxide, was successfully applied to mouse plasma samples and could be adapted for use with other biological fluids.

  3. How interactions between microbial resource demands, soil organic matter stoichiometry, and substrate reactivity determine the direction and magnitude of soil respiratory responses to warming.

    PubMed

    Billings, Sharon A; Ballantyne, Ford

    2013-01-01

    Recent empirical and theoretical advances inform us about multiple drivers of soil organic matter (SOM) decomposition and microbial responses to warming. Absent from our conceptual framework of how soil respiration will respond to warming are adequate links between microbial resource demands, kinetic theory, and substrate stoichiometry. Here, we describe two important concepts either insufficiently explored in current investigations of SOM responses to temperature, or not yet addressed. First, we describe the complete range of responses for how warming may change microbial resource demands, physiology, community structure, and total biomass. Second, we describe how any relationship between SOM activation energy of decay and carbon (C) and nitrogen (N) stoichiometry can alter the relative availability of C and N as temperature changes. Changing availabilities of C and N liberated from their organic precursors can feedback to microbial resource demands, which in turn influence the aggregated respiratory response to temperature we observe. An unsuspecting biogeochemist focused primarily on temperature sensitivity of substrate decay thus cannot make accurate projections of heterotrophic CO2 losses from diverse organic matter reservoirs in a warming world. We establish the linkages between enzyme kinetics, SOM characteristics, and potential for microbial adaptation critical for making such projections. By examining how changing microbial needs interact with inherent SOM structure and composition, and thus reactivity, we demonstrate the means by which increasing temperature could result in increasing, unchanging, or even decreasing respiration rates observed in soils. We use this exercise to highlight ideas for future research that will develop our abilities to predict SOM feedbacks to climate.

  4. DISCO interacting protein 2 determines direction of axon projection under the regulation of c-Jun N-terminal kinase in the Drosophila mushroom body.

    PubMed

    Nitta, Yohei; Sugie, Atsushi

    2017-04-07

    Precisely controlled axon guidance for complex neuronal wiring is essential for appropriate neuronal function. c-Jun N-terminal kinase (JNK) was found to play a role in axon guidance recently as well as in cell proliferation, protection and apoptosis. In spite of many genetic and molecular studies on these biological processes regulated by JNK, how JNK regulates axon guidance accurately has not been fully explained thus far. To address this question, we use the Drosophila mushroom body (MB) as a model since the α/β axons project in two distinct directions. Here we show that DISCO interacting protein 2 (DIP2) is required for the accurate direction of axonal guidance. DIP2 expression is under the regulation of Basket (Bsk), the Drosophila homologue of JNK. We additionally found that the Bsk/DIP2 pathway is independent from the AP-1 transcriptional factor complex pathway, which is directly activated by Bsk. In conclusion, our findings revealed DIP2 as a novel effector downstream of Bsk modulating the direction of axon projection.

  5. Finite-element analysis to determine effect of monolimb flexibility on structural strength and interaction between residual limb and prosthetic socket.

    PubMed

    Lee, Winson C C; Zhang, Ming; Boone, David A; Contoyannis, Bill

    2004-01-01

    Monolimb refers to a kind of transtibial prostheses having the socket and shank molded into one piece of thermoplastic material. One of its characteristics is that the shank is made of a material that can deform during walking, which can simulate ankle joint motion to some extent. Changes in shank geometry can alter the stress distribution within the monolimb and at the residual limb-socket interface and, respectively, affect the deformability and structural integrity of the prosthesis and comfort perceived by amputees. This paper describes the development of a finite-element model for the study of the structural behavior of monolimbs with different shank designs and the interaction between the limb and socket during walking. The von Mises stress distributions in monolimbs with different shank designs at different walking phases are reported. With the use of distortion energy theory, possible failure was predicted. The effect of the stiffness of the monolimb shanks on the stress distribution at the limb-socket interface was studied. The results show a trend--the peak stress applied to the limb was lowered as the shank stiffness decreased. This information is useful for future monolimb optimization.

  6. Interaction of the Transcription Start Site Core Region and Transcription Factor YY1 Determine Ascorbate Transporter SVCT2 Exon 1a Promoter Activity

    PubMed Central

    Qiao, Huan; May, James M.

    2012-01-01

    Transcription of the ascorbate transporter, SVCT2, is driven by two distinct promoters in exon 1 of the transporter sequence. The exon 1a promoter lacks a classical transcription start site and little is known about regulation of promoter activity in the transcription start site core (TSSC) region. Here we present evidence that the TSSC binds the multifunctional initiator-binding protein YY1. Electrophoresis shift assays using YY1 antibody showed that YY1 is present as one of two major complexes that specifically bind to the TSSC. The other complex contains the transcription factor NF-Y. Mutations in the TSSC that decreased YY1 binding also impaired the exon 1a promoter activity despite the presence of an upstream activating NF-Y/USF complex, suggesting that YY1 is involved in the regulation of the exon 1a transcription. Furthermore, YY1 interaction with NF-Y and/or USF synergistically enhanced the exon 1a promoter activity in transient transfections and co-activator p300 enhanced their synergistic activation. We propose that the TSSC plays a vital role in the exon 1a transcription and that this function is partially carried out by the transcription factor YY1. Moreover, co-activator p300 might be able to synergistically enhance the TSSC function via a “bridge” mechanism with upstream sequences. PMID:22532872

  7. Comparative Transcriptomic Analysis Reveals That Ethylene/H2O2-Mediated Hypersensitive Response and Programmed Cell Death Determine the Compatible Interaction of Sand Pear and Alternaria alternata

    PubMed Central

    Wang, Hong; Lin, Jing; Chang, Youhong; Jiang, Cai-Zhong

    2017-01-01

    A major restriction on sand pear (Pyrus pyrifolia) production is black spot disease caused by the necrotrophic fungus Alternaria alternata. However, the pear response mechanism to A. alternata is unknown at the molecular level. Here, host responses of a resistant cultivar Cuiguan (CG) and a susceptible cultivar Sucui1 (SC1) to A. alternata infection were investigated. We found that the primary necrotic lesion formed at 1 dpi and the expansion of lesions was aggressive in SC1. Data from transcriptomic profiles using RNA-Seq technology identified a large number of differentially expressed genes (DEGs) between CG and SC1 in the early phase of A. alternata infection. K-mean cluster and Mapman analysis revealed that genes involved in ethylene (ET) biosynthesis and ET signaling pathway, such as ACS, ACOs, and ERFs, and in hypersensitive response (HR) and programmed cell death (PCD) were significantly enriched and up-regulated in the susceptible cultivar SC1. Conversely, genes involved in response to hydrogen peroxide and superoxide were differentially up-regulated in the resistant cultivar CG after inoculation with the fungus. Furthermore, ET levels were highly accumulated in SC1, but not in CG. Higher activities of detoxifying enzymes such as catalases were detected in CG. Our results demonstrate that the ET-/H2O2-mediated PCD and detoxifying processes play a vital role in the interaction of pear and A. alternata. PMID:28261248

  8. Interaction of colloidal nanoparticles with their local environment: the (ionic) nanoenvironment around nanoparticles is different from bulk and determines the physico-chemical properties of the nanoparticles

    PubMed Central

    Pfeiffer, Christian; Rehbock, Christoph; Hühn, Dominik; Carrillo-Carrion, Carolina; de Aberasturi, Dorleta Jimenez; Merk, Vivian; Barcikowski, Stephan; Parak, Wolfgang J.

    2014-01-01

    The physico-chemical properties of colloidal nanoparticles (NPs) are influenced by their local environment, as, in turn, the local environment influences the physico-chemical properties of the NPs. In other words, the local environment around NPs has a profound impact on the NPs, and it is different from bulk due to interaction with the NP surface. So far, this important effect has not been addressed in a comprehensive way in the literature. The vicinity of NPs can be sensitively influenced by local ions and ligands, with effects already occurring at extremely low concentrations. NPs in the Hückel regime are more sensitive to fluctuations in the ionic environment, because of a larger Debye length. The local ion concentration hereby affects the colloidal stability of the NPs, as it is different from bulk owing to Debye Hückel screening caused by the charge of the NPs. This can have subtle effects, now caused by the environment to the performance of the NP, such as for example a buffering effect caused by surface reaction on ultrapure ligand-free nanogold, a size quenching effect in the presence of specific ions and a significant impact on fluorophore-labelled NPs acting as ion sensors. Thus, the aim of this review is to clarify and give an unifying view of the complex interplay between the NP's surface with their nanoenvironment. PMID:24759541

  9. Live Imaging of Host-Parasite Interactions in a Zebrafish Infection Model Reveals Cryptococcal Determinants of Virulence and Central Nervous System Invasion

    PubMed Central

    Tenor, Jennifer L.; Oehlers, Stefan H.; Yang, Jialu L.

    2015-01-01

    ABSTRACT The human fungal pathogen Cryptococcus neoformans is capable of infecting a broad range of hosts, from invertebrates like amoebas and nematodes to standard vertebrate models such as mice and rabbits. Here we have taken advantage of a zebrafish model to investigate host-pathogen interactions of Cryptococcus with the zebrafish innate immune system, which shares a highly conserved framework with that of mammals. Through live-imaging observations and genetic knockdown, we establish that macrophages are the primary immune cells responsible for responding to and containing acute cryptococcal infections. By interrogating survival and cryptococcal burden following infection with a panel of Cryptococcus mutants, we find that virulence factors initially identified as important in causing disease in mice are also necessary for pathogenesis in zebrafish larvae. Live imaging of the cranial blood vessels of infected larvae reveals that C. neoformans is able to penetrate the zebrafish brain following intravenous infection. By studying a C. neoformans FNX1 gene mutant, we find that blood-brain barrier invasion is dependent on a known cryptococcal invasion-promoting pathway previously identified in a murine model of central nervous system invasion. The zebrafish-C. neoformans platform provides a visually and genetically accessible vertebrate model system for cryptococcal pathogenesis with many of the advantages of small invertebrates. This model is well suited for higher-throughput screening of mutants, mechanistic dissection of cryptococcal pathogenesis in live animals, and use in the evaluation of therapeutic agents. PMID:26419880

  10. Ionization behavior of amino lipids for siRNA delivery: determination of ionization constants, SAR, and the impact of lipid pKa on cationic lipid-biomembrane interactions.

    PubMed

    Zhang, Jingtao; Fan, Haihong; Levorse, Dorothy A; Crocker, Louis S

    2011-03-01

    Ionizable amino lipids are being pursued as an important class of materials for delivering small interfering RNA (siRNA) therapeutics, and research is being conducted to elucidate the structure-activity relationships (SAR) of these lipids. The pK(a) of cationic lipid headgroups is one of the critical physiochemical properties of interest due to the strong impact of lipid ionization on the assembly and performance of these lipids. This research focused on developing approaches that permit the rapid determination of the relevant pK(a) of the ionizable amino lipids. Two distinct approaches were investigated: (1) potentiometric titration of amino lipids dissolved in neutral surfactant micelles; and (2) pH-dependent partitioning of a fluorescent dye to cationic liposomes formulated from amino lipids. Using the approaches developed here, the pK(a) values of cationic lipids with distinct headgroups were measured and found to be significantly lower than calculated values. It was also found that lipid-lipid interaction has a strong impact on the pK(a) values of lipids. Lysis of model biomembranes by cationic lipids was used to evaluate the impact of lipid pK(a) on the interaction between cationic lipids and cell membranes. It was found that cationic lipid-biomembrane interaction depends strongly on lipid pK(a) and solution pH, and this interaction is much stronger when amino lipids are highly charged. The presence of an optimal pK(a) range of ionizable amino lipids for siRNA delivery was suggested based on these results. The pK(a) methods reported here can be used to support the SAR screen of cationic lipids for siRNA delivery, and the information revealed through studying the impact of pK(a) on the interaction between cationic lipids and cell membranes will contribute significantly to the design of more efficient siRNA delivery vehicles.

  11. Interaction of high-density and low-density lipoproteins to solid surfaces coated with cholesterol as determined by an optical fiber-based biosensor

    NASA Astrophysics Data System (ADS)

    Singh, Bal R.; Poirier, Michelle A.

    1993-05-01

    In recent years, the use of fiber optics has become an important tool in biomedicine and biotechnology. We are involved in developing and employing a new system which, through the use of fiber optics, may be capable of measuring the content of cholesterol and lipoproteins in blood samples in real time. In the optical fiber-based biosensor, a laser beam having a wavelength of 512 nm (green light) is launched into an optical fiber, which transmits the light to its distal end. An evanescent wave (travelling just outside the fiber core) is used to excite rhodamine-labelled HDL or LDL which become bound to the fiber or to fiber-bound molecules. The fluorescence (red light) is coupled back into the fiber and detected with a photodiode. Preliminary work has involved testing of high density lipoprotein (HDL) binding to a cholesterol-coated fiber and to a bare fiber and low density lipoprotein (LDL) binding to a cholesterol-coated fiber. A significant difference was observed in the binding rate of HDL (5 (mu) g/mL and lower) to a bare fiber as opposed to a cholesterol-coated fiber. The binding rate of HDL (5 (mu) g/mL) to a bare fiber was 7.5 (mu) V/sec and to a cholesterol-coated fiber was 3.5 (mu) V/sec. We have calculated the binding affinity of LDL to a cholesterol- coated fiber as 1.4 (mu) M-1. These preliminary results suggest that the optical fiber-based biosensor can provide a unique and promising approach to the analysis of lipoprotein interaction with solid surfaces and with cholesterol. More importantly, the results suggest that this technique may be used to assess the binding of blood proteins to artificial organs/tissues, and to measure the amount of cholesterol, HDL and LDL in less than a minute.

  12. Interactions with successional stage and nutrient status determines the life-form-specific effects of increased soil temperature on boreal forest floor vegetation

    PubMed Central

    Hedwall, Per-Ola; Skoglund, Jerry; Linder, Sune

    2015-01-01

    The boreal forest is one of the largest terrestrial biomes and plays a key role for the global carbon balance and climate. The forest floor vegetation has a strong influence on the carbon and nitrogen cycles of the forests and is sensitive to changes in temperature conditions and nutrient availability. Additionally, the effects of climate warming on forest floor vegetation have been suggested to be moderated by the tree layer. Data on the effects of soil warming on forest floor vegetation from the boreal forest are, however, very scarce. We studied the effects on the forest floor vegetation in a long-term (18 years) soil warming and fertilization experiment in a Norway spruce stand in northern Sweden. During the first 9 years, warming favored early successional species such as grasses and forbs at the expense of dwarf shrubs and bryophytes in unfertilized stands, while the effects were smaller after fertilization. Hence, warming led to significant changes in species composition and an increase in species richness in the open canopy nutrient limited forest. After another 9 years of warming and increasing tree canopy closure, most of the initial effects had ceased, indicating an interaction between forest succession and warming. The only remaining effect of warming was on the abundance of bryophytes, which contrary to the initial phase was strongly favored by warming. We propose that the suggested moderating effects of the tree layer are specific to plant life-form and conclude that the successional phase of the forest may have a considerable impact on the effects of climate change on forest floor vegetation and its feedback effects on the carbon and nitrogen cycles, and thus on the climate. PMID:25750720

  13. Intra- and Interspecific Interactions as Proximate Determinants of Sexual Dimorphism and Allometric Trajectories in the Bottlenose Dolphin Tursiops truncatus (Cetacea, Odontoceti, Delphinidae)

    PubMed Central

    2016-01-01

    Feeding adaptation, social behaviour, and interspecific interactions related to sexual dimorphism and allometric growth are particularly challenging to be investigated in the high sexual monomorphic Delphinidae. We used geometric morphometrics to extensively explore sexual dimorphism and ontogenetic allometry of different projections of the skull and the mandible of the bottlenose dolphin Tursiops truncatus. Two-dimensional landmarks were recorded on the dorsal, ventral, lateral, and occipital views of the skull, and on the lateral view of the left and the right mandible of 104 specimens from the Mediterranean and the North Seas, differing environmental condition and degree of interspecific associations. Landmark configurations were transformed, standardized and superimposed through a Generalized Procrustes Analysis. Size and shape differences between adult males and females were respectively evaluated through ANOVA on centroid size, Procrustes ANOVA on Procrustes distances, and MANOVA on Procrustes coordinates. Ontogenetic allometry was investigated by multivariate regression of shape coordinates on centroid size in the largest homogenous sample from the North Sea. Results evidenced sexual dimorphic asymmetric traits only detected in the adults of the North Sea bottlenose dolphins living in monospecific associations, with females bearing a marked incision of the cavity hosting the left tympanic bulla. These differences were related to a more refined echolocalization system that likely enhances the exploitation of local resources by philopatric females. Distinct shape in immature versus mature stages and asymmetric changes in postnatal allometry of dorsal and occipital traits, suggest that differences between males and females are established early during growth. Allometric growth trajectories differed between males and females for the ventral view of the skull. Allometric trajectories differed among projections of skull and mandible, and were related to dietary

  14. Intra- and Interspecific Interactions as Proximate Determinants of Sexual Dimorphism and Allometric Trajectories in the Bottlenose Dolphin Tursiops truncatus (Cetacea, Odontoceti, Delphinidae).

    PubMed

    de Francesco, Maria Carla; Loy, Anna

    2016-01-01

    Feeding adaptation, social behaviour, and interspecific interactions related to sexual dimorphism and allometric growth are particularly challenging to be investigated in the high sexual monomorphic Delphinidae. We used geometric morphometrics to extensively explore sexual dimorphism and ontogenetic allometry of different projections of the skull and the mandible of the bottlenose dolphin Tursiops truncatus. Two-dimensional landmarks were recorded on the dorsal, ventral, lateral, and occipital views of the skull, and on the lateral view of the left and the right mandible of 104 specimens from the Mediterranean and the North Seas, differing environmental condition and degree of interspecific associations. Landmark configurations were transformed, standardized and superimposed through a Generalized Procrustes Analysis. Size and shape differences between adult males and females were respectively evaluated through ANOVA on centroid size, Procrustes ANOVA on Procrustes distances, and MANOVA on Procrustes coordinates. Ontogenetic allometry was investigated by multivariate regression of shape coordinates on centroid size in the largest homogenous sample from the North Sea. Results evidenced sexual dimorphic asymmetric traits only detected in the adults of the North Sea bottlenose dolphins living in monospecific associations, with females bearing a marked incision of the cavity hosting the left tympanic bulla. These differences were related to a more refined echolocalization system that likely enhances the exploitation of local resources by philopatric females. Distinct shape in immature versus mature stages and asymmetric changes in postnatal allometry of dorsal and occipital traits, suggest that differences between males and females are established early during growth. Allometric growth trajectories differed between males and females for the ventral view of the skull. Allometric trajectories differed among projections of skull and mandible, and were related to dietary

  15. The determination of acrylamide in environmental and drinking waters by large-volume injection - hydrophilic-interaction liquid chromatography and tandem mass spectrometry.

    PubMed

    Backe, Will J; Yingling, Virginia; Johnson, Todd

    2014-03-21

    A simple and sensitive analytical method was developed to quantify levels of acrylamide in environmental and drinking waters. The analytical method consisted of solvent exchanging acrylamide from 2mL of water into 2mL of dichloromethane using acetonitrile as an intermediate. The sample was then directly analyzed by large-volume (750μL) injection - hydrophilic-interaction liquid chromatography and tandem mass spectrometry. The method detection limit and reporting level were 2.4ng/L and 17ng/L of acrylamide, respectively. The recovery of acrylamide during solvent exchange was 95±2.8% and the matrix effects were 12±2.2% in river water. The use of atmospheric-pressure chemical ionization reduced matrix effects; however, it also reduced method sensitivity by a factor of 2.2 compared to electrospray ionization. Matrix effects were compensated for by the use of an isotopically-labeled internal standard and the method accuracy was 89±3.0% at 25ng/L of acrylamide and 102±2.6% at 250ng/L of acrylamide. The precision of the method was less than 6% relative standard deviation at both 25ng/L and 250ng/L of acrylamide. Samples from a sand-and-gravel mine and a drinking-water treatment plant were acquired to demonstrate the method. The concentrations of acrylamide at the sand-and-gravel mine were up to 280ng/L. In the drinking-water treatment plant, the concentration of acrylamide was approximately double in the finished drinking water when compared to other stages in the drinking-water treatment process. Disinfection or fluoridation may result in higher concentrations of acrylamide in finished drinking water; however, further research in this area is necessary.

  16. Local density and group size interacts with age and sex to determine direction and rate of social dispersal in a polygynous mammal

    PubMed Central

    Marjamäki, Paula H; Contasti, Adrienne L; Coulson, Tim N; McLoughlin, Philip D

    2013-01-01

    Movement away from an area or social group in response to increasing density (density-dependent dispersal) is known for most species; why it evolves is fundamental to our understanding of ecology and evolution. However, we have yet to fully appreciate how individuals of varying conditions (e.g., age and sex) might differently consider effects of density (quorum) when deciding to disperse or not, and scale dependence in their sense of quorum. We tracked movements of all individuals of a naturalized population of feral horses (Equus ferus caballus; Sable Island National Park Reserve, Nova Scotia, Canada) during a period of rapid population growth (N increased from 375 to 484 horses from 2008 to 2010). Permanent dispersal from breeding groups (bands) was positively density dependent for all age and sex categories with respect to local density (horses/km2, bounded by the 99th percentile of individual movements [8000 m]), but was negatively and positively density dependent for males and females, respectively, in relation to group (band) size. Dispersal was generally female biased, with the exception of foals which moved with their mothers (no sex effect), and for yearlings and subadults when band sizes were smaller than average, in which case males dispersed at higher rates than females. Dispersal distance was positively related to local density. We conclude that dispersal rate can be both positively and negatively density dependent for feral horses, contingent on the state of individuals and the scale at which quorum with respect to choosing to disperse or not is assessed. Scale effects and interactions of density-dependent and sex- and age-biased dispersal may have both ecological and evolutionary consequences through effects on resource and mate competition. PMID:24101995

  17. Pro-inflammatory chemokine-chemokine receptor interactions within the Ewing sarcoma microenvironment determine CD8(+) T-lymphocyte infiltration and affect tumour progression.

    PubMed

    Berghuis, Dagmar; Santos, Susy J; Baelde, Hans J; Taminiau, Antonie Hm; Egeler, R Maarten; Schilham, Marco W; Hogendoorn, Pancras Cw; Lankester, Arjan C

    2011-02-01

    Ewing sarcoma is an aggressive round cell sarcoma with poor patient prognosis, particularly in cases of advanced-stage disease. Dynamic tumor-host immune interations within the tumor microenvironment may polarize in situ immune responses and shape tumor development and/or progression. To gain insight into the nature of tumour-host immune interactions within the Ewing sarcoma microenvironment, the presence and spatial distribution of infiltrating CD8(+) /CD4(+) T-lymphocytes were evaluated in therapy-naive Ewing sarcoma. Expression profiling of 40 different chemokines and several chemokine receptors was performed in therapy-naive tumours and cell lines by qPCR, immunohistochemistry, and flow cytometry. Considerable inter-tumour variation was observed regarding density, type, and distribution of infiltrating T-lymphocytes. Tumour-infiltrating T-cells contained significantly higher percentages of CD8(+) T-lymphocytes as compared to stroma-infiltrating cells, suggesting preferential migration of this T-cell type into tumour areas. Gene expression levels of several type 1-associated, pro-inflammatory chemokines (CXCR3- and CCR5-ligands CXCL9, CXCL10, and CCL5) correlated positively with infiltrating (CD8(+) ) T-lymphocyte numbers expressing corresponding chemokine receptors. Survival analyses demonstrated an impact of tumour-infiltrating, and not stroma-infiltrating, CD8(+) T-lymphocytes on tumour progression. At protein level, both tumour and stromal cells expressed the IFNγ-inducible chemokines CXCL9 and CXCL10. CCR5-ligand CCL5 was exclusively expressed by non-tumoural stromal/infiltrating cells. Together, our results indicate that an inflammatory immune microenvironment with high expression of type 1-associated chemokines may be critical for the recruitment of (CD8(+) ) T-lymphocytes expressing corresponding chemokine receptors. The observed impact of tumour-infiltrating (CD8(+) ) T-lymphocytes is consistent with a role for adaptive anti-tumour immunity in the

  18. Hydrophilic-interaction liquid chromatography-tandem mass spectrometric determination of erythrocyte 5-phosphoribosyl 1-pyrophosphate in patients with hypoxanthine-guanine phosphoribosyltransferase deficiency.

    PubMed

    Hasegawa, Hiroshi; Shinohara, Yoshihiko; Nozaki, Sayako; Nakamura, Makiko; Oh, Koei; Namiki, Osamu; Suzuki, Kiyotaka; Nakahara, Akihiko; Miyazawa, Mari; Ishikawa, Ken; Himeno, Takahiro; Yoshida, Sayaka; Ueda, Takanori; Yamada, Yasukazu; Ichida, Kimiyoshi

    2015-01-22

    Mutations in the gene encoding hypoxanthine-guanine phosphoribosyltransferase (HPRT) cause Lesch-Nyhan disease (LND) and its variants (LNV). Due to the technical problems for measuring the HPRT activity in vitro, discordances between the residual HPRT activity and the clinical severity were found. 5-Phosphoribosyl 1-pyrophosphate (PRPP) is a substrate for HPRT. Since increased PRPP concentrations were observed in erythrocytes from patients with LND and LNV, we have turned our attention to erythrocyte PRPP as a biomarker for the phenotype classification. In the present work, a method for determination of PRPP concentration in erythrocyte was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM). Packed erythrocyte samples were deproteinized by heating and the supernatants were injected into the LC-MS/MS system. All measurement results showed good precision with RSD <6%. PRPP concentrations of nine normal male subjects, four male patents with LND and six male patients with LNV were compared. The PRPP concentrations in erythrocyte from patients with LND were markedly increased compared with those from normal subjects, and those from patients with LNV were also increased but the degree was smaller than those with LND. The increase pattern of PRPP concentration in erythrocyte from patients with HPRT deficiency was consistent with the respective phenotypes and was correlated with the disease severity. PRPP concentration was suggested to give us supportive information for the diagnosis and the phenotype classification of LND and LNV.

  19. To Float or Not to Float: How Interactions between Light and Dissolved Inorganic Carbon Species Determine the Buoyancy of Stratiotes aloides

    PubMed Central

    Harpenslager, Sarah F.; Smolders, Alfons J. P.; Kieskamp, Ariët A. M.; Roelofs, Jan G. M.; Lamers, Leon P. M.

    2015-01-01

    Structural diversity formed by dense, floating Stratiotes aloides stands, generates hotspots of biodiversity of flora and fauna in wetlands. However, only part of the populations become emergent and provide this important facilitation. Since it has been hypothesised that its buoyancy depends on the rates of underwater photosynthesis, we investigated the role of dissolved CO2 availability and PAR on photosynthesis, biomass production and buoyancy in a controlled greenhouse experiment. Photosynthesis and growth were strongly influenced by both PAR and CO2 availability. At low PAR, plants formed less biomass and produced no emergent leaves, even when CO2 was abundant. At low CO2 levels, S. aloides switched to HCO3- use, resulting in a lower photosynthetic O2 production, decreased emergent leaf formation and increased CaCO3 precipitation on its leaves, all of which impaired buoyancy. At high PAR, low CO2 availability resulted in slower colonisation of the water layer, whereas CO2 availability did not influence PAR-limited plants. Our study shows that site conditions, rather than the sole abundance of potentially facilitating species, may strongly determine whether or not they form the structure necessary to act as a facilitator for biodiversity in aquatic environments. PMID:25909504

  20. To Float or Not to Float: How Interactions between Light and Dissolved Inorganic Carbon Species Determine the Buoyancy of Stratiotes aloides.

    PubMed

    Harpenslager, Sarah F; Smolders, Alfons J P; Kieskamp, Ariët A M; Roelofs, Jan G M; Lamers, Leon P M

    2015-01-01

    Structural diversity formed by dense, floating Stratiotes aloides stands, generates hotspots of biodiversity of flora and fauna in wetlands. However, only part of the populations become emergent and provide this important facilitation. Since it has been hypothesised that its buoyancy depends on the rates of underwater photosynthesis, we investigated the role of dissolved CO2 availability and PAR on photosynthesis, biomass production and buoyancy in a controlled greenhouse experiment. Photosynthesis and growth were strongly influenced by both PAR and CO2 availability. At low PAR, plants formed less biomass and produced no emergent leaves, even when CO2 was abundant. At low CO2 levels, S. aloides switched to HCO3- use, resulting in a lower photosynthetic O2 production, decreased emergent leaf formation and increased CaCO3 precipitation on its leaves, all of which impaired buoyancy. At high PAR, low CO2 availability resulted in slower colonisation of the water layer, whereas CO2 availability did not influence PAR-limited plants. Our study shows that site conditions, rather than the sole abundance of potentially facilitating species, may strongly determine whether or not they form the structure necessary to act as a facilitator for biodiversity in aquatic environments.

  1. Energy and macronutrient content of familiar beverages interact with pre-meal intervals to determine later food intake, appetite and glycemic response in young adults.

    PubMed

    Panahi, Shirin; Luhovyy, Bohdan L; Liu, Ting Ting; Akhavan, Tina; El Khoury, Dalia; Goff, H Douglas; Anderson, G Harvey

    2013-01-01

    The objective was to compare the effects of pre-meal consumption of familiar beverages on appetite, food intake, and glycemic response in healthy young adults. Two short-term experiments compared the effect of consumption at 30 (experiment 1) or 120 min (experiment 2) before a pizza meal of isovolumetric amounts (500 mL) of water (0 kcal), soy beverage (200 kcal), 2% milk (260 kcal), 1% chocolate milk (340 kcal), orange juice (229 kcal) and cow's milk-based infant formula (368 kcal) on food intake and subjective appetite and blood glucose before and after a meal. Pre-meal ingestion of chocolate milk and infant formula reduced food intake compared to water at 30 min, however, beverage type did not affect food intake at 2h. Pre-meal blood glucose was higher after chocolate milk than other caloric beverages from 0 to 30 min (experiment 1), and after chocolate milk and orange juice from 0 to 120 min (experiment 2). Only milk reduced post-meal blood glucose in both experiments, suggesting that its effects were independent of meal-time energy intake. Combined pre- and post-meal blood glucose was lower after milk compared to chocolate milk and orange juice, but did not differ from other beverages. Thus, beverage calorie content and inter-meal intervals are primary determinants of food intake in the short-term, but macronutrient composition, especially protein content and composition, may play the greater role in glycemic control.

  2. The interaction between litter, N input, and allocation requirement determines invader success and N retention in a simulated clonal wetland ecosystem

    NASA Astrophysics Data System (ADS)

    Martina, J. P.; Currie, W.; Goldberg, D. E.

    2012-12-01

    Wetlands are highly dynamic ecosystems in terms of C and N cycling, as well as one of the most invaded habitats worldwide. It is, therefore, important to disentangle the complex set of mechanisms and feedbacks influencing potential alterations of C and N cycling due to invasive wetland plants. Through factorial sets of simulations, we used a newly developed community-ecosystem model, called MONDRIAN, to run 'in silico' experiments to explore the integrated processes involved in determining invasion success and resulting effects/feedbacks to C and N cycling. MONDRIAN is an individual based model, simulating growth and competition for nutrients among individual ramets, as well as clonal connections and horizontal expansion. Simulated ecosystem N cycling both drives, and is driven by, plant growth, litter production, and biogeochemistry of litter and sediment organic matter. Using MONDRIAN, we set up a multiple-factorial experiment testing (1) the effects of N loading, (2) allocation requirements for daughter ramet establishment, and (3) litter suppression on the ability of invasive species to successfully colonize, persist, and potentially outcompete native species (n=3, 3168 total model runs). Five hypothetical species were used in the model runs, with all species having identical traits, e.g., growth rates, but differing in their maximum size. The smallest three species were considered native species and attempted "invader" species included all five size classes. Species were grown in monoculture and in invasion scenarios to determine the effects of competition. Simulation results showed that when each species was grown in monoculture, higher allocation requirements led to significantly decreased population sizes and, to a lesser extent, rates of net primary production (NPP), especially for species of larger maximum size. For example, the negative effects to population size of increased allocation requirements were 4x that of NPP for the largest species, but only 1

  3. Interaction of cetylpyridine bromide with nucleic acids and determination of nucleic acids at nanogram levels based on the enhancement of resonance Rayleigh light scattering.

    PubMed

    Liu, Rutao; Yang, Jinghe; Wu, Xia

    2002-07-01

    Resonance Rayleigh light scattering (RRLS) spectra of cetylpyridine bromide (CPB)-nucleic acid system and their analytical application have been first studied. The effective factors and optimum conditions of the reaction have been investigated. After CPB and nucleic acid are mixed together, a new absorption peak located at 300 nm appeared, which is due to the formation of new ion associate of CPB-nucleic acid. The new associate can result in two apparent RRLS peaks at 310-400 and 460-480 nm. The RRLS peak of the corrected spectra located at 290-350 nm, which indicate that the RRLS is originated from the absorption of CPB-nucleic acid associate. The peak at 460-480 nm disappears in the corrected RRLS spectra, which indicated that this peak is originated from the strong line emission of the Xe lamp. Under the optimum conditions, the enhanced intensity of RRLS is proportional to the concentration of nucleic acid in the range of 5.0 x 10(-9)-5.0 x 10(-5) g ml(-1) for calf thymus DNA (ctDNA), 1.0 x 10(-8)-4.0 x 10(-5) g ml(-1) for fish sperm DNA (fsDNA) and 1.0 x 10(-8)-5.0 x 10(-5) g ml(-1) for yeast RNA (yRNA). The detection limits (S/N = 3) are 4.3, 8.7 and 7.4 ng ml(-1), respectively. Synthetic samples were determined satisfactorily.

  4. Determining Best Estimates and Uncertainties in Cloud Microphysical Parameters from ARM Field Data: Implications for Models, Retrieval Schemes and Aerosol-Cloud-Radiation Interactions

    SciTech Connect

    McFarquhar, Greg

    2015-12-28

    We proposed to analyze in-situ cloud data collected during ARM/ASR field campaigns to create databases of cloud microphysical properties and their uncertainties as needed for the development of improved cloud parameterizations for models and remote sensing retrievals, and for evaluation of model simulations and retrievals. In particular, we proposed to analyze data collected over the Southern Great Plains (SGP) during the Mid-latitude Continental Convective Clouds Experiment (MC3E), the Storm Peak Laboratory Cloud Property Validation Experiment (STORMVEX), the Small Particles in Cirrus (SPARTICUS) Experiment and the Routine AAF Clouds with Low Optical Water Depths (CLOWD) Optical Radiative Observations (RACORO) field campaign, over the North Slope of Alaska during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) and the Mixed-Phase Arctic Cloud Experiment (M-PACE), and over the Tropical Western Pacific (TWP) during The Tropical Warm Pool International Cloud Experiment (TWP-ICE), to meet the following 3 objectives; derive statistical databases of single ice particle properties (aspect ratio AR, dominant habit, mass, projected area) and distributions of ice crystals (size distributions SDs, mass-dimension m-D, area-dimension A-D relations, mass-weighted fall speeds, single-scattering properties, total concentrations N, ice mass contents IWC), complete with uncertainty estimates; assess processes by which aerosols modulate cloud properties in arctic stratus and mid-latitude cumuli, and quantify aerosol’s influence in context of varying meteorological and surface conditions; and determine how ice cloud microphysical, single-scattering and fall-out properties and contributions of small ice crystals to such properties vary according to location, environment, surface, meteorological and aerosol conditions, and develop parameterizations of such effects.In this report we describe the accomplishments that we made on all 3 research objectives.

  5. Thermal rate constants for R+N2H2 --> RH+N2H (R=H, OH, NH2) determined from multireference configuration interaction and variational transition state theory calculations

    NASA Astrophysics Data System (ADS)

    Linder, Douglas P.; Duan, Xiaofeng; Page, Michael

    1996-04-01

    Ab initio electronic structure calculations were performed to determine features of the potential energy surface for abstraction of a hydrogen atom from N2H2 by H, OH, and NH2. Based on multireference configuration interaction calculations with basis sets up to correlation consistent polarized valence triple zeta, the barrier heights determined for these reactions are 4.3, 3.0, and 4.4 kcal/mol, respectively. Using features of the potential energy surface along minimum energy paths determined at the complete active space self-consistent-field level of theory, variational transition state theory calculations were performed to determine the rate coefficients over the temperature range 300-3000 K. The temperature dependent computed rate coefficients for the three reactions are well represented by the following three-parameter expressions: kH(T) =1.41×10-19T2.63 exp(115.8/T) cm3 molec-1 s-1, kOH(T)=9.84×10-23 T3.40 exp(686.3/T) cm3 molec-1 s-1, and kNH2(T)=1.46×10-25T4.05 exp(810.5/T) cm3 molec-1 s-1. Abstraction from N2H2 is predicted to occur at a significantly slower rate than analogous abstractions from the isoelectronic HNO.

  6. Sulphate radical generation through interaction of peroxymonosulphate with Co(II) for in-line sample preparation aiming at spectrophotometric flow-based determination of phosphate and phosphite in fertilizers.

    PubMed

    Crispino, Carla C; Kamogawa, Marcos Y; Ferreira, José R; Zagatto, Elias A G

    2016-09-01

    An advanced oxidative process relying on the interaction of peroxymonosulphate and cobalt(II) was implemented for generating the sulphate radicals in flow analysis, in order to accomplish in-line sample preparation thus improving the spectrophotometric determination of phosphate and phosphite in liquid foliar fertilizers. To this end, a flow-batch system with a heated chamber was designed. The sample was handled twice, with and without the step of phosphite oxidation to phosphate, and the formed orthophosphate was quantified after interaction with the vanadate-molybdate reagent. Phosphite was determined as the difference in analytical signals corresponding to sample handling with and without the oxidation step. Influence of Co(II) on the peroxymonosulphate activation, reagent concentrations and added volumes, acidity, temperature and heating time were investigated like aiming at to improve analytical recovery and measurement repeatability, as well as the and system ruggedness. The 6.6-20.0mgL(-1) P2O5 standards were in-line prepared from a single stock solution. Detection limits were estimated as 0.8 and 0.1mgL(-1) for P2O5 and P-PO4. Twenty-four samples are were run per hour, and results are were in agreement with those obtained by the official procedure.

  7. Interaction of 7-n-alkoxycoumarins with cytochrome P-450(2) and their partitioning into liposomal membranes. Assessment of methods for determination of membrane partition coefficients.

    PubMed Central

    Vermeir, M; Boens, N; Heirwegh, K P

    1992-01-01

    A study was made of the binding of 7-ethoxy-, 7-n-propoxy- and 7-n-pentoxy-coumarin to cytochrome P-450(2) reconstituted into large unilamellar liposomes composed of a mixture of egg L-alpha-phosphatidylcholine, egg phosphatidylethanolamine and dipalmitoyl phosphatidic acid (2:1:0.06, by weight). The apparent spectral dissociation constants Ksapp. increased linearly with increasing proteoliposomal concentration. When both cytochrome P-450(2) and NADPH:cytochrome P-450 reductase were reconstituted into liposomes, the apparent Michaelis constants Kmapp. for O-dealkylation of 7-methoxy-, 7-ethoxy- and 7-n-propoxy-coumarin showed a similar dependence on the proteoliposomal concentration. The results were in accordance with models for kinetic or equilibrium processes in biphasic systems containing membrane-bound catalytic or acceptor sites, in which a linear solute partition in the bilayer membrane is postulated. The methyl, ethyl and n-propyl ether were readily dealkylated. However, the O-dealkylation rate of 7-n-butoxycoumarin was low and became very small for longer alkyl ethers. Both the effective dissociation constants and effective Michaelis constants decreased with elongation of the alkyl side chain of the coumarins. From plots of the apparent dissociation constants and apparent Michaelis constants against the lipid volume fraction of the proteoliposomes, the membrane partition coefficients for several homologues were calculated. When protein-free liposomes were added to 7-n-alkoxycoumarin solutions, the fluorescence intensity of the coumarins decreased and eventually became negligible in the presence of an excess of liposomal material. On the assumption that the overall fluorescence can be ascribed exclusively to the fraction of 7-n-alkoxycoumarin molecules present in the aqueous phase, partition coefficients for liposomal accumulation of the test compounds could be determined directly. For several coumarin ethers, comparable values were derived for the membrane

  8. A simultaneous determination method for 5-fluorouracil and its metabolites in human plasma with linear range adjusted by in-source collision-induced dissociation using hydrophilic interaction liquid chromatography-electrospray ionization-tandem mass spectrometry.

    PubMed

    Ishii, Hideaki; Shimada, Miki; Yamaguchi, Hiroaki; Mano, Nariyasu

    2016-11-01

    We applied a new technique for quantitative linear range shift using in-source collision-induced dissociation (CID) to complex biological fluids to demonstrate its utility. The technique was used in a simultaneous quantitative determination method of 5-fluorouracil (5-FU), an anticancer drug for various solid tumors, and its metabolites in human plasma by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). To control adverse effects after administration of 5-FU, it is important to monitor the plasma concentration of 5-FU and its metabolites; however, no simultaneous determination method has yet been reported because of vastly different physical and chemical properties of compounds. We developed a new analytical method for simultaneously determining 5-FU and its metabolites in human plasma by LC/ESI-MS/MS coupled with the technique for quantitative linear range shift using in-source CID. Hydrophilic interaction liquid chromatography using a stationary phase with zwitterionic functional groups, phosphorylcholine, was suitable for separation of 5-FU from its nucleoside and interfering endogenous materials. The addition of glycerin into acetonitrile-rich eluent after LC separation improved the ESI-MS response of high polar analytes. Based on the validation results, linear range shifts by in-source CID is the reliable technique even with complex biological samples such as plasma. Copyright © 2016 John Wiley & Sons Ltd.

  9. Isopiestic Determination of the Osmotic and Activity Coefficients of NaCl + SrCl2 + H2O at 298.15 K, and Representation with an Extended Ion-Interaction Model

    SciTech Connect

    Clegg, S L; Rard, J A; Miller, D G

    2004-11-09

    Isopiestic vapor-pressure measurements were made at 298.15 K for aqueous NaCl + SrCl{sub 2} solutions, using NaCl(aq) as the reference standard. The measurements for these ternary solutions were made at NaCl ionic strength fractions of y{sub 1} = 0.17066, 0.47366, and 0.82682 for the water activity range 0.9835 {ge} a{sub w} {ge} 0.8710. Our results, and those from two previous isopiestic studies, were combined and used with previously determined parameters for NaCl(aq) and those for SrCl{sub 2}(aq) determined here to evaluate the mixing parameters{sup S}{Theta}{sub Na,Sr} = (0.0562 {+-} 0.0007) kg {center_dot} mol{sup -1} and {Psi}{sub Na,Sr,Cl} = -(0.00705 {+-} 0.00017) kg{sup 2} {center_dot} mol{sup -2} for an extended form of Pitzer's ion-interaction model. These model parameters are valid for ionic strengths of I {le} 7.0 mol {center_dot} kg{sup -1}, where higher-order electrostatic effects have been included in the mixture model. If the fitting range is extended to the saturated solution molalities, then {sup S}{Theta}{sub Na,Sr} = (0.07885 {+-} 0.00195) kg {center_dot} mol{sup -1} and {Psi}{sub Na,Sr,Cl} = -(0.01230 {+-} 0.00033) kg{sup 2} {center_dot} mol{sup -2}. The extended ion-interaction model parameters obtained from available isopiestic data for SrCl{sub 2}(aq) at 298.15 K yield recommended values of the water activities and osmotic and activity coefficients.

  10. Pulsed electron spin nutation spectroscopy for weakly exchange-coupled multi-spin molecular systems with nuclear hyperfine couplings: a general approach to bi- and triradicals and determination of their spin dipolar and exchange interactions

    NASA Astrophysics Data System (ADS)

    Ayabe, Kazuki; Sato, Kazunobu; Nakazawa, Shigeaki; Nishida, Shinsuke; Sugisaki, Kenji; Ise, Tomoaki; Morita, Yasushi; Toyota, Kazuo; Shiomi, Daisuke; Kitagawa, Masahiro; Suzuki, Shuichi; Okada, Keiji; Takui, Takeji

    2013-10-01

    Weakly exchange-coupled biradicals have attracted much attention in terms of their dynamic nuclear polarisation application in NMR spectroscopy for biological systems or the use of synthetic electron-spin qubits in quantum information processing/quantum-computing technology. Analogues multi-partite molecular systems are important in entering a new phase of the relevant fields. Many stable organic biradicals known so far have nitrogen nuclei at their electron spin sites, where singly occupied molecular orbitals are dominating and large hyperfine couplings occur. A salient feature of such weakly exchange-coupled molecular systems in terms of electronic spin structures is underlain by small zero-field splitting (ZFS) parameters comparable with nuclear hyperfine and/or exchange interactions. Pulse-based electron spin nutation (ESN) spectroscopy of weakly exchange-coupled biradicals, applicable to oriented or non-oriented media, has proven to be a useful and facile approach to the determination of ZFS parameters, which reflect relatively short distances between unpaired electron spins. In the present study, we first treat two-dimensional single-crystal ESN spectroscopy (Q-band) of a 15N-labelled weakly exchange-coupled biradical, showing the nuclear hyperfine effects on the ESN phenomena from both the experimental and theoretical side. ESN spectroscopy is transition moment spectroscopy, in which the nutation frequency as a function of the microwave irradiation strength ω1 (angular frequency) for any cases of weakly exchange-coupled systems can be treated. The results provide a testing ground for the simplified but general approach to the ESN analysis. In this study, we have invoked single-crystal electron-electron double resonance measurements on a typical biradical well incorporated in a diamagnetic host lattice and checked the accuracy of our ESN analysis for the spin dipolar tensor and exchange interaction. Next, we extend the general approach to analogues multi

  11. Determination of carnitine and acylcarnitines in human urine by means of microextraction in packed sorbent and hydrophilic interaction chromatography-ultra-high-performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Magiera, Sylwia; Baranowski, Jacek

    2015-05-10

    A method using semi-automatic microextraction by packed sorbent (eVol®-MEPS) and hydrophilic interaction chromatography-ultra-high-performance liquid chromatography-tandem mass spectrometry (HILIC-UHPLC-MS/MS) was described for the simultaneous determination of carnitine and acylcarnitines in human urine. The optimal conditions of MEPS extraction were obtained using C2 of M1 (C8+SCX) phase as a sorbent. Chromatographic separation of the analytes was achieved within 2.5min on Acquity UPLC BEH HILIC column using a gradient elution program with water containing 5mM ammonium acetate and acetonitrile as the mobile phase. The detection was performed on a triple-quadrupole tandem mass spectrometer in a positive ion mode via electrospray ionization (ESI). The linearity of the calibration curves for all compounds was found over a range from 0.1ng/mL to 500ng/mL. The method afforded satisfactory results in terms of sensitivity, specificity, precision, accuracy, recovery as well as stability of the analyte under various conditions. The method was used successfully for determination of carnitine and acylcarnitines in human urine.

  12. Voltammetric studies on the potent carcinogen, 7,12-dimethylbenz[a]anthracene: Adsorptive stripping voltammetric determination in bulk aqueous forms and human urine samples and detection of DNA interaction on pencil graphite electrode.

    PubMed

    Yardim, Y; Keskin, E; Levent, A; Ozsöz, M; Sentürk, Z

    2010-01-15

    7,12-Dimethylbenz[a]anthracene (DMBA), is a widely studied polycyclic aromatic hydrocarbon that has long been recognized as a very potent carcinogen. Initially, the electrochemical oxidation of DMBA at the glassy carbon and pencil graphite electrodes in non-aqueous media (dimethylsulphoxide with lithium perchlorate) was studied by cyclic voltammetry. DMBA was irreversibly oxidized in two steps at high positive potentials, resulting in the ill-resolved formation of a couple with a reduction and re-oxidation wave at much lower potentials. Special attention was given to the use of adsorptive stripping voltammetry together with a medium exchange procedure on disposable pencil graphite electrode in aqueous solutions over the pH range of 3.0-9.0. The response was characterized with respect to pH of the supporting electrolyte, pre-concentration time and accumulation potential. Using square-wave stripping mode, the compound yielded a well-defined voltammetric response in acetate buffer, pH 4.8 at +1.15V (vs. Ag/AgCl) (a pre-concentration step being carried out at a fixed potential of +0.60V for 360s). The process could be used to determine DMBA concentrations in the range 2-10nM, with an extremely low detection limit of 0.194nM (49.7ngL(-1)). The applicability to assay of spiked human urine samples was also illustrated. Finally, the interaction of DMBA with fish sperm double-stranded DNA based on decreasing of the oxidation signal of adenine base was studied electrochemically by using differential pulse voltammetry with a pencil graphite electrode at the surface and also in solution. The favorable signal-to-noise characteristics of biosensor resulted in low detection limit (ca. 46nM) following a 300-s interaction. These results displayed that the electrochemical DNA-based biosensor could be used for the sensitive, rapid, simple and cost effective detection of DMBA-DNA interaction.

  13. The interactive brain hypothesis

    PubMed Central

    Di Paolo, Ezequiel; De Jaegher, Hanne

    2012-01-01

    Enactive approaches foreground the role of interpersonal interaction in explanations of social understanding. This motivates, in combination with a recent interest in neuroscientific studies involving actual interactions, the question of how interactive processes relate to neural mechanisms involved in social understanding. We introduce the Interactive Brain Hypothesis (IBH) in order to help map the spectrum of possible relations between social interaction and neural processes. The hypothesis states that interactive experience and skills play enabling roles in both the development and current function of social brain mechanisms, even in cases where social understanding happens in the absence of immediate interaction. We examine the plausibility of this hypothesis against developmental and neurobiological evidence and contrast it with the widespread assumption that mindreading is crucial to all social cognition. We describe the elements of social interaction that bear most directly on this hypothesis and discuss the empirical possibilities open to social neuroscience. We propose that the link between coordination dynamics and social understanding can be best grasped by studying transitions between states of coordination. These transitions form part of the self-organization of interaction processes that characterize the dynamics of social engagement. The patterns and synergies of this self-organization help explain how individuals understand each other. Various possibilities for role-taking emerge during interaction, determining a spectrum of participation. This view contrasts sharply with the observational stance that has guided research in social neuroscience until recently. We also introduce the concept of readiness to interact to describe the practices and dispositions that are summoned in situations of social significance (even if not interactive). This latter idea links interactive factors to more classical observational scenarios. PMID:22701412

  14. Comparison of the quantitative performances and measurement uncertainty estimates obtained during method validation versus routine applications of a novel hydrophilic interaction chromatography method for the determination of cidofovir in human plasma.

    PubMed

    Lecomte, F; Hubert, C; Demarche, S; De Bleye, C; Dispas, A; Jost, M; Frankenne, F; Ceccato, A; Rozet, E; Hubert, Ph

    2012-01-05

    Method validation is essential to ensure that an analytical method is fit for its intended purpose. Additionally, it is advisable to estimate measurement uncertainty in order to allow a correct interpretation of the results generated by analytical methods. Measurement uncertainty can be efficiently estimated during method validation as a top-down approach. However, method validation predictions of the quantitative performances of the assay and estimations of measurement uncertainty may be far away from the real performances obtained during the routine application of this assay. In this work, the predictions of the quantitative performances and measurement uncertainty estimations obtained from a method validation are compared to those obtained during routine applications of a bioanalytical method. For that purpose, a new hydrophilic interaction chromatography (HILIC) method was used. This method was developed for the determination of cidofovir, an antiviral drug, in human plasma. Cidofovir (CDV) is a highly polar molecule presenting three ionizable functions. Therefore, it is an interesting candidate for determination by HILIC mode. CDV is an acyclic cytidine monophosphate analog that has a broad antiviral spectrum and is currently undergoing evaluation in clinical trials as a topical agent for treatment of papillomavirus infections. The analytical conditions were optimized by means of design of experiments approach in order to obtain robust analytical conditions. These ones were absolutely necessary to enable the comparisons mentioned above. After a sample clean-up by means of solid phase extraction, the chromatographic analysis was performed on bare silica stationary phase using a mixture of acetonitrile-ammonium hydrogen carbonate (pH 7.0; 20mM) (72:28, v/v) as mobile phase. This newly developed bioanalytical method was then fully validated according to FDA (Food and Drug Administration) requirements using a total error approach that guaranteed that each future

  15. Rapid and simultaneous determination of hexapeptides (Ac-EEMQRR-amide and H2N-EEMQRR-amide) in anti-wrinkle cosmetics by hydrophilic interaction liquid chromatography-solid phase extraction preparation and hydrophilic interaction liquid chromatography with tandem mass spectrometry.

    PubMed

    Zhou, Wanlong; Wang, Perry G; Krynitsky, Alexander J; Rader, Jeanne I

    2011-11-04

    A rapid method for the simultaneous determination of Ac-EEMQRR-amide and H(2)N-EEMQRR-amide in cosmetic products was developed and evaluated. This analytical procedure involved extracting samples with 0.1:0.1:85:15 (v:v) trifluoroacetic acid (TFA):formic acid:acetonitrile (ACN):water and determination by hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-MS/MS). Samples showing serious ion suppression were further cleaned up using HILIC-SPE prior to HILIC-MS/MS analysis. Stable isotopically labeled peptides, corresponding to the above two peptides, were used as internal standards to correct for loss of recovery and matrix effects. Electrospray ionization (ESI) in the positive mode was used. The linear range was 2.0-1000 ng/mL for Ac-EEMQRR-amide and 25.0-2500 ng/mL for H(2)N-EEMQRR-amide. Thirteen commercial products were analyzed for the two peptides using this method. The amounts of Ac-EEMQRR-amide in the samples ranged from none detected to 42.3 μg/g. H(2)N-EEMQRR-amide was not detected in any of the samples. The recoveries for Ac-EEMQRR-amide and H(2)N-EEMQRR-amide ranged from 85% to 110% and 84% to 119%, respectively, at the spiking level of 30 μg/g.

  16. Interacting faults

    NASA Astrophysics Data System (ADS)

    Peacock, D. C. P.; Nixon, C. W.; Rotevatn, A.; Sanderson, D. J.; Zuluaga, L. F.

    2017-04-01

    The way that faults interact with each other controls fault geometries, displacements and strains. Faults rarely occur individually but as sets or networks, with the arrangement of these faults producing a variety of different fault interactions. Fault interactions are characterised in terms of the following: 1) Geometry - the spatial arrangement of the faults. Interacting faults may or may not be geometrically linked (i.e. physically connected), when fault planes share an intersection line. 2) Kinematics - the displacement distributions of the interacting faults and whether the displacement directions are parallel, perpendicular or oblique to the intersection line. Interacting faults may or may not be kinematically linked, where the displacements, stresses and strains of one fault influences those of the other. 3) Displacement and strain in the interaction zone - whether the faults have the same or opposite displacement directions, and if extension or contraction dominates in the acute bisector between the faults. 4) Chronology - the relative ages of the faults. This characterisation scheme is used to suggest a classification for interacting faults. Different types of interaction are illustrated using metre-scale faults from the Mesozoic rocks of Somerset and examples from the literature.

  17. Mapping Murine Corneal Neovascularization and Weight Loss Virulence Determinants in the Herpes Simplex Virus 1 Genome and the Detection of an Epistatic Interaction between the UL and IRS/US Regions

    PubMed Central

    Lee, Kyubin; Kolb, Aaron W.; Larsen, Inna; Craven, Mark

    2016-01-01

    ABSTRACT Herpes simplex virus 1 (HSV-1) most commonly causes recrudescent labial ulcers; however, it is also the leading cause of infectious blindness in developed countries. Previous research in animal models has demonstrated that the severity of HSV-1 ocular disease is influenced by three main factors: host innate immunity, host immune response, and viral strain. We have previously shown that mixed infection with two avirulent HSV-1 strains (OD4 and CJ994) results in recombinants with a wide range of ocular disease phenotype severity. Recently, we developed a quantitative trait locus (QTL)-based computational approach (vQTLmap) to identify viral single nucleotide polymorphisms (SNPs) predicted to influence the severity of the ocular disease phenotypes. We have now applied vQTLmap to identify HSV-1 SNPs associated with corneal neovascularization and mean peak percentage weight loss (MPWL) using 65 HSV-1 OD4-CJ994 recombinants. The vQTLmap analysis using Random Forest for neovascularization identified phenotypically meaningful nonsynonymous SNPs in the ICP4, UL41 (VHS), UL42, UL46 (VP11/12), UL47 (VP13/14), UL48 (VP22), US3, US4 (gG), US6 (gD), and US7 (gI) coding regions. The ICP4 gene was previously identified as a corneal neovascularization determinant, validating the vQTLmap method. Further analysis detected an epistatic interaction for neovascularization between a segment of the unique long (UL) region and a segment of the inverted repeat short (IRS)/unique short (US) region. Ridge regression was used to identify MPWL-associated nonsynonymous SNPs in the UL1 (gL), UL2, UL4, UL49 (VP22), UL50, and ICP4 coding regions. The data provide additional insights into virulence gene and epistatic interaction discovery in HSV-1. IMPORTANCE Herpes simplex virus 1 (HSV-1) typically causes recurrent cold sores; however, it is also the leading source of infectious blindness in develo