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Sample records for homology-dependent interactions determine

  1. Non-Mendelian inheritance and homology-dependent effects in ciliates.

    PubMed

    Meyer, Eric; Garnier, Olivier

    2002-01-01

    Ciliates are single-celled eukaryotes that harbor two kinds of nuclei. The germline micronuclei function only to perpetuate the genome during sexual reproduction; the macronuclei are polyploid, somatic nuclei that differentiate from the micronuclear lineage at each sexual generation. Macronuclear development involves extensive and reproducible rearrangements of the genome, including chromosome fragmentation and precise excision of numerous internal sequence elements. In Paramecium and Tetrahymena, homology-dependent maternal effects have been evidenced by transformation of the vegetative macronucleus with germline sequences containing internal eliminated sequences (short single-copy elements), which can result in a specific inhibition of the excision of the homologous elements during development of a new macronucleus in the sexual progeny of transformed clones. Furthermore, transformation of the Paramecium maternal macronucleus with cloned macronuclear sequences can specifically induce new fragmentation patterns or internal deletions in the zygotic macronucleus. These experiments show that the processing of many germline sequences in the developing macronucleus is sensitive to the presence and copy number of homologous sequences in the maternal macronucleus. The generality and sequence specificity of this transnuclear, epigenetic regulation of rearrangements suggest that it is mediated by pairing interactions between zygotic sequences and sequences originating from the maternal macronucleus, presumably RNA molecules. Alternative macronuclear versions of the genome can be maternally inherited across sexual generations, suggesting a molecular model for some of the long-known cases of non-Mendelian inheritance, and in particular for the developmental determination and maternal inheritance of mating types in Paramecium tetraurelia. PMID:11931229

  2. Genomic assay reveals tolerance of DNA damage by both translesion DNA synthesis and homology-dependent repair in mammalian cells.

    PubMed

    Izhar, Lior; Ziv, Omer; Cohen, Isadora S; Geacintov, Nicholas E; Livneh, Zvi

    2013-04-16

    DNA lesions can block replication forks and lead to the formation of single-stranded gaps. These replication complications are mitigated by DNA damage tolerance mechanisms, which prevent deleterious outcomes such as cell death, genomic instability, and carcinogenesis. The two main tolerance strategies are translesion DNA synthesis (TLS), in which low-fidelity DNA polymerases bypass the blocking lesion, and homology-dependent repair (HDR; postreplication repair), which is based on the homologous sister chromatid. Here we describe a unique high-resolution method for the simultaneous analysis of TLS and HDR across defined DNA lesions in mammalian genomes. The method is based on insertion of plasmids carrying defined site-specific DNA lesions into mammalian chromosomes, using phage integrase-mediated integration. Using this method we show that mammalian cells use HDR to tolerate DNA damage in their genome. Moreover, analysis of the tolerance of the UV light-induced 6-4 photoproduct, the tobacco smoke-induced benzo[a]pyrene-guanine adduct, and an artificial trimethylene insert shows that each of these three lesions is tolerated by both TLS and HDR. We also determined the specificity of nucleotide insertion opposite these lesions during TLS in human genomes. This unique method will be useful in elucidating the mechanism of DNA damage tolerance in mammalian chromosomes and their connection to pathological processes such as carcinogenesis. PMID:23530190

  3. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms.

    PubMed

    Wu, Qingfa; Ding, Shou-Wei; Zhang, Yongjiang; Zhu, Shuifang

    2015-01-01

    A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed. PMID:26047558

  4. YU238259 Is a Novel Inhibitor of Homology-dependent DNA Repair that Exhibits Synthetic Lethality and Radiosensitization in Repair-deficient Tumors

    PubMed Central

    Stachelek, Gregory C.; Peterson-Roth, Elizabeth; Liu, Yanfeng; Fernandez, Rafael J.; Pike, Luke R. G.; Qian, Jack M.; Abriola, Laura; Hoyer, Denton; Hungerford, William; Merkel, Janie; Glazer, Peter M.

    2015-01-01

    Radiation therapy and DNA-damaging chemotherapy are frequently utilized in the treatment of solid tumors. Innate or acquired resistance to these therapies remains a major clinical challenge in oncology. The development of small molecules that sensitize cancers to established therapies represents an attractive approach to extending survival and quality of life in patients. Here, we demonstrate that YU238259, a member of a novel class of DNA double-strand break repair inhibitors, exhibits potent synthetic lethality in the setting of DNA damage response and DNA repair defects. YU238259 specifically inhibits homology-dependent DNA repair (HDR), but not non-homologous end-joining (NHEJ), in cell-based GFP reporter assays. Treatment with YU238259 is not only synergistic with ionizing radiation (IR), etoposide, and PARP inhibition, but this synergism is heightened by BRCA2-deficiency. Further, growth of BRCA2-deficient human tumor xenografts in nude mice is significantly delayed by YU238259 treatment even in the absence of concomitant DNA-damaging therapy. The cytotoxicity of these small molecules in repair-deficient cells results from an accumulation of unresolved DNA double-strand breaks. These findings suggest that YU238259 or related small molecules may have clinical benefit to patients with advanced BRCA2-negative tumors, either as a monotherapy or as an adjuvant to radiotherapy and certain chemotherapies. PMID:26116172

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

    PubMed

    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.

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

    PubMed

    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

  7. 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

  8. Computational learning on specificity-determining residue-nucleotide interactions

    PubMed Central

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Moses, Alan M.; Zhang, Zhaolei

    2015-01-01

    The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein–DNA interactions across different DNA binding families. PMID:26527718

  9. 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.

  10. Dark Matter Self Interaction Limits: Determination and Implications

    NASA Astrophysics Data System (ADS)

    Lessard, Paul

    2007-05-01

    The first studies of the lensing events around the Bullet cluster have shown that the dark matter halos of galaxy clusters are collisionless. This rather fortunate structure in the universe becomes an excellent laboratory for setting limits on the source of dark matter particle interaction. Markevitch et al. in 2004 explored three simple methods for determining the dark matter self interaction cross section to mass ratio.. A new strong and weak lensing derived density map of the cluster has been created, advancing the accuracy of these limits. A subsequent Markevitch et al. paper was released April of this year with a full n-body simulation of the collision putting giving us the best, although not the strongest, limit on the dark matter self interaction cross-section to mass ratio. Furthermore we are now at such a point as to ask what these limits tell us. Axions and SUSY wimps theoretically fall well under this threshold leaving their DM candidacy untouched if not strengthened. Other candidates like Q-balls however, are not guaranteed to fall below this limit. It is my goal to characterize Q-ball dark matter scenarios coincident with this new experimental limit. To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2007.NWS07.C1.7

  11. Particle-Surface Interaction Model and Method of Determining Particle-Surface Interactions

    NASA Technical Reports Server (NTRS)

    Hughes, David W. (Inventor)

    2012-01-01

    A method and model of predicting particle-surface interactions with a surface, such as the surface of a spacecraft. The method includes the steps of: determining a trajectory path of a plurality of moving particles; predicting whether any of the moving particles will intersect a surface; predicting whether any of the particles will be captured by the surface and/or; predicting a reflected trajectory and velocity of particles reflected from the surface.

  12. Interactions among thermal parameters determine offspring sex under temperature-dependent sex determination.

    PubMed

    Warner, Daniel A; Shine, Richard

    2011-01-22

    In many animals, temperatures experienced by developing embryos determine offspring sex (e.g. temperature-dependent sex determination, TSD), but most studies focus strictly on the effects of mean temperature, with little emphasis on the importance of thermal fluctuations. In the jacky dragon (Amphibolurus muricatus), an Australian lizard with TSD, data from nests in the field demonstrate that offspring sex ratios are predictable from thermal fluctuations but not from mean nest temperatures. To clarify this paradox, we incubated eggs in a factorial experiment with two levels of mean temperature and three levels of diel fluctuation. We show that offspring sex is determined by an interaction between these critical thermal parameters. Intriguingly, because these two thermal descriptors shift in opposing directions throughout the incubation season, this interactive effect inhibits seasonal shifts in sex ratio. Hence, our results suggest that TSD can yield offspring sex ratios that resemble those produced under genotypic sex-determining systems. These findings raise important considerations for understanding the diversity of TSD reaction norms, for designing experiments that evaluate the evolutionary significance of TSD, and for predicting sex ratios under past and future climate change scenarios.

  13. Interactions among thermal parameters determine offspring sex under temperature-dependent sex determination

    PubMed Central

    Warner, Daniel A.; Shine, Richard

    2011-01-01

    In many animals, temperatures experienced by developing embryos determine offspring sex (e.g. temperature-dependent sex determination, TSD), but most studies focus strictly on the effects of mean temperature, with little emphasis on the importance of thermal fluctuations. In the jacky dragon (Amphibolurus muricatus), an Australian lizard with TSD, data from nests in the field demonstrate that offspring sex ratios are predictable from thermal fluctuations but not from mean nest temperatures. To clarify this paradox, we incubated eggs in a factorial experiment with two levels of mean temperature and three levels of diel fluctuation. We show that offspring sex is determined by an interaction between these critical thermal parameters. Intriguingly, because these two thermal descriptors shift in opposing directions throughout the incubation season, this interactive effect inhibits seasonal shifts in sex ratio. Hence, our results suggest that TSD can yield offspring sex ratios that resemble those produced under genotypic sex-determining systems. These findings raise important considerations for understanding the diversity of TSD reaction norms, for designing experiments that evaluate the evolutionary significance of TSD, and for predicting sex ratios under past and future climate change scenarios. PMID:20685704

  14. Determination and characterization of metronidazole–kaolin interaction

    PubMed Central

    Aleanizy, Fadilah Sfouq; Alqahtani, Fulwah; Al Gohary, Omaimah; El Tahir, Eram; Al Shalabi, Rania

    2014-01-01

    The needs for safe, therapeutically effective antidiarrheal combination continuously lead to effective treatment. When administered simultaneously, metronidazole–kaolin interactions have been reported by FDA but not studied. This paper is the first to study metronidazole–kaolin interactions. Adsorption isotherms of a metronidazole–kaolin antidiarrheal combination from aqueous solutions at an in vivo simulated pH conditions were obtained at 37 ± 0.5 °C. Langmuir constants for the adsorption are 10.8225, 41.3223 mg g−1 and 11.60, 2.56 l g−1 aimed at the monolayer capacity, and the equilibrium constant at pH 1.2 and 6.8, respectively. pH effect on adsorption of known concentration of metronidazole by kaolin was also studied over the range 1.2–8. A gradual increase in the adsorbed amount was noted with increasing the pH. Elution studies by different eluents showed that drug recovery from adsorbent surface was pH-dependent via competitive mechanism. The elution followed the sequence: 0.1 M HCl > 0.1 M NaCl > H2O. Adsorption–desorption studies revealed physical adsorption. The equilibrium concentration of metronidazole decreased as the adsorbent concentration was increased in the systems. The dissolution profiles (USP) of commercially available tablets (Riazole® 500 mg) were obtained alone and in the presence of either (ORS®) rehydration salts and 9 or 18 g of kaolin powder. The percentage drug released versus time: 95.01% in 25 min, 101.02% in 30 min, 67.63% in 60 min, 60.59% in 60 min, respectively. The percentage drug released versus time was increased with ORS® due to common ion effect [Cl−], while, it was decreased with kaolin due to adsorption. The mechanism of reaction of Riazole® (500 mg) tablets in the different dissolution media, confirms with Korsmeyer–Peppas model. The interaction between metronidazole and kaolin was characterized by melting point determinations, differential scanning calorimetry analysis and

  15. Determining a Skyrme-type effective interaction from realistic two-nucleon interaction

    SciTech Connect

    Manisa, K.

    2011-07-15

    The Variational Monte Carlo (VMC) method is employed to determine characteristics of symmetric and asymmetric nuclear matter. The realistic Urbana v14 nucleon-nucleon interaction potential of Lagaris and Pandharipande was used in the VMC calculations with addition of a phenomenological density-dependent term to simulate many-body interactions. A new Skyrme parameter set SKaan-U14 is found to consistently reproduce the characteristics of the nuclear matter obtained from VMC calculations. The properties of symmetric and asymmetric nuclear matter are calculated by the new Skyrme parameter set. The results obtained by using the new Skyrme parameter set are compared with results obtained by different Skyrme parameter sets in the literature.

  16. Interaction Determined Electron Energy Levels in One-Dimension

    NASA Astrophysics Data System (ADS)

    Pepper, Michael; Kumar, Sanjeev; Thomas, Kalarikad; Smith, Luke; Creeth, Graham; Farrer, Ian; Ritchie, David; Jones, Geraint; Jonathan, Griffiths; UCL Collaboration; Cavendish Laboratory Collaboration

    2015-03-01

    We have investigated electron transport in a quasi-one dimensional electron gas in the GaAs-AlGaAs heterostructure designed so that the confinement potential can be progressively weakened. This causes the energy levels to decrease in energy relative to each other, however this decrease occurs at different rates, a feature attributed to the energy being determined by both confinement and the electron-electron repulsion which varies with the shape of the wavefunction. It is found that the initial ground state crosses the higher levels so resulting in missing plateaux of quantised conductance. A change in the nature of the ground state to a more extended form causes an increase in the capacitance between the confining gates and the electrons. Both crossings and anti-crossings of the levels are found and these will be discussed along with other consequences of the form of the level interactions. The effects of level crossing on the spin dependent 0.7 structure will be presented. Supported by EPSRC (UK).

  17. 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.

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

    DOEpatents

    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.

  19. Ideology and Interaction: Debating Determinisms in Literacy Studies

    ERIC Educational Resources Information Center

    Collin, Ross; Street, Brian V.

    2014-01-01

    In this exchange, Street and Collin debate the merits of the interaction model of literacy that Collin outlined in a recent issue of Reading Research Quarterly. Built as a complement and a counter to Street's ideological model of literacy, Collin's interaction model defines literacies as technologies that coevolve with sociocultural…

  20. 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

  1. Steric interactions determine side-chain conformations in protein cores.

    PubMed

    Caballero, D; Virrueta, A; O'Hern, C S; Regan, L

    2016-09-01

    We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modeling residues in the context of a particular protein environment, with both intra- and inter-residue steric interactions, is sufficient to specify which of the allowed side-chain conformations is adopted. This model predicts 97% of the side-chain conformations of Leu, Ile, Val, Phe, Tyr, Trp and Thr core residues to within 20°. Although the hard-sphere dipeptide model predicts the observed side-chain dihedral angle distributions for both Thr and Ser, the model including the protein environment predicts side-chain conformations to within 20° for only 60% of core Ser residues. Thus, this approach can identify the amino acids for which hard-sphere interactions alone are sufficient and those for which additional interactions are necessary to accurately predict side-chain conformations in protein cores. We also show that our approach can predict alternate side-chain conformations of core residues, which are supported by the observed electron density.

  2. 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…

  3. 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.

  4. Charged Group Surface Accessibility Determines Micelleplexes Formation and Cellular Interaction

    PubMed Central

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

    2015-01-01

    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. In this article, we investigated charged group presentation on the micelle surfaces and their interaction with miRNA using thermodynamics, biochemistry, and molecular dynamics simulation. Charged group accessibility on cationic micelle surfaces was shown as a mechanism to alter micelleplex formation and stability. PMID:25866141

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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…

  13. Sugar interaction with metals in aqueous solution: indirect determination from infrared and direct determination from nuclear magnetic resonance spectroscopy.

    PubMed

    Rondeau, Philippe; Sers, Sandrine; Jhurry, Dhanjay; Cadet, Frederic

    2003-04-01

    In this article, mid-infrared Fourier transform (Mid-FT-IR) and carbon thirteen nuclear magnetic resonance (13C NMR) spectroscopy have been used to determine possible interactions between sucrose and various alkali or alkaline earth metals in aqueous solution. In the presence of these metals, significant shifts in the absorption bands of sucrose were noted by mid-FT-IR coupled with principal component analysis (PCA). These shifts were explained on the basis of weakening of the H-bond network between sucrose and water and possible interactions between sucrose and the metal ion. Factorial maps were established and the spectral patterns obtained show that these interactions vary according to the nature of the metal ion. 13C NMR analysis showed that the carbon atoms of sucrose undergo shielding or deshielding in the presence of metal ions in aqueous solutions. Two factors were invoked to account for the variation of chemical shifts: the rupture of hydrogen bonds due to hydration of the metal ion and the possible coordination of the metal ion to the oxygen atoms of sucrose. PMID:14658645

  14. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

    PubMed

    Syedbasha, Mohameedyaseen; Linnik, Janina; Santer, Deanna; O'Shea, Daire; Barakat, Khaled; Joyce, Michael; Khanna, Nina; Tyrrell, D Lorne; Houghton, Michael; Egli, Adrian

    2016-01-01

    A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.

  15. 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.

  16. 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.

  17. fourSig: a method for determining chromosomal interactions in 4C-Seq data

    PubMed Central

    Williams, Rex L.; Starmer, Joshua; Mugford, Joshua W.; Calabrese, J. Mauro; Mieczkowski, Piotr; Yee, Della; Magnuson, Terry

    2014-01-01

    The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates. PMID:24561615

  18. Ecological resistance, seed density and their interactions determine patterns of invasion in a California coastal grassland.

    PubMed

    Thomsen, Meredith A; D'Antonio, Carla M; Suttle, Kenwyn B; Sousa, Wayne P

    2006-02-01

    Relatively little experimental evidence is available regarding how ecological resistance and propagule density interact in their effects on the establishment of invasive exotic species. We examined the independent and interactive effects of neighbour cover (biotic resistance), winter vs. spring water addition (abiotic resistance) and seed density on the invasion of the European perennial grass Holcus lanatus into a California coastal grassland dominated by exotic annual grasses. We found that decreased competition from resident exotic grasses had no effect. In contrast, increased late-season water availability eroded the abiotic resistance offered by naturally dry conditions, facilitating invasion. Finally, watering treatment and seed density interacted strongly in determining seedling survival: while seedling mortality was close to 100% in ambient and winter water addition plots, survivor numbers increased with seed density in spring-watered plots. Thus, decreased abiotic resistance can amplify the effect of increased propagule density on seedling establishment, thereby increasing the likelihood of invasion.

  19. 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. PMID:17285319

  20. CIA, a novel estrogen receptor coactivator with a bifunctional nuclear receptor interacting determinant.

    PubMed

    Sauvé, F; McBroom, L D; Gallant, J; Moraitis, A N; Labrie, F; Giguère, V

    2001-01-01

    Coregulators for nuclear receptors (NR) are factors that either enhance or repress their transcriptional activity. Both coactivators and corepressors have been shown to use similar but functionally distinct NR interacting determinants containing the core motifs LxxLL and PhixxPhiPhi, respectively. These interactions occur through a hydrophobic cleft located on the surface of the ligand-binding domain (LBD) of the NR and are regulated by ligand-dependent activation function 2 (AF-2). In an effort to identify novel coregulators that function independently of AF-2, we used the LBD of the orphan receptor RVR (which lacks AF-2) as bait in a yeast two-hybrid screen. This strategy led to the cloning of a nuclear protein referred to as CIA (coactivator independent of AF-2 function) that possesses both repressor and activator functions. Strikingly, we observed that CIA not only interacts with RVR and Rev-ErbAalpha in a ligand-independent manner but can also form complexes with estrogen receptor alpha (ERalpha) and ERbeta in vitro and enhances ERalpha transcriptional activity in the presence of estradiol (E(2)). CIA-ERalpha interactions were found to be independent of AF-2 and enhanced by the antiestrogens EM-652 and ICI 182,780 but not by 4-hydroxytamoxifen and raloxifene. We further demonstrate that CIA-ERalpha interactions require the presence within CIA of a novel bifunctional NR recognition determinant containing overlapping LxxLL and PhixxPhiPhi motifs. The identification and functional characterization of CIA suggest that hormone binding can create a functional coactivator interaction interface in the absence of AF-2.

  1. 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

  2. Unusual role of epilayer–substrate interactions in determining orientational relations in van der Waals epitaxy

    PubMed Central

    Liu, Lei; Siegel, David A.; Chen, Wei; Liu, Peizhi; Guo, Junjie; Duscher, Gerd; Zhao, Chong; Wang, Hao; Wang, Wenlong; Bai, Xuedong; McCarty, Kevin F.; Zhang, Zhenyu; Gu, Gong

    2014-01-01

    Using selected-area low-energy electron diffraction analysis, we showed strict orientational alignment of monolayer hexagonal boron nitride (h-BN) crystallites with Cu(100) surface lattices of Cu foil substrates during atmospheric pressure chemical vapor deposition. In sharp contrast, the graphene–Cu(100) system is well-known to assume a wide range of rotations despite graphene’s crystallographic similarity to h-BN. Our density functional theory calculations uncovered the origin of this surprising difference: The crystallite orientation is determined during nucleation by interactions between the cluster’s edges and the substrate. Unlike the weaker B– and N–Cu interactions, strong C–Cu interactions rearrange surface Cu atoms, resulting in the aligned geometry not being a distinct minimum in total energy. The discovery made in this specific case runs counter to the conventional wisdom that strong epilayer–substrate interactions enhance orientational alignment in epitaxy and sheds light on the factors that determine orientational relation in van der Waals epitaxy of 2D materials. PMID:25385622

  3. A pipeline for determining protein-protein interactions and proximities in the cellular milieu.

    PubMed

    Subbotin, Roman I; Chait, Brian T

    2014-11-01

    It remains extraordinarily challenging to elucidate endogenous protein-protein interactions and proximities within the cellular milieu. The dynamic nature and the large range of affinities of these interactions augment the difficulty of this undertaking. Among the most useful tools for extracting such information are those based on affinity capture of target bait proteins in combination with mass spectrometric readout of the co-isolated species. Although highly enabling, the utility of affinity-based methods is generally limited by difficulties in distinguishing specific from nonspecific interactors, preserving and isolating all unique interactions including those that are weak, transient, or rapidly exchanging, and differentiating proximal interactions from those that are more distal. Here, we have devised and optimized a set of methods to address these challenges. The resulting pipeline involves flash-freezing cells in liquid nitrogen to preserve the cellular environment at the moment of freezing; cryomilling to fracture the frozen cells into intact micron chunks to allow for rapid access of a chemical reagent and to stabilize the intact endogenous subcellular assemblies and interactors upon thawing; and utilizing the high reactivity of glutaraldehyde to achieve sufficiently rapid stabilization at low temperatures to preserve native cellular interactions. In the course of this work, we determined that relatively low molar ratios of glutaraldehyde to reactive amines within the cellular milieu were sufficient to preserve even labile and transient interactions. This mild treatment enables efficient and rapid affinity capture of the protein assemblies of interest under nondenaturing conditions, followed by bottom-up MS to identify and quantify the protein constituents. For convenience, we have termed this approach Stabilized Affinity Capture Mass Spectrometry. Here, we demonstrate that Stabilized Affinity Capture Mass Spectrometry allows us to stabilize and elucidate

  4. 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.

  5. 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

  6. 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. PMID:25413866

  7. Spatial and temporal factors determine auditory-visual interactions in human saccadic eye movements.

    PubMed

    Frens, M A; Van Opstal, A J; Van der Willigen, R F

    1995-08-01

    In this paper, we show that human saccadic eye movements toward a visual target are generated with a reduced latency when this target is spatially and temporally aligned with an irrelevant auditory nontarget. This effect gradually disappears if the temporal and/or spatial alignment of the visual and auditory stimuli are changed. When subjects are able to accurately localize the auditory stimulus in two dimensions, the spatial dependence of the reduction in latency depends on the actual radial distance between the auditory and the visual stimulus. If, however, only the azimuth of the sound source can be determined by the subjects, the horizontal target separation determines the strength of the interaction. Neither saccade accuracy nor saccade kinematics were affected in these paradigms. We propose that, in addition to an aspecific warning signal, the reduction of saccadic latency is due to interactions that take place at a multimodal stage of saccade programming, where the perceived positions of visual and auditory stimuli are represented in a common frame of reference. This hypothesis is in agreement with our finding that the saccades often are initially directed to the average position of the visual and the auditory target, provided that their spatial separation is not too large. Striking similarities with electrophysiological findings on multisensory interactions in the deep layers of the midbrain superior colliculus are discussed.

  8. Interactions and Diffusion in Fine-Stranded β-lactoglobulin Gels Determined via FRAP and Binding

    PubMed Central

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

    2014-01-01

    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. PMID:24411257

  9. 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

    2014-01-01

    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.

  10. Determination of the interaction using FTIR within the composite gel polymer electrolyte

    NASA Astrophysics Data System (ADS)

    Huang, Yun; Ma, Xiaoyan; Wang, Xu; Liang, Xiao

    2013-01-01

    In the previous research, the gel polymer electrolyte (GPE) which consisted of poly(methyl methacrylate) (PMMA) matrix, propylene carbonate (PC), LiClO4 and OREC (Rectorite modified with dodecyl benzyl dimethyl ammonium chloride), achieved satisfactory properties. In the paper, the interaction between components was quantitatively determined. Characterization of interaction of Cdbnd O in PC and PMMA with Li+ and OH group on OREC surface has been thoroughly examined using FTIR, respectively. The quantitative analysis of FTIR shows that the absorptivity coefficient a of PMMA/LiClO4, PC/LiClO4, PC/OREC and PMMA/OREC is 0.902, 0.113, 0.430 and 0.753, respectively, which means that the Li+ or OH bonded Cdbnd O is more sensitive than the free Cdbnd O in FTIR spectra. The limit value of bonded Cdbnd O equivalent fraction of PMMA/LiClO4, PC/LiClO4, PC/OREC and PMMA/OREC is 17%, 94%, 57% and 20%, respectively, which implies that all the interaction within the components is reversible and the intensity of interaction is ordered as PC/LiClO4, PC/OREC, PMMA/OREC and PMMA/LiClO4.

  11. 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

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

    PubMed

    Roach, Deborah Ann

    2012-10-01

    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.

  13. 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

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

    PubMed

    Roach, Deborah Ann

    2012-10-01

    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

  15. Abiotic and biotic interactions determine whether increased colonization is beneficial or detrimental to metapopulation management.

    PubMed

    Southwell, Darren M; Rhodes, Jonathan R; McDonald-Madden, Eve; Nicol, Sam; Helmstedt, Kate J; McCarthy, Michael A

    2016-06-01

    Increasing the colonization rate of metapopulations can improve persistence, but can also increase exposure to threats. To make good decisions, managers must understand whether increased colonization is beneficial or detrimental to metapopulation persistence. While a number of studies have examined interactions between metapopulations, colonization, and threats, they have assumed that threat dynamics respond linearly to changes in colonization. Here, we determined when to increase colonization while explicitly accounting for non-linear dependencies between a metapopulation and its threats. We developed patch occupancy metapopulation models for species susceptible to abiotic, generalist, and specialist threats and modeled the total derivative of the equilibrium proportion of patches occupied by each metapopulation with respect to the colonization rate. By using the total derivative, we developed a rule for determining when to increase metapopulation colonization. This rule was applied to a simulated metapopulation where the dynamics of each threat responded to increased colonization following a power function. Before modifying colonization, we show that managers must understand: (1) whether a metapopulation is susceptible to a threat; (2) the type of threat acting on a metapopulation; (3) which component of threat dynamics might depend on colonization, and; (4) the likely response of a threat-dependent variable to changes in colonization. The sensitivity of management decisions to these interactions increases uncertainty in conservation planning decisions.

  16. Cell-Binding Assays for Determining the Affinity of Protein-Protein Interactions: Technologies and Considerations.

    PubMed

    Hunter, S A; Cochran, J R

    2016-01-01

    Determining the equilibrium-binding affinity (Kd) of two interacting proteins is essential not only for the biochemical study of protein signaling and function but also for the engineering of improved protein and enzyme variants. One common technique for measuring protein-binding affinities uses flow cytometry to analyze ligand binding to proteins presented on the surface of a cell. However, cell-binding assays require specific considerations to accurately quantify the binding affinity of a protein-protein interaction. Here we will cover the basic assumptions in designing a cell-based binding assay, including the relevant equations and theory behind determining binding affinities. Further, two major considerations in measuring binding affinities-time to equilibrium and ligand depletion-will be discussed. As these conditions have the potential to greatly alter the Kd, methods through which to avoid or minimize them will be provided. We then outline detailed protocols for performing direct- and competitive-binding assays against proteins displayed on the surface of yeast or mammalian cells that can be used to derive accurate Kd values. Finally, a comparison of cell-based binding assays to other types of binding assays will be presented. PMID:27586327

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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. PMID:26973872

  2. 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

  3. 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

  4. 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

  5. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  6. Susceptibility to ulcerative colitis in Hungarian patients determined by gene-gene interactions

    PubMed Central

    Sarlos, Patricia; Varszegi, Dalma; Csongei, Veronika; Magyari, Lili; Jaromi, Luca; Nagy, Lajos; Melegh, Bela

    2014-01-01

    AIM: To study the inflammatory bowel disease-5 locus (IBD5) and interleukin-23 receptor (IL23R) gene variants in UC patients and test for gene-gene interaction. METHODS: The study population (n = 625) was comprised of 320 unrelated ulcerative colitis (UC) patients with Caucasian origin and 316 age- and gender-matched, healthy controls. Five variants in the IBD5 locus (IGR2198a_1 rs11739135, IGR2096a_1 rs12521868, IGR2230a_1 rs17622208, SLC22A4 rs1050152 and SLC22A5 rs2631367) and two of the IL23R gene (rs1004819, rs2201841) were analysed. PCR and restriction fragment length polymorphism methods were used for genotyping, the SLC22A4 rs1050152 genotypes were determined by direct sequencing. Interactions and specific genotype combinations of the seven variants were tested by binary logistic regression analysis. The IL23R genotypes were stratified by IBD5 genotypes for further interaction analyses. RESULTS: For the IL23R rs1004819 A allele we found significantly higher allele frequency (P = 0.032) in UC patients compared to control subjects. The SNP rs1004819 showed significant association with UC risk for carriers (P = 0.004, OR = 1.606; 95%CI: 1.160-2.223) and the SNP rs2201841 for homozygotes (P = 0.030, OR = 1.983; 95%CI: 1.069-3.678). Individually none of the IBD5 markers conferred risk to UC development. There was no evidence for statistical interaction either between IBD5 loci and IL23R genes using logistic regression analysis. After genotype stratification, we could detect a positive association on the background of rs1004819 A allele for SLC22A4 T, SLC22A5 C, IGR2198a_1 C or IGR2096a_1 T allele, the highest OR was calculated in the presence of SLC22A4 T allele (P = 0.005, OR = 2.015; 95%CI: 1.230-3.300). There was no association with UC for any combinations of rs1004819 and IGR2230a_1. The IL23R rs2201841 homozygous genotype and IBD5 carrier status together did not confer susceptibility for UC. CONCLUSION: The present study has shown that UC susceptibility

  7. Determination of metformin and its prodrugs in human and rat blood by hydrophilic interaction liquid chromatography.

    PubMed

    Huttunen, Kristiina M; Rautio, Jarkko; Leppänen, Jukka; Vepsäläinen, Jouko; Keski-Rahkonen, Pekka

    2009-10-15

    Simple and specific hydrophilic interaction liquid chromatography (HILIC) method with ultraviolet (UV) detection was developed for the simultaneous determination of highly water-soluble metformin and its more lipophilic prodrugs in human and rat blood samples. The sample preparation was accomplished by precipitating proteins with acetonitrile, which enabled the direct injection of supernatants to the HPLC. Chromatographic separation was performed on an analytical normal phase silica column using a mixture of 0.01 M ammonium acetate pH 5.0 and acetonitrile (40:60, v/v) as a mobile phase at flow rate of 1 ml/min and at the wavelength of 235 nm. The method was validated in terms of specificity, linearity, accuracy, precision, recovery, and analyte stability. The UV-HILIC method was suitable for detecting both metformin and one of its more lipophilic prodrugs simultaneously in human and rat blood samples.

  8. 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

    2016-01-01

    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

  9. 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

  10. Determination of the Cytostatic and Cytocidal Activities of Antimalarial Compounds and their Combination Interactions

    PubMed Central

    Sherlach, Katy S.; Roepe, Paul D.

    2014-01-01

    Determining the antiplasmodial activity of candidate antimalarial drugs in vitro identifies new therapies for drug-resistant malaria. Importantly though, activity can be either growth-inhibitory (cytostatic) or parasite-kill (cytocidal), or both. The simple methods described here can allow for distinction between these, as well as definition of drug interactions between two or more compounds. The latter is important in the definition of novel drug combination therapy for malaria. These methods involve live malarial parasite red blood cell culture, routine pharmacology, high-throughput detection of parasite DNA with fluorescent reporters, and routine mathematical analysis of dose – response curves. The techniques and approaches are accessible to most laboratories and require minimal special equipment beyond a fluorescent plate reader and tissue culture facilities. PMID:25445179

  11. 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.

  12. Intershell Interaction in a Double Wall Carbon Nanotube with Determined Chiral Indices under a Torsional Strain

    NASA Astrophysics Data System (ADS)

    Lin, Letian; Cui, Taoran; Washburn, Sean; Qin, Lu-Chang

    2011-03-01

    We have used a double wall carbon nanotube to build a torsional pendulum. The nanotube worked as a torsional bearing for a metal block. An external electric field was used to rotate the metal block to cause a fully elastic torsional deformation on the nanotube. Nano-beam electron diffraction patterns were taken before and while the nanotube was twisted. By analysis of the shift of the diffraction patterns, we were able to determine the nanotube chiral indices and measure the inner-shell torisonal responses to the torsional stress applied on the outer-shell. The inter-shell interactions and nanotube shear modulus were also calculated and discussed in connection to the theoretical estimations.

  13. 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. PMID:23497901

  14. 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.

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

    DOE PAGESBeta

    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 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

  16. 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.

  17. Carbon mineralizability determines interactive effects on mineralization of pyrogenic organic matter and soil organic carbon.

    PubMed

    Whitman, Thea; Zhu, Zihua; Lehmann, Johannes

    2014-12-01

    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 preincubations, 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 preincubated for 6 months. Over the longer term, both the 6-month and 1-day preincubated soils experienced net ∼10% decreases in SOC mineralization with PyOM additions. Additionally, the duration of preincubation affected interactions, indicating that there may be no optimal preincubation time for SOC mineralization studies. We show conclusively that mineralizability of SOC in relation to PyOM-C is an important determinant of the effect of PyOM additions on SOC mineralization. PMID:25361379

  18. 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.

  19. 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

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

    PubMed

    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 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.

  1. Pollutant threshold concentration determination in marine ecosystems using an ecological interaction endpoint.

    PubMed

    Wang, Changyou; Liang, Shengkang; Guo, Wenting; Yu, Hua; Xing, Wenhui

    2015-09-01

    The threshold concentrations of pollutants are determined by extrapolating single-species effect data to community-level effects. This assumes the most sensitive endpoint of the life cycle of individuals and the species sensitivity distribution from single-species toxic effect tests, thus, ignoring the ecological interactions. The uncertainties due to this extrapolation can be partially overcome using the equilibrium point of a customized ecosystem. This method incorporates ecological interactions and integrates the effects on growth, survival, and ingestion into a single effect measure, the equilibrium point excursion in the customized ecosystem, in order to describe the toxic effects on plankton. A case study showed that the threshold concentration of copper calculated with the endpoint of the equilibrium point was 10 μg L(-1), which is significantly different from the threshold calculated with a single-species endpoint. The endpoint calculated using this method provides a more relevant measure of the ecological impact than any single individual-level endpoint. PMID:25982547

  2. 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

  3. 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…

  4. 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.

  5. Density-based Energy Decomposition Analysis for Intermolecular Interactions with Variationally Determined Intermediate State Energies

    SciTech Connect

    Wu, Q.; Ayers, P.W.; Zhang, Y.

    2009-10-28

    The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented with the Wu-Yang algorithm [Q. Wu and W. Yang, J. Chem. Phys. 118, 2498 (2003) ]. This variational process dispenses with the Heitler-London antisymmetrization of wave functions used in most previous methods and calculates the electrostatic and Pauli repulsion energies together without any distortion of the frozen density, an important fact that enables a clean separation of these two terms from the relaxation (i.e., polarization and charge transfer) terms. The new EDA also employs the constrained density functional theory approach [Q. Wu and T. Van Voorhis, Phys. Rev. A 72, 24502 (2005)] to separate out charge transfer effects. Because the charge transfer energy is based on the density flow in real space, it has a small basis set dependence. Applications of this decomposition to hydrogen bonding in the water dimer and the formamide dimer show that the frozen density energy dominates the binding in these systems, consistent with the noncovalent nature of the interactions. A more detailed examination reveals how the interplay of electrostatics and the Pauli repulsion determines the distance and angular dependence of these hydrogen bonds.

  6. 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.

  7. 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

    2015-05-01

    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. PMID:25905890

  8. 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.

  9. 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.

  10. Histamine H2 receptor signaling × environment interactions determine susceptibility to experimental allergic encephalomyelitis

    PubMed Central

    Saligrama, Naresha; Case, Laure K.; Krementsov, Dimitry N.; Teuscher, Cory

    2014-01-01

    Histamine and its receptors are important in both multiple sclerosis and experimental allergic encephalomyelitis (EAE). C57BL/6J (B6) mice deficient for the histamine H2 receptor (H2RKO) are less susceptible to EAE and exhibit blunted Th1 responses. However, whether decreased antigen-specific T-cell effector responses in H2RKO mice were due to a lack of H2R signaling in CD4+ T cells or antigen-presenting cells has remained unclear. We generated transgenic mice expressing H2R specifically in T cells on the H2RKO background, and, using wild-type B6 and H2RKO mice as controls, induced EAE either in the presence or absence of the ancillary adjuvant pertussis toxin (PTX), which models the effects of infectious inflammatory stimuli on autoimmune disease. We monitored the mice for clinical signs of EAE and neuropathology, as well as effector T-cell responses using flow cytometry. EAE severity and neuropathology in H2RKO mice expressing H2R exclusively in T cells become equal to those in wild-type B6 mice only when PTX is used to elicit disease. EAE complementation was associated with frequencies of CD4+IFN-γ+ and CD4+IL-17+ cells that are equal to or greater than those in wild-type B6, respectively. Thus, the regulation of encephalitogenic T-cell responses and EAE susceptibility by H2R signaling in CD4+ T cells is dependent on gene × environment interactions.—Saligrama, N., Case, L. K., Krementsov, D. N., Teuscher, C. Histamine H2 receptor signaling × environment interactions determine susceptibility to experimental allergic encephalomyelitis. PMID:24371118

  11. 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]. PMID:27098911

  12. 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

  13. Oxygen and energy availability interact to determine flight performance in the Glanville fritillary butterfly.

    PubMed

    Fountain, Toby; Melvin, Richard G; Ikonen, Suvi; Ruokolainen, Annukka; Woestmann, Luisa; Hietakangas, Ville; Hanski, Ilkka

    2016-05-15

    Flying insects have the highest known mass-specific demand for oxygen, which makes it likely that reduced availability of oxygen might limit sustained flight, either instead of or in addition to the limitation due to metabolite resources. The Glanville fritillary butterfly (Melitaea cinxia) occurs as a large metapopulation in which adult butterflies frequently disperse between small local populations. Here, we examine how the interaction between oxygen availability and fuel use affects flight performance in the Glanville fritillary. Individuals were flown under either normoxic (21 kPa O2) or hypoxic (10 kPa O2) conditions and their flight metabolism was measured. To determine resource use, levels of circulating glucose, trehalose and whole-body triglyceride were recorded after flight. Flight performance was significantly reduced in hypoxic conditions. When flown under normoxic conditions, we observed a positive correlation among individuals between post-flight circulating trehalose levels and flight metabolic rate, suggesting that low levels of circulating trehalose constrains flight metabolism. To test this hypothesis experimentally, we measured the flight metabolic rate of individuals injected with a trehalase inhibitor. In support of the hypothesis, experimental butterflies showed significantly reduced flight metabolic rate, but not resting metabolic rate, in comparison to control individuals. By contrast, under hypoxia there was no relationship between trehalose and flight metabolic rate. Additionally, in this case, flight metabolic rate was reduced in spite of circulating trehalose levels that were high enough to support high flight metabolic rate under normoxic conditions. These results demonstrate a significant interaction between oxygen and energy availability for the control of flight performance.

  14. Membrane interactions in nerve myelin: II. Determination of surface charge from biochemical data.

    PubMed Central

    Inouye, H; Kirschner, D A

    1988-01-01

    In our accompanying paper (Inouye and Kirschner, 1988) we calculated the surface charge density at the extracellular surfaces in peripheral and central nervous system (PNS; CNS) myelins from observations on the dependency of the width of the extracellular space on pH and ionic strength. Here, we have determined the surface charge density of the membrane surfaces in myelin from its chemical composition and the localization of some of its molecular components. We then analyzed the attractive and repulsive forces between the apposed surfaces and calculated equilibrium periods for comparison with the measured values. The biochemical model accounts for the observed isoelectric range of the myelin period and, with the surface charge reduced (possibly by divalent cation binding or a space charge approximation), the model also accounts for the dependency of period on pH above the isoelectric range. At the extracellular (and cytoplasmic) surfaces the contribution of lipid (with pI approximately 2) to the net surface charge is about the same in both PNS and CNS myelin, whereas the contribution of protein depends on which ones are exposed at the two surfaces. The protein conformation and localization modulate the surface charge of the lipid, resulting in positively-charged cytoplasmic surfaces (pI approximately 9) and negatively-charged extracellular surfaces (pI approximately 2-4). The net negative charge at the extracellular surface is due in CNS myelin to lipid, and in PNS myelin to both lipid and (PO) glycoprotein. The net positive charge at the cytoplasmic surface is due in CNS myelin mostly to basic protein, and in PNS myelin to PO glycoprotein and basic protein. The invariance of the cytoplasmic packing may be due to specific short-range interactions. Our models demonstrate how the particular myelin proteins and their localization and conformation can account for the differences in inter-membrane interactions in CNS and PNS myelins. PMID:3345333

  15. A dual-light reporter system to determine the efficiency of protein–protein interactions in mammalian cells

    PubMed Central

    Nasim, M. T.; Trembath, R. C.

    2005-01-01

    Methods for determining protein–protein interactions in mammalian cells typically rely on single reporter functions and are susceptible to variations between samples particularly in regard to levels of transcription, processing and translation. A method has been developed for determining protein–protein interactions in mammalian cells, which bypasses these variables confounding single reporter assays. The approach utilizes two units of gene expression linked to reporter functions that are interposed by a deactivation–activation unit in such a way that the downstream expression unit is switched off. Hence upstream expression occurs regardless of protein–protein interaction, leading to the production of the upstream reporter. In the event of protein–protein interactions, the downstream expression unit is switched on leading to dual reporter read outs. Thus, the ratio of the two reporter activities provides a measure to determine the efficiency of protein–protein interactions. To access the system we screened a mutant of BMPR2 where the interaction between BMPR-II and LIMK is abrogated. BMPR-II is a type II receptor of the TGFβ superfamily and plays a key role in the pathogenesis of familial pulmonary arterial hypertension. This system has potential for high-throughput screening of libraries (peptide, chemical, cDNA, etc.) to isolate agents that are capable of interfering with highly selective protein–protein interaction. PMID:15824058

  16. 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.

  17. Metal-sulfur valence orbital interaction energies in metal-dithiolene complexes: determination of charge and overlap interaction energies by comparison of core and valence ionization energy shifts.

    PubMed

    Wiebelhaus, Nicholas J; Cranswick, Matthew A; Klein, Eric L; Lockett, L Tori; Lichtenberger, Dennis L; Enemark, John H

    2011-11-01

    The electronic interactions between metals and dithiolenes are important in the biological processes of many metalloenzymes as well as in diverse chemical and material applications. Of special note is the ability of the dithiolene ligand to support metal centers in multiple coordination environments and oxidation states. To better understand the nature of metal-dithiolene electronic interactions, new capabilities in gas-phase core photoelectron spectroscopy for molecules with high sublimation temperatures have been developed and applied to a series of molecules of the type Cp(2)M(bdt) (Cp = η(5)-cyclopentadienyl, M = Ti, V, Mo, and bdt = benzenedithiolato). Comparison of the gas-phase core and valence ionization energy shifts provides a unique quantitative energy measure of valence orbital overlap interactions between the metal and the sulfur orbitals that is separated from the effects of charge redistribution. The results explain the large amount of sulfur character in the redox-active orbitals and the 'leveling' of oxidation state energies in metal-dithiolene systems. The experimentally determined orbital interaction energies reveal a previously unidentified overlap interaction of the predominantly sulfur HOMO of the bdt ligand with filled π orbitals of the Cp ligands, suggesting that direct dithiolene interactions with other ligands bound to the metal could be significant for other metal-dithiolene systems in chemistry and biology.

  18. Using a local-interaction model to determine the resistance to penetration of projectiles into sandy soil

    NASA Astrophysics Data System (ADS)

    Kotov, V. L.; Balandin, V. V.; Bragov, A. M.; Linnik, E. Yu.; Balandin, V. V.

    2013-07-01

    A local-interaction model describing the penetration of axisymmetric projectiles into sandy soil at a constant velocity is studied experimentally and theoretically. Two approaches to the determination of the parameters of the quadratic local-interaction model are considered. The first approach is based on the use of the solution of the problem of spherical-cavity expansion taking into account the dynamic compressibility and shear resistance of soil. In the second approach, model parameters are determined based on the experimental dependence of the resistance to penetration of conical projectiles into a sandy soil on the impact velocity. Good agreement was obtained between the results of experiments, two-dimensional numerical calculations, and calculations for the local interaction model based on the solution of the spherical-cavity expansion problem and used to determine the maximum resistance to penetration of conical and spherical projectiles.

  19. 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

  20. Assessment of Magnetostatic Interaction Effects on Thellier Paleointensity Determination by Experimental Simulations

    NASA Astrophysics Data System (ADS)

    Zheng, Z.; Zhao, X.

    2009-05-01

    The ability to control magnetic interactions between grains is of fundamental importance in paleointensity studies. We continued to perform experimental simulations to help understand the effect of magnetostatic interaction on Thellier type paleointensity experiments, using artificial synthesized magnetite grains mixed with both pseudo-single domain (PSD) and multidomain (MD) particles. Magnetite powders were mixed either with an Aron ceramic or were dispersed in matrix of Seto porcelain clay. The effects of interaction between grains can be observed from the magnetic behavior of specimens with different inter-grain distances. The maximum effect of domain's interaction can be estimated by comparing the behavior of specimens with large inter-grain distance (i.e., mostly dispersed-grains) with that of ideal non-interacting SD grains. Our results clearly show that (1) the interaction between grains (rather than domain's interaction) has particular disastrous effects on the Thellier-Coe paleointensity experiment; (2) interaction of large inter- grain distance samples adds an almost negative constant value to the applied external field (i.e., acting as an internal demagnetizing field); (3) interaction in shorter inter-grain distance samples mainly generates the difference in blocking and unblocking temperatures of the sample. Detailed results will be presented and discussed at the meeting.

  1. Characteristics of the interaction of calcium with casein submicelles as determined by analytical affinity chromatography

    SciTech Connect

    Jang, H.D.; Swaisgood, H.E. )

    1990-12-01

    Interaction of calcium with casein submicelles was investigated in CaCl2 and calcium phosphate buffers and with synthetic milk salt solutions using the technique of analytical affinity chromatography. Micelles that had been prepared by size exclusion chromatography with glycerolpropyl controlled-pore glass from fresh raw skim milk that had never been cooled, were dialyzed at room temperature against calcium-free imidazole buffer, pH 6.7. Resulting submicelles were covalently immobilized on succinamidopropyl controlled-pore glass (300-nm pore size). Using 45Ca to monitor the elution retardation, the affinity of free Ca2+ and calcium salt species was determined at temperatures of 20 to 40 degrees C and pH 6.0 to 7.5. Increasing the pH in this range or increasing the temperature strengthened the binding of calcium to submicelles, similar to previous observations with individual caseins. However, the enthalpy change obtained from the temperature dependence was considerably greater than that reported for alpha s1- and beta-caseins. Furthermore, the elution profiles for 45Ca in milk salt solutions were decidedly different from those in CaCl2 or calcium phosphate buffers and the affinities were also greater. For example, at pH 6.7 and 30 degrees C the average dissociation constant for the submicelle-calcium complex is 0.074 mM for CaCl2 and calcium phosphate buffers, vs 0.016 mM for the milk salt solution. The asymmetric frontal boundaries and higher average affinities observed with milk salts may be due to binding of calcium salts with greater affinity in addition to the binding of free Ca2+ in these solutions.

  2. Male-male competition, female mate choice and their interaction: determining total sexual selection.

    PubMed

    Hunt, John; Breuker, Casper J; Sadowski, Jennifer A; Moore, Allen J

    2009-01-01

    Empirical studies of sexual selection typically focus on one of the two mechanisms of sexual selection without integrating these into a description of total sexual selection, or study total sexual selection without quantifying the contributions of all of the mechanisms of sexual selection. However, this can provide an incomplete or misleading view of how sexually selected traits evolve if the mechanisms of sexual selection are opposing or differ in form. Here, we take a two-fold approach to advocate a direction for future studies of sexual selection. We first show how a quantitative partitioning and examination of sexual selection mechanisms can inform by identifying illustrative studies that describe both male-male competition and female mate choice acting on the same trait. In our sample, the most common trait where this occurred was body size, and selection was typically linear. We found that male-male competition and female mate choice can be reinforcing or opposing, although the former is most common in the literature. The mechanisms of sexual selection can occur simultaneously or sequentially, and we found they were more likely to be opposing when the mechanisms operated sequentially. The degree and timing that these mechanisms interact have important implications for the operation of sexual selection and needs to be considered in designing studies. Our examples highlight where empirical data are needed. We especially lack standardized measures of the form and strength of selection imposed by each mechanism of sexual selection and how they combine to determine total sexual selection. Secondly, using quantitative genetic principles, we outline how the selection imposed by individual mechanisms can be measured and combined to estimate the total strength and form of sexual selection. We discuss the evolutionary consequences of combining the mechanisms of sexual selection and interpreting total sexual selection. We suggest how this approach may result in

  3. Genetic and environmental interactions determine seizure susceptibility in epileptic EL mice.

    PubMed

    Todorova, M T; Mantis, J G; Le, M; Kim, C Y; Seyfried, T N

    2006-10-01

    Gene identification has progressed rapidly for monogenic epilepsies, but complex gene-environmental interactions have hindered progress in gene identification for multifactorial epilepsies. We analyzed the role of environmental risk factors in the inheritance of multifactorial idiopathic generalized epilepsy in the EL mouse. Seizure susceptibility was evaluated in the EL (E) and seizure-resistant ABP/LeJ (A) parental mouse strains and in their AEF1 and AEF2 hybrid offspring using a handling-induced seizure test. The seizure test was administered in three environments (environments I, II and III) that differed with respect to the number of seizure tests administered (one test or four tests) and the age of the mice when tested (young or old). The inheritance of seizure susceptibility appeared dominant after repetitive seizure testing in young or old mice, but recessive after a single test in old mice. Heritability was high (0.67-0.77) in each environment. Significant quantitative trait loci (QTL) that were associated with environments I and III (repetitive testing) were found on chromosomes 2 and 9 and colocalized with previously mapped El2 and El4, respectively. The El2 QTL found in environment I associated only with female susceptibility. A novel QTL, El-N, for age-dependent predisposition to seizures was found on proximal chromosome 9 only in environment II. The findings indicate that environmental risk factors determine the genetic architecture of seizure susceptibility in EL mice and suggest that QTL for complex epilepsies should be defined in terms of the environment in which they are expressed.

  4. 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.

  5. N terminus determinants of MinC from Neisseria gonorrhoeae mediate interaction with FtsZ but do not affect interaction with MinD or homodimerization.

    PubMed

    Greco-Stewart, V; Ramirez-Arcos, S; Liao, M; Dillon, J R

    2007-06-01

    While bacterial cell division has been widely studied in rod-shaped bacteria, the mechanism of cell division in round (coccal) bacteria remains largely enigmatic. In the present study, interaction between the cell division inhibitor MinC from Neisseria gonorrhoeae (MinC(Ng)) and the gonococcal cell division proteins MinD(Ng) and FtsZ(Ng) are demonstrated. Protein truncation and site-directed mutagenic approaches determined which N-terminal residues were essential for cell division inhibition by MinC(Ng) using cell morphology as an indicator of protein functionality. Truncation from or mutation at the 13th amino acid of the N terminus of MinC(Ng) resulted in loss of protein function. Bioinformatic analyses predicted that point mutations of L35P and L68P would affect the alpha-helical conformation of the protein and we experimentally showed that these mutations alter the functionality of MinC(Ng). The bacterial two-hybrid system showed that interaction of MinC(Ng) with FtsZ(Ng) is abrogated upon truncation of 13 N-terminal residues while MinC(Ng)-MinD(Ng) interaction or MinC(Ng) homodimerization is unaffected. These data confirm interactions among gonococcal cell division proteins and determine the necessity of the 13th amino acid for MinC(Ng) function. PMID:17287984

  6. The Subfamily-Specific Interaction between Kv2.1 and Kv6.4 Subunits Is Determined by Interactions between the N- and C-termini

    PubMed Central

    Bocksteins, Elke; Mayeur, Evy; Van Tilborg, Abbi; Regnier, Glenn; Timmermans, Jean-Pierre; Snyders, Dirk J.

    2014-01-01

    The “silent” voltage-gated potassium (KvS) channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-terminus, but unexpectedly also with the Kv3.1 N-terminus. We confirmed this interaction by Fluorescence Resonance Energy Transfer (FRET) and co-immunoprecipitation (co-IP) using N-terminal Kv3.1 and Kv6.4 fragments. However, full-length Kv3.1 and Kv6.4 subunits do not form heterotetramers at the plasma membrane. Therefore, additional interactions between the Kv6.4 and Kv2.1 subunits should be important in the Kv2.1/Kv6.4 subfamily-specificity. Using FRET and co-IP approaches with N- and C-terminal fragments we observed that the Kv6.4 C-terminus physically interacts with the Kv2.1 N-terminus but not with the Kv3.1 N-terminus. The N-terminal amino acid sequence CDD which is conserved between Kv2 and KvS subunits appeared to be a key determinant since charge reversals with arginine substitutions abolished the interaction between the N-terminus of Kv2.1 and the C-terminus of both Kv2.1 and Kv6.4. In addition, the Kv6.4(CKv3.1) chimera in which the C-terminus of Kv6.4 was replaced by the corresponding domain of Kv3.1, disrupted the assembly with Kv2.1. These results indicate that the subfamily-specific Kv2.1/Kv6.4 heterotetramerization is determined by interactions between Kv2.1 and Kv6.4 that involve both the N- and C-termini in which the conserved N-terminal CDD sequence plays a key role. PMID:24901643

  7. Contextual interactions determine whether the Drosophila homeodomain protein, Vnd, acts as a repressor or activator

    PubMed Central

    Yu, Zhongxin; Syu, Li-Jyun; Mellerick, Dervla M.

    2005-01-01

    At the molecular level, members of the NKx2.2 family of transcription factors establish neural compartment boundaries by repressing the expression of homeobox genes specific for adjacent domains [Muhr et al. (2001) Cell, 104, 861–873; Weiss et al. (1998) Genes Dev., 12, 3591–3602]. The Drosophila homologue, vnd, interacts genetically with the high-mobility group protein, Dichaete, in a manner suggesting co-operative activation [Zhao and Skeath (2002) Development, 129, 1165–1174]. However, evidence for direct interactions and transcriptional activation is lacking. Here, we present molecular evidence for the interaction of Vnd and Dichaete that leads to the activation of target gene expression. Two-hybrid interaction assays indicate that Dichaete binds the Vnd homeodomain, and additional Vnd sequences stabilize this interaction. In addition, Vnd has two activation domains that are typically masked in the intact protein. Whether vnd can activate or repress transcription is context-dependent. Full-length Vnd, when expressed as a Gal4 fusion protein, acts as a repressor containing multiple repression domains. A divergent domain in the N-terminus, not found in vertebrate Vnd-like proteins, causes the strongest repression. The co-repressor, Groucho, enhances Vnd repression, and these two proteins physically interact. The data presented indicate that the activation and repression domains of Vnd are complex, and whether Vnd functions as a transcriptional repressor or activator depends on both intra- and inter-molecular interactions. PMID:15640442

  8. 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.

  9. 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

  10. Determination of the specific interaction between sulfonylurea-incorporated polymer and rat islets.

    PubMed

    Park, Keun-Hong; Song, Soo Chang; Akaike, Toshihiro

    2002-03-01

    A SU derivative, mimicking glibenclamide in chemical structure, was synthesized to incorporate it into a water-soluble polymeric backbone as a biospecific and stimulating polymer for insulin secretion. The ability of insulin secretion was examined with different glucose concentrations (3.3 and 11.6 mM). Although the vinylated SU did not exhibit significant activity compared to the control, the SU-incorporated copolymer could enhance insulin secretion as much as or more than glibenclamide did. In this study, a polymer fluorescence-labeled with rodamine-B isothiocyanate was used to visualize the interactions and we found that the labeled polymer was strongly absorbed to rat islets, probably due to its specific interaction mediated by SU receptors on the cell membrane. To verify the specific interaction between the SU (K+ channel closer)-incorporated copolymer and rat islets, cells were pretreated with diazoxide, an agonist of ATP-sensitive K+ channels (K+ channel opener), before adding the incorporated polymer to the cell culture medium. This treatment suppressed the action of SUs on rat islets. A confocal laser microscopic study further confirmed this interaction. The results of this study provided evidence that the SU-incorporated copolymer stimulates insulin secretion through specific interactions of SU moieties in the polymer with rat islets.

  11. Molecular simulation of carbon dioxide, brine, and clay mineral interactions and determination of contact angles.

    PubMed

    Tenney, Craig M; Cygan, Randall T

    2014-01-01

    Capture and subsequent geologic storage of CO2 in deep brine reservoirs plays a significant role in plans to reduce atmospheric carbon emission and resulting global climate change. The interaction of CO2 and brine species with mineral surfaces controls the ultimate fate of injected CO2 at the nanoscale via geochemistry, at the pore-scale via capillary trapping, and at the field-scale via relative permeability. We used large-scale molecular dynamics simulations to study the behavior of supercritical CO2 and aqueous fluids on both the hydrophilic and hydrophobic basal surfaces of kaolinite, a common clay mineral. In the presence of a bulk aqueous phase, supercritical CO2 forms a nonwetting droplet above the hydrophilic surface of kaolinite. This CO2 droplet is separated from the mineral surface by distinct layers of water, which prevent the CO2 droplet from interacting directly with the mineral surface. Conversely, both CO2 and H2O molecules interact directly with the hydrophobic surface of kaolinite. In the presence of bulk supercritical CO2, nonwetting aqueous droplets interact with the hydrophobic surface of kaolinite via a mixture of adsorbed CO2 and H2O molecules. Because nucleation and precipitation of minerals should depend strongly on the local distribution of CO2, H2O, and ion species, these nanoscale surface interactions are expected to influence long-term mineralization of injected carbon dioxide.

  12. Functional regions of Candida albicans hyphal cell wall protein Als3 that determine interaction with the oral bacterium Streptococcus gordonii

    PubMed Central

    Bamford, Caroline V.; Nobbs, Angela H.; Barbour, Michele E.; Lamont, Richard J.

    2015-01-01

    The opportunistic pathogen Candida albicans colonizes the oral cavity and gastrointestinal tract. Adherence to host cells, extracellular matrix and salivary glycoproteins that coat oral surfaces, including prostheses, is an important prerequisite for colonization. In addition, interactions of C. albicans with commensal oral streptococci are suggested to promote retention and persistence of fungal cells in mixed-species communities. The hyphal filament specific cell wall protein Als3, a member of the Als protein family, is a major determinant in C. albicans adherence. Here, we utilized site-specific in-frame deletions within Als3 expressed on the surface of heterologous Saccharomyces cerevisiae to determine regions involved in interactions of Als3 with Streptococcus gordonii. N-terminal region amino acid residue deletions Δ166–225, Δ218–285, Δ270–305 and Δ277–286 were each effective in inhibiting binding of Strep. gordonii to Als3. In addition, these deletions differentially affected biofilm formation, hydrophobicity, and adherence to silicone and human tissue proteins. Deletion of the central repeat domain (Δ434–830) did not significantly affect interaction of Als3 with Strep. gordonii SspB protein, but affected other adherence properties and biofilm formation. Deletion of the amyloid-forming region (Δ325–331) did not affect interaction of Als3 with Strep. gordonii SspB adhesin, suggesting this interaction was amyloid-independent. These findings highlighted the essential function of the N-terminal domain of Als3 in mediating the interaction of C. albicans with S. gordonii, and suggested that amyloid formation is not essential for the inter-kingdom interaction. PMID:25332379

  13. Functional regions of Candida albicans hyphal cell wall protein Als3 that determine interaction with the oral bacterium Streptococcus gordonii.

    PubMed

    Bamford, Caroline V; Nobbs, Angela H; Barbour, Michele E; Lamont, Richard J; Jenkinson, Howard F

    2015-01-01

    The opportunistic pathogen Candida albicans colonizes the oral cavity and gastrointestinal tract. Adherence to host cells, extracellular matrix and salivary glycoproteins that coat oral surfaces, including prostheses, is an important prerequisite for colonization. In addition, interactions of C. albicans with commensal oral streptococci are suggested to promote retention and persistence of fungal cells in mixed-species communities. The hyphal filament specific cell wall protein Als3, a member of the Als protein family, is a major determinant in C. albicans adherence. Here, we utilized site-specific in-frame deletions within Als3 expressed on the surface of heterologous Saccharomyces cerevisiae to determine regions involved in interactions of Als3 with Streptococcus gordonii. N-terminal region amino acid residue deletions Δ166-225, Δ218-285, Δ270-305 and Δ277-286 were each effective in inhibiting binding of Strep. gordonii to Als3. In addition, these deletions differentially affected biofilm formation, hydrophobicity, and adherence to silicone and human tissue proteins. Deletion of the central repeat domain (Δ434-830) did not significantly affect interaction of Als3 with Strep. gordonii SspB protein, but affected other adherence properties and biofilm formation. Deletion of the amyloid-forming region (Δ325-331) did not affect interaction of Als3 with Strep. gordonii SspB adhesin, suggesting this interaction was amyloid-independent. These findings highlighted the essential function of the N-terminal domain of Als3 in mediating the interaction of C. albicans with S. gordonii, and suggested that amyloid formation is not essential for the inter-kingdom interaction.

  14. The Role of Solvent Heterogeneity in Determining the Dispersion Interaction Between Nanoassemblies

    SciTech Connect

    Chun, Jaehun; Mundy, Christopher J.; Schenter, Gregory K.

    2015-05-07

    Understanding fundamental nanoassembly processes on intermediate scales beween the molecular and the continuum requires an in-depth analysis of the coupling between particle interactions and molecular detail. This is because the discrete nature of the solvent becomes comparable to the characteristic length scales of assembly molecular fluctuations. Utilizing the spatial density resonse of a solvent to a surface in conjunction with the Clausius-Mossotti equation, we present a simple theory relating the discrete nature of solvent to dispersion interactions. Our study reveals that dispersion interactions are indeed sensitive to the spatial variation of solvent density, manifesting in dramatic deviations in van der Waals forces from the conventional formulation (e.g. with uniform solvent density). This study provides the first steps toward incorporating molecular scale principles that underlie hydration forces where the detailed nature of solvent responses play a significant role.

  15. Experimentally determined swelling pressures and geochemical interactions of compacted Wyoming bentonite with highly alkaline solutions

    NASA Astrophysics Data System (ADS)

    Karnland, Ola; Olsson, Siv; Nilsson, Ulf; Sellin, Patrik

    The estimated quantity of cement for construction and sealing purposes is around 9E5 kg in the planned Swedish KBS3 repository for nuclear waste. The highly alkaline cement pore fluid (pH > 12) may affect other components in the repository, and especially the bentonite buffer is of concern. In this study, we simulated possible interactions between cement and bentonite by contacting highly compacted bentonite with high molar hydroxide solutions in a series of laboratory experiments. Wyoming bentonite (MX-80) and purified homo-ionic Na- and Ca-montmorillonite were used for tests with 0.1, 0.3 and 1.0 M NaOH, and saturated Ca(OH) 2 solutions. Pressure cells with permeable filters were loaded with compacted discs of bentonite at the proposed buffer density (2000 kg/m 3 at full water saturation). A hydroxide solution was circulated on one side of the cell and an isotonic chloride solution on the other during a minimum of 45 days. Swelling pressure and solution pH were monitored during the tests and the change in the solution composition and bentonite mineralogy were determined after completed tests. No effect on swelling pressure was observed in tests with 0.1 M NaOH (pH 12.9) or saturated Ca(OH) 2 solutions (pH 12.4) and the mineralogical/chemical changes of the clay were minimal. The bentonite swelling pressure was significantly reduced in the tests with 0.3 (pH 13.3) and 1.0 M (pH 13.8) NaOH solutions. The reduction seems to be due to an instant osmotic effect, and to a continuous dissolution of silica minerals, resulting in mass loss and, consequently, a decrease in density. At these high pH, the release of silica was dominating and the CEC of the clay increased by 20-25%. The structural formula of the smectite and X-ray diffraction tests for non-expandability (Greene-Kelly test) provided strong evidence that the dissolution of montmorillonite proceeds incongruently through an initial step of beidellitization. The calculated rate of silica release from

  16. 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

  17. 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…

  18. 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.

  19. 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

  20. Determination of the critical residues responsible for cardiac myosin binding protein C's interactions.

    PubMed

    Bhuiyan, Md Shenuarin; Gulick, James; Osinska, Hanna; Gupta, Manish; Robbins, Jeffrey

    2012-12-01

    Despite early demonstrations of myosin binding protein C's (MyBP-C) interaction with actin, different investigators have reached different conclusions regarding the relevant and necessary domains mediating this binding. Establishing the detailed structure-function relationships is needed to fully understand cMyBP-C's ability to impact on myofilament contraction as mutations in different domains are causative for familial hypertrophic cardiomyopathy. We defined cMyBP-C's N-terminal structural domains that are necessary or sufficient to mediate interactions with actin and/or the head region of the myosin heavy chain (S2-MyHC). Using a combination of genetics and functional assays, we defined the actin binding site(s) present in cMyBP-C. We confirmed that cMyBP-C's C1 and m domains productively interact with actin, while S2-MyHC interactions are restricted to the m domain. Using residue-specific mutagenesis, we identified the critical actin binding residues and distinguished them from the residues that were critical for S2-MyHC binding. To validate the structural and functional significance of these residues, we silenced the endogenous cMyBP-C in neonatal rat cardiomyocytes (NRC) using cMyBP-C siRNA, and replaced the endogenous cMyBP-C with normal or actin binding-ablated cMyBP-C. Replacement with actin binding-ablated cMyBP-C showed that the mutated protein did not incorporate into the sarcomere normally. Residues responsible for actin and S2-MyHC binding are partially present in overlapping domains but are unique. Expression of an actin binding-deficient cMyBP-C resulted in abnormal cytosolic distribution of the protein, indicating that interaction with actin is essential for the formation and/or maintenance of normal cMyBP-C sarcomeric distribution.

  1. Interaction Mechanism of Oil-in-Water Emulsions with Asphaltenes Determined Using Droplet Probe AFM.

    PubMed

    Shi, Chen; Zhang, Ling; Xie, Lei; Lu, Xi; Liu, Qingxia; Mantilla, Cesar A; van den Berg, Frans G A; Zeng, Hongbo

    2016-03-15

    Emulsions with interface-active components at the oil/water interface have long been of fundamental and practical interest in many fields. In this work, the interaction forces between two oil droplets in water in the absence/presence of asphaltenes were directly measured using droplet probe atomic force microscopy (AFM) and analyzed using a theoretical model based on Reynolds lubrication theory and the augmented Young-Laplace equation by including the effects of disjoining pressure. It was revealed that the interaction forces measured between two pristine oil droplets (i.e., toluene) could be well described by the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, while an additional steric interaction should be included in the presence of asphaltenes in the oil. The surface interaction and the stability of oil droplets in aqueous solution were demonstrated to be significantly influenced by the asphaltenes concentration in oil, salt concentration, pH, and presence of divalent ions (Ca(2+)) in water. Adsorbed asphaltenes at the oil/water interface led to more negative surface potential of the oil/water interface and also induced steric repulsion between oil droplets, inhibiting the drop coalescence and stabilizing the oil-in-water emulsion. Lower pH of aqueous solution could lead to less negative surface potential and weaken the repulsion between oil droplets. Addition of divalent ions (Ca(2+)) was found to disrupt the protecting effects of adsorbed asphaltenes at oil/water interface and induce coalescence of oil droplets. Our results provide a useful methodology for quantifying the interaction forces and investigating the properties of asphaltenes at the oil/water interfaces and provide insights into the stabilization mechanism of oil-in-water emulsions due to asphaltenes in oil production and water treatment.

  2. 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.

  3. 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.

  4. Evolution of species interactions determines microbial community productivity in new environments.

    PubMed

    Fiegna, Francesca; Moreno-Letelier, Alejandra; Bell, Thomas; Barraclough, Timothy G

    2015-05-01

    Diversity generally increases ecosystem productivity over short timescales. Over longer timescales, both ecological and evolutionary responses to new environments could alter productivity and diversity-productivity relationships. In turn, diversity might affect how component species adapt to new conditions. We tested these ideas by culturing artificial microbial communities containing between 1 and 12 species in three different environments for ∼60 generations. The relationship between community yields and diversity became steeper over time in one environment. This occurred despite a general tendency for the separate yields of isolates of constituent species to be lower at the end if they had evolved in a more diverse community. Statistical comparisons of community and species yields showed that species interactions had evolved to be less negative over time, especially in more diverse communities. Diversity and evolution therefore interacted to enhance community productivity in a new environment. PMID:25387206

  5. Evolution of species interactions determines microbial community productivity in new environments

    PubMed Central

    Fiegna, Francesca; Moreno-Letelier, Alejandra; Bell, Thomas; Barraclough, Timothy G

    2015-01-01

    Diversity generally increases ecosystem productivity over short timescales. Over longer timescales, both ecological and evolutionary responses to new environments could alter productivity and diversity–productivity relationships. In turn, diversity might affect how component species adapt to new conditions. We tested these ideas by culturing artificial microbial communities containing between 1 and 12 species in three different environments for ∼60 generations. The relationship between community yields and diversity became steeper over time in one environment. This occurred despite a general tendency for the separate yields of isolates of constituent species to be lower at the end if they had evolved in a more diverse community. Statistical comparisons of community and species yields showed that species interactions had evolved to be less negative over time, especially in more diverse communities. Diversity and evolution therefore interacted to enhance community productivity in a new environment. PMID:25387206

  6. 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.

  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. Flexibility and extracellular opening determine the interaction between ligands and insect sulfakinin receptors

    PubMed Central

    Yu, Na; Zotti, Moises João; Scheys, Freja; Braz, Antônio S. K.; Penna, Pedro H. C.; Nachman, Ronald J.; Smagghe, Guy

    2015-01-01

    Despite their fundamental importance for growth, the mechanisms that regulate food intake are poorly understood. Our previous work demonstrated that insect sulfakinin (SK) signaling is involved in inhibiting feeding in an important model and pest insect, the red flour beetle Tribolium castaneum. Because the interaction of SK peptide and SK receptors (SKR) initiates the SK signaling, we have special interest on the structural factors that influence the SK-SKR interaction. First, the three-dimensional structures of the two T. castaneum SKRs (TcSKR1 and TcSKR2) were generated from molecular modeling and they displayed significance in terms of the outer opening of the cavity and protein flexibility. TcSKR1 contained a larger outer opening of the cavity than that in TcSKR2, which allows ligands a deep access into the cavity through cell membrane. Second, normal mode analysis revealed that TcSKR1 was more flexible than TcSKR2 during receptor-ligand interaction. Third, the sulfated SK (sSK) and sSK-related peptides were more potent than the nonsulfated SK, suggesting the importance of the sulfate moiety. PMID:26267367

  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. 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

  11. Mechanistic aspects of peptide-membrane interactions determined by optical, dielectric and piezoelectric techniques: an overview.

    PubMed

    Oliveira, Maria D L; Franco, Octavio L; Nascimento, Jessica M; de Melo, Celso P; Andrade, Cesar A S

    2013-11-01

    Antimicrobial peptides (AMPs) have been isolated from a wide variety of organisms that include microorganisms, plants, insects, frogs and mammals. As part of the innate immune system expressed in many tissues, AMPs are able to provide protection against invasion of foreign microorganisms and exhibit a broad spectrum of activity against bacteria, fungi and/or virus. Non-AMPs cell-penetrating peptides have been used as carriers for overcoming the membrane barrier and helping in the delivery of various molecules into the cell. Physicochemical peptide-lipid interactions studies can provide us with reliable molecular information about microbe defense response, including the elucidation of the prevailing mechanisms of its action, such as the barrel-stave, toroidal pore, carpet and detergent-like models. In this paper, we present an overview of the peptide-lipid mechanisms of interaction as well as discuss alternative techniques that could help to elucidate the peptides functionality. Quartz crystal microbalance (QCM), surface plasmon resonance (SPR) spectroscopy and electrochemical impedance spectroscopy (EIS) are useful techniques to investigate in details of the peptide-membrane interaction. The techniques here discussed could also offer specific and low-cost methods that can to shed some light over the different modes of action of AMPs, contributing to the development of drugs against infectious diseases.

  12. Molecular determinants of the interactions between proteins and ssDNA

    PubMed Central

    Mishra, Garima; Levy, Yaakov

    2015-01-01

    ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB–ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6–65 nt. In addition to charge–charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB–ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs. PMID:25855635

  13. Molecular determinants of the DprA−RecA interaction for nucleation on ssDNA

    PubMed Central

    Lisboa, Johnny; Andreani, Jessica; Sanchez, Dyana; Boudes, Marion; Collinet, Bruno; Liger, Dominique; van Tilbeurgh, Herman; Guérois, Raphael; Quevillon-Cheruel, Sophie

    2014-01-01

    Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, DprAM238 and RecAF230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA−RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA. PMID:24782530

  14. Microcalorimetric and SAXS determination of PEO-SDS interactions: the effect of cosolutes formed by ions.

    PubMed

    Barbosa, Aparecida Mageste; Santos, Igor José Boggione; Ferreira, Guilherme Max Dias; da Silva, Maria do Carmo Hespanhol; Teixeira, Alvaro Vianna Novaes de Carvalho; da Silva, Luis Henrique Mendes

    2010-09-23

    The effect of different ionic cosolutes (NaCl, Na(2)SO(4), Li(2)SO(4), NaSCN, Na(2)[Fe(CN)(5)NO], and Na(3)[Co(NO)(6)]) on the interaction between sodium dodecyl sulfate (SDS) and poly(ethylene oxide) (PEO) was examined by small-angle X-ray scattering (SAXS) and isothermal titration calorimetric techniques. The critical aggregation concentration values (cac), the saturation concentration (C(2)), the integral enthalpy change for aggregate formation (ΔH(agg)(int)) and the standard free energy change of micelle adsorption on the macromolecule chain (ΔΔG(agg)) were derived from the calorimetric titration curves. In the presence of 1.00 mmol L(-1) cosolute, no changes in the parameters were observed when compared with those obtained for SDS-PEO interactions in pure water. For NaCl, Na(2)SO(4), Li(2)SO(4), and NaSCN at 10.0 and 100 mmol L(-1), the cosolute presence lowered cac, increased C(2), and the PEO-SDS aggregate became more stable. In the presence of Na(2)[Fe(CN)(5)NO], the calorimetric titration curves changed drastically, showing a possible reduction in the PEO-SDS degree of interaction, possibility disrupting the formed nanostructure; however, the SAXS data confirmed, independent of the small energy observed, the presence of aggregates adsorbed on the polymer chain.

  15. Chemical cross-linking and mass spectrometry to determine the subunit interaction network in a recombinant human SAGA HAT subcomplex.

    PubMed

    Nguyen-Huynh, Nha-Thi; Sharov, Grigory; Potel, Clément; Fichter, Pélagie; Trowitzsch, Simon; Berger, Imre; Lamour, Valérie; Schultz, Patrick; Potier, Noëlle; Leize-Wagner, Emmanuelle

    2015-08-01

    Understanding the way how proteins interact with each other to form transient or stable protein complexes is a key aspect in structural biology. In this study, we combined chemical cross-linking with mass spectrometry to determine the binding stoichiometry and map the protein-protein interaction network of a human SAGA HAT subcomplex. MALDI-MS equipped with high mass detection was used to follow the cross-linking reaction using bis[sulfosuccinimidyl] suberate (BS3) and confirm the heterotetrameric stoichiometry of the specific stabilized subcomplex. Cross-linking with isotopically labeled BS3 d0-d4 followed by trypsin digestion allowed the identification of intra- and intercross-linked peptides using two dedicated search engines: pLink and xQuest. The identified interlinked peptides suggest a strong network of interaction between GCN5, ADA2B and ADA3 subunits; SGF29 is interacting with GCN5 and ADA3 but not with ADA2B. These restraint data were combined to molecular modeling and a low-resolution interacting model for the human SAGA HAT subcomplex could be proposed, illustrating the potential of an integrative strategy using cross-linking and mass spectrometry for addressing the structural architecture of multiprotein complexes.

  16. 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.

  17. Uncontrollable and unpredictable stress interacts with subclinical depression and anxiety scores in determining anxiety response.

    PubMed

    Havranek, Michael M; Bolliger, Bianca; Roos, Sophie; Pryce, Christopher R; Quednow, Boris B; Seifritz, Erich

    2016-01-01

    According to learned helplessness theory, uncontrollable stress is assumed to be a critical etiological factor in the pathogenesis of depression. In contrast, unpredictability of stressors is assumed to facilitate the development of sustained anxiety. Despite the frequent co-morbidity of depression and anxiety disorders, these two factors have rarely been studied simultaneously in humans. Therefore, we investigated whether there are interaction effects of uncontrollability and unpredictability on anxiety response in healthy participants. Seventy-nine healthy participants performed a visual dot probe task with emotional faces, while receiving mild electrical shocks in four different conditions (2 × 2 factorial design). In (un)controllable conditions, participants were (not) able to attenuate shock intensity. In (un)predictable conditions, participants were (not) able to anticipate shock occurrence. Before the experiment, participants' subclinical depression and anxiety scores were measured using the Beck Depression and Anxiety Inventories (BDI/BAI). During the experiment, continuous skin conductance and self-reported state anxiety were assessed and attentional biases towards angry faces were calculated. As expected, participants showed greater anxiety in uncontrollable compared to controllable and in unpredictable compared to predictable conditions. Additionally, anxiety decreased within the test sessions in participants with low BDI/BAI scores but not in participants with higher BDI/BAI scores. Most importantly, controllability and predictability interacted with each other and with BDI/BAI scores with regard to anxiety. Our results provide evidence that uncontrollability and unpredictability of stressors not only have separate but also interaction effects on several anxiety measures in susceptible individuals and may provide insights into the psychological mechanisms underlying a depressive/anxiety co-morbidity.

  18. 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. PMID:27459778

  19. Arsenic species interactions with a porous carbon electrode as determined with an electrochemical quartz crystal microbalance

    PubMed Central

    Morallón, Emilia; Arias-Pardilla, Joaquín; Calo, J.M.; Cazorla-Amorós, D.

    2009-01-01

    The interactions of arsenic species with platinum and porous carbon electrodes were investigated with an electrochemical quartz crystal microbalance (EQCM) and cyclic voltammetry in alkaline solutions. It is shown that the redox reactions in arsenic-containing solutions, due to arsenic reduction/deposition, oxidation/desorption, and electrocatalyzed oxidation by Pt can be readily distinguished with the EQCM. This approach was used to show that the arsenic redox reactions on the carbon electrode are mechanistically similar to that on the bare Pt electrode. This could not be concluded with just classical cyclic voltammetry alone due to the obfuscation of the faradaic features by the large capacitative effects of the carbon double layer. For the porous carbon electrode, a continual mass loss was always observed during potential cycling, with or without arsenic in the solution. This was attributed to electrogasification of the carbon. The apparent mass loss per cycle was observed to decrease with increasing arsenic concentration due to a net mass increase in adsorbed arsenic per cycle that increased with arsenic concentration, offsetting the carbon mass loss. Additional carbon adsorption sites involved in arsenic species interactions are created during electrogasification, thereby augmenting the net uptake of arsenic per cycle. It is demonstrated that EQCM, and in particular the information given by the behavior of the time derivative of the mass vs. potential, or massogram, is very useful for distinguishing arsenic species interactions with carbon electrodes. It may also prove to be effective for investigating redox/adsorption/desorption behavior of other species in solution with carbon materials as well. PMID:20161369

  20. Arsenic species interactions with a porous carbon electrode as determined with an electrochemical quartz crystal microbalance.

    PubMed

    Morallón, Emilia; Arias-Pardilla, Joaquín; Calo, J M; Cazorla-Amorós, D

    2009-06-30

    The interactions of arsenic species with platinum and porous carbon electrodes were investigated with an electrochemical quartz crystal microbalance (EQCM) and cyclic voltammetry in alkaline solutions. It is shown that the redox reactions in arsenic-containing solutions, due to arsenic reduction/deposition, oxidation/desorption, and electrocatalyzed oxidation by Pt can be readily distinguished with the EQCM. This approach was used to show that the arsenic redox reactions on the carbon electrode are mechanistically similar to that on the bare Pt electrode. This could not be concluded with just classical cyclic voltammetry alone due to the obfuscation of the faradaic features by the large capacitative effects of the carbon double layer.For the porous carbon electrode, a continual mass loss was always observed during potential cycling, with or without arsenic in the solution. This was attributed to electrogasification of the carbon. The apparent mass loss per cycle was observed to decrease with increasing arsenic concentration due to a net mass increase in adsorbed arsenic per cycle that increased with arsenic concentration, offsetting the carbon mass loss. Additional carbon adsorption sites involved in arsenic species interactions are created during electrogasification, thereby augmenting the net uptake of arsenic per cycle.It is demonstrated that EQCM, and in particular the information given by the behavior of the time derivative of the mass vs. potential, or massogram, is very useful for distinguishing arsenic species interactions with carbon electrodes. It may also prove to be effective for investigating redox/adsorption/desorption behavior of other species in solution with carbon materials as well.

  1. 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.

  2. Uncontrollable and unpredictable stress interacts with subclinical depression and anxiety scores in determining anxiety response.

    PubMed

    Havranek, Michael M; Bolliger, Bianca; Roos, Sophie; Pryce, Christopher R; Quednow, Boris B; Seifritz, Erich

    2016-01-01

    According to learned helplessness theory, uncontrollable stress is assumed to be a critical etiological factor in the pathogenesis of depression. In contrast, unpredictability of stressors is assumed to facilitate the development of sustained anxiety. Despite the frequent co-morbidity of depression and anxiety disorders, these two factors have rarely been studied simultaneously in humans. Therefore, we investigated whether there are interaction effects of uncontrollability and unpredictability on anxiety response in healthy participants. Seventy-nine healthy participants performed a visual dot probe task with emotional faces, while receiving mild electrical shocks in four different conditions (2 × 2 factorial design). In (un)controllable conditions, participants were (not) able to attenuate shock intensity. In (un)predictable conditions, participants were (not) able to anticipate shock occurrence. Before the experiment, participants' subclinical depression and anxiety scores were measured using the Beck Depression and Anxiety Inventories (BDI/BAI). During the experiment, continuous skin conductance and self-reported state anxiety were assessed and attentional biases towards angry faces were calculated. As expected, participants showed greater anxiety in uncontrollable compared to controllable and in unpredictable compared to predictable conditions. Additionally, anxiety decreased within the test sessions in participants with low BDI/BAI scores but not in participants with higher BDI/BAI scores. Most importantly, controllability and predictability interacted with each other and with BDI/BAI scores with regard to anxiety. Our results provide evidence that uncontrollability and unpredictability of stressors not only have separate but also interaction effects on several anxiety measures in susceptible individuals and may provide insights into the psychological mechanisms underlying a depressive/anxiety co-morbidity. PMID:26669536

  3. 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.

  4. Determination of cluster size in particle-nucleus interactions at 50 and 400 GeV

    SciTech Connect

    Irfan, M.; Khushnood, H.; Shakeel, A.; Zafar, M.; Shafi, M.

    1984-07-01

    We have investigated the formation of clusters and their sizes in 50-GeV ..pi../sup -/-nucleus and 400-GeV proton-nucleus interactions. The maximum multiplicity of charged shower particles constituting the clusters at the two incident energies is observed to be four. Furthermore, the cluster size has been found to be independent of the gray-particle multiplicity and hence the target mass. The cluster size has also been observed to be independent of the energy and identity of the impinging hadrons.

  5. Triple SILAC to Determine Stimulus Specific Interactions in the Wnt Pathway

    PubMed Central

    2011-01-01

    Many important regulatory functions are performed by dynamic multiprotein complexes that adapt their composition and activity in response to different stimuli. Here we employ quantitative affinity purification coupled with mass spectrometry to efficiently separate background from specific interactors but add an additional quantitative dimension to explicitly characterize stimulus-dependent interactions. This is accomplished by SILAC in a triple-labeling format, in which pull-downs with bait, with bait and stimulus, and without bait are quantified against each other. As baits, we use full-length proteins fused to the green fluorescent protein and expressed under endogenous control. We applied this technology to Wnt signaling, which is important in development, tissue homeostasis, and cancer, and investigated interactions of the key components APC, Axin-1, DVL2, and CtBP2 with differential pathway activation. Our screens identify many known Wnt signaling complex components and link novel candidates to Wnt signaling, including FAM83B and Girdin, which we found as interactors to multiple Wnt pathway players. Girdin binds to DVL2 independent of stimulation with the ligand Wnt3a but to Axin-1 and APC in a stimulus-dependent manner. The core destruction complex itself, which regulates beta-catenin stability as the key step in canonical Wnt signaling, remained essentially unchanged. PMID:22011079

  6. 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. PMID:27402761

  7. Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity.

    PubMed

    Abhinav, K V; Sharma, Kaushal; Swaminathan, C P; Surolia, A; Vijayan, M

    2015-02-01

    Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in β-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in β-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin. PMID:25664742

  8. 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

  9. Conformational Transition Between Four and Five-Stranded Phenylalanine Zippers Determined by a Local Packing Interaction

    SciTech Connect

    Liu,J.; Zheng, Q.; Deng, Y.; Kallenbach, N.; Lu, M.

    2006-01-01

    Alpha-helical coiled coils play a crucial role in mediating specific protein-protein interactions. However, the rules and mechanisms that govern helix-helix association in coiled coils remain incompletely understood. Here we have engineered a seven heptad 'Phe-zipper' protein (Phe-14) with phenylalanine residues at all 14 hydrophobic a and d positions, and generated a further variant (Phe-14{sub M}) in which a single core Phe residue is substituted with Met. Phe-14 forms a discrete {alpha}-helical pentamer in aqueous solution, while Phe-14M folds into a tetrameric helical structure. X-ray crystal structures reveal that in both the tetramer and the pentamer the a and d side-chains interlock in a classical knobs-into-holes packing to produce parallel coiled-coil structures enclosing large tubular cavities. However, the presence of the Met residue in the apolar interface of the tetramer markedly alters its local coiled-coil conformation and superhelical geometry. Thus, short-range interactions involving the Met side-chain serve to preferentially select for tetramer formation, either by inhibiting a nucleation step essential for pentamer folding or by abrogating an intermediate required to form the pentamer. Although specific trigger sequences have not been clearly identified in dimeric coiled coils, higher-order coiled coils, as well as other oligomeric multi-protein complexes, may require such sequences to nucleate and direct their assembly.

  10. Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity.

    PubMed

    Abhinav, K V; Sharma, Kaushal; Swaminathan, C P; Surolia, A; Vijayan, M

    2015-02-01

    Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in β-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in β-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.

  11. 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.

  12. Which shape characteristics of the intermolecular interaction of liquid water determine its compressibility ?

    NASA Astrophysics Data System (ADS)

    Yasutomi, Makoto

    2016-05-01

    We consider a fluid of spherical particles with a pair potential given by a hard core repulsion and a tail, and show that the isothermal compressibility of liquid water is determined by the degree of steepness of the soft repulsion near the hard-core contact. This helps us understand the thermodynamic mechanism that causes the compressibility anomaly of liquid water.

  13. 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…

  14. 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

  15. 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

    2015-07-01

    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.

  16. 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.

  17. Immunoendocrine interactions during chronic cysticercosis determine male mouse feminization: role of IL-6.

    PubMed

    Morales-Montor, J; Baig, S; Mitchell, R; Deway, K; Hallal-Calleros, C; Damian, R T

    2001-10-15

    Taenia crassiceps cysticercosis results in an impressive feminization in male mice during chronic infection, characterized by increased serum estradiol levels 100 times their normal values, while those of testosterone and dihydrotestosterone are decreased by 85 and 95% respectively. Concomitantly, the levels of follicle-stimulating hormone and IL-6 are increased 70 and 90 times their normal values in the infected male mice. Since a specific Th1/Th2 shift of the immune response has been previously reported during the chronic infection, and this shift may be associated with the feminization process, we proposed that this shift is induced by immunoendocrine interactions during the disease, and this gives way to a change in the initial resistance to the infection in the male mice, which become as susceptible as female mice. To confirm this hypothesis, we depleted immune system activity in two different ways: total body irradiation and neonatal thymectomy. Our results show that when immune system activity is depleted using either strategy, the male mice do not feminize, and the levels of follicle-stimulating hormone and IL-6 are inhibited. Depletion of IL-6 using IL-6(-/-) knockout mice does not produce the feminization process stated above, while restitution of the IL-6(-/-) knockout, irradiated, and thymectomized mice with murine recombinant IL-6 restores the feminization process. Expression of the IL-6 gene was found only in the testes and spleen of infected animals. Our results illustrate the importance of immunoendocrine interactions during a parasitic disease and show a possible new mechanism of parasite establishment in an initially resistant host.

  18. Hydrogen bonding mediated by key orbital interactions determines hydration enthalpy differences of phosphate water clusters.

    PubMed

    Ruben, Eliza A; Chapman, Michael S; Evanseck, Jeffrey D

    2007-10-25

    Electronic structure calculations have been carried out to provide a molecular interpretation for dihydrogen phosphate stability in water relative to that of metaphosphate. Specifically, hydration enthalpies of biologically important metaphosphate and dihydrogen phosphate with one to three waters have been computed with second-order Møller-Plesset perturbation and density functional theory (B3LYP) with up to the aug-cc-pvtz basis set and compared to experiment. The inclusion of basis set superposition error corrections and supplemental diffuse functions are necessary to predict hydration enthalpies within experimental uncertainty. Natural bond orbital analysis is used to rationalize underlying hydrogen bond configurations and key orbital interactions responsible for the experimentally reported difference in hydration enthalpies between metaphosphate and dihydrogen phosphate. In general, dihydrogen phosphate forms stronger hydrogen bonds compared to metaphosphate due to a greater charge transfer or enhanced orbital overlap between the phosphoryl oxygen lone pairs, n(O), and the antibonding O-H bond of water. Intramolecular distal lone pair repulsion with the donor n(O) orbital of dihydrogen phosphate distorts symmetric conformations, which improves n(O) and sigma*(O-H) overlap and ultimately the hydrogen bond strength. Unlike metaphosphate, water complexed to dihydrogen phosphate can serve as both a hydrogen bond donor and a hydrogen bond acceptor, which results in cooperative charge transfer and a reduction of the energy gap between n(O) and sigma*(O-H), leading to stronger hydrogen bonds. This study offers insight into how orbital interactions mediate hydrogen bond strengths with potential implications on the understanding of the kinetics and mechanism in enzymatic phosphoryl transfer reactions.

  19. 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

  20. Interactions between environmental variables determine immunity in the Indian meal moth Plodia interpunctella.

    PubMed

    Triggs, Alison; Knell, Robert J

    2012-03-01

    1. Animals raised in good environmental conditions are expected to have more resources to invest in immunity than those raised in poor conditions. Variation in immune activity and parasite resistance in response to changes in environmental temperature, population density and food quality have been shown in many invertebrate species. 2. Almost all studies to date have examined the effects of individual variables in isolation. The aim of this study was to address whether environmental factors interact to produce synergistic effects on phenoloxidase (PO) activity and haemocyte count, both indicators of immune system activity. Temperature, food quality and density were varied in a fully factorial design for a total of eight treatment combinations. 3. Strong interactions between the three environmental variables led to the magnitude and in some cases the direction of the effect of most variables changing as the other environmental factors were altered. Overall, food quality had the most important and consistent influence, larvae raised on a good-quality diet having substantially higher PO activity in every case and substantially higher haemocyte counts in all treatments except unheated/low density. 4. When food quality was good, the larvae showed 'density-dependent prophylaxis': raising their investment in immunity when population density is high. When food quality was poor and the temperature low, however, those larvae raised at high densities invested less in immunity. 5. Increased temperature is often thought to lead to increased immune reactivity in ectotherms, but we found that the effect of temperature was strongly dependent on the values of other environmental variables. PO activity increased with temperature when larvae were raised on good food or when density was high, but when food was poor and density low, a higher temperature led to reduced PO activity. A higher temperature led to higher haemocyte counts when density was high and food quality was poor, but

  1. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

    PubMed Central

    Harcombe, William R.; Riehl, William J.; Dukovski, Ilija; Granger, Brian R.; Betts, Alex; Lang, Alex H.; Bonilla, Gracia; Kar, Amrita; Leiby, Nicholas; Mehta, Pankaj; Marx, Christopher J.; Segrè, Daniel

    2014-01-01

    Summary The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of structured communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice, and applied it to engineered consortia. First, we predicted, and experimentally confirmed, the species-ratio to which a 2-species mutualistic consortium converges, and the equilibrium composition of a newly engineered 3-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding, that the net outcome is beneficial, highlights the complex nature of metabolic interactions in microbial communities, while at the same time demonstrating their predictability. PMID:24794435

  2. Genes and environment interact to determine the fitness costs of resistance to Bacillus thuringiensis

    PubMed Central

    Raymond, Ben; Sayyed, Ali H; Wright, Denis J

    2005-01-01

    Genes which provide resistance to novel challenges such as pesticides, toxins or pathogens often impose fitness costs on individuals with a resistant phenotype. Studies of resistance to Bacillus thuringiensis and its insecticidal Cry toxins indicate that fitness costs may be variable and cryptic. Using two field populations (Karak and Serd4) of the diamondback moth, Plutella xylostella, we tested the hypothesis that the costs associated with resistance to the B. thuringiensis toxin Cry1Ac would be evident when insects were grown under poor environmental conditions, namely limited or poor quality resources. On a poor quality resource, a cultivar of Brassica oleracea var. capitata with varietal resistance to P. xylostella, only one resistant population, Karak, showed reduced fitness. Conversely, when we limited a high quality resource, Brassica pekinensis, by imposing larval competition, only resistant Serd4 insects had reduced survival at high larval densities. Furthermore, Cry1Ac resistance in Serd4 insects declined when reared at high larval densities while resistance at low densities fluctuated but did not decline significantly. These results confirm the hypothesis that resistance costs can appear under stressful conditions and demonstrate that the fitness cost of resistance to Bacillus thuringiensis can depend on the particular interaction between genes and the environment. PMID:16011928

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

    PubMed

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

    2016-06-21

    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. PMID:27245174

  4. 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.

  5. Reproductive and socioeconomic determinants of child survival: confounded, interactive, and age-dependent effects.

    PubMed

    Kost, K; Amin, S

    1992-01-01

    Studies of infant and child mortality have evolved to distinguish between two sets of explanatory variables-factors related to reproductive or maternal characteristics and socioeconomic factors, generally described as characteristics of the family or household. Almost all multivariate analyses include variables from each of these two sets, but there has been little consideration of the relationship between them. We examine how these two sets of variables jointly affect mortality. We test first for confounded effects by examining socioeconomic effects while excluding and then including reproductive variables in nested multivariate models. Next, we look for age-dependent effects among the explanatory variables and find that reproductive and socioeconomic factors affect mortality at differing ages of children. Finally, we examine interactive effects of the two sets of variables. We conclude that the higher mortality observed among the low status groups is not a result of greater concentration of poor reproductive patterns in those groups. Instead, higher status groups probably have more resources available for combating the negative effects of the same high-risk reproductive patterns. PMID:1514117

  6. Lifetime number of mates interacts with female age to determine reproductive success in female guppies.

    PubMed

    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.

  7. Locality interactions with prominence in determining the scope of phrasal lengthening

    PubMed Central

    Byrd, Dani; Riggs, Daylen

    2009-01-01

    Temporal lengthening of gestures and segments located in a boundary-adjacent syllable has been found in both pre- and postboundary contexts. However, the temporal extent or scope of this lengthening, particularly in the articulatory domain, is not well described. We address the question of scope of prosodic lengthening by considering specifically whether prominence interacts with boundary-related articulatory lengthening in such a way that prominent elements not immediately at a phrase edge are lengthened relative to the same prominent elements phrase-medially (i.e. at a considerable distance from a boundary). Articulatory kinematic data were collected for three subjects to analyze consonant constrictions of prominent syllables located (1) either immediately before or after a boundary and (2) two and three syllables away from that boundary. The results indicate that, as expected, gestures undergo prosodic lengthening when immediately local to the phase boundary. However, some subjects did display prosodic lengthening at a small remove from the boundary for a prominent syllable. This effect was strongest in the postboundary condition. These results suggest that a consideration of prominence may be relevant in understanding the temporal patterning of boundary-related articulatory lengthening. PMID:19888443

  8. 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.

  9. Reversible movement of switch 1 loop of myosin determines actin interaction

    PubMed Central

    Kintses, Bálint; Gyimesi, Máté; Pearson, David S; Geeves, Michael A; Zeng, Wei; Bagshaw, Clive R; Málnási-Csizmadia, András

    2007-01-01

    The conserved switch 1 loop of P-loop NTPases is implicated as a central element that transmits information between the nucleotide-binding pocket and the binding site of the partner proteins. Recent structural studies have identified two states of switch 1 in G-proteins and myosin, but their role in the transduction mechanism has yet to be clarified. Single tryptophan residues were introduced into the switch 1 region of myosin II motor domain and studied by rapid reaction methods. We found that in the presence of MgADP, two states of switch 1 exist in dynamic equilibrium. Actin binding shifts the equilibrium towards one of the MgADP states, whereas ATP strongly favors the other. In the light of electron cryo-microscopic and X-ray crystallographic results, these findings lead to a specific structural model in which the equilibrium constant between the two states of switch 1 is coupled to the strength of the actin–myosin interaction. This has implications for the enzymatic mechanism of G-proteins and possibly P-loop NTPases in general. PMID:17213877

  10. 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.

  11. Determination of oxidized phosphatidylcholines by hydrophilic interaction liquid chromatography coupled to Fourier transform mass spectrometry.

    PubMed

    Sala, Pia; Pötz, Sandra; Brunner, Martina; Trötzmüller, Martin; Fauland, Alexander; Triebl, Alexander; Hartler, Jürgen; Lankmayr, Ernst; Köfeler, Harald C

    2015-04-14

    A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates.

  12. 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. PMID:24112322

  13. Ethyl glucuronide determination in meconium and hair by hydrophilic interaction liquid chromatography-tandem mass spectrometry.

    PubMed

    Tarcomnicu, Isabela; van Nuijs, Alexander L N; Aerts, Katrien; De Doncker, Mireille; Covaci, Adrian; Neels, Hugo

    2010-03-20

    Ethyl glucuronide (EtG) detection in non-conventional matrices, such as hair and meconium, can provide useful information on alcohol abuse over a long time frame, for example during pregnancy or after a withdrawal treatment. This study reports on the development, validation and application of a new hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method for the analysis of EtG in meconium and hair. For each matrix, the sample preparation and the chromatographic separation were thoroughly optimised. Additionally, experiments with reversed-phase liquid chromatography were also performed in the development stages. Analyses were carried out using a Phenomenex Luna HILIC column (150 mm x 3 mm, 5 microm) and a mobile phase composed by ammonium acetate 2mM and acetonitrile, in gradient. Different SPE cartridges (Oasis MAX, Oasis WAX, aminopropyl silica) and solvents were tested in order to obtain the highest recoveries and cleanest extracts. Optimal results were obtained for meconium with aminopropyl cartridges, while for hair an incubation of 16 h with 2 mL of water and acetonitrile (50/50, v/v) provided good results. The analytical method was validated for both matrices (meconium and hair) by assessing linearity, precision, accuracy, recovery and limit of quantification. The calibration curve concentrations ranged from 50 to 1200 pg/mg for meconium and from 20 to 1000 pg/mg for hair. Real meconium and hair samples were analyzed and results were consistent with literature. PMID:20061101

  14. Fluorescence spectroscopic study of serum albumin-bromadiolone interaction: fluorimetric determination of bromadiolone.

    PubMed

    Deepa, Subbiah; Mishra, Ashok K

    2005-07-01

    Bromadiolone (BRD), a substituted 4-hydroxycoumarin derivative, is known to possess anti-coagulant activity with acute toxicity. In this paper, we report a study on the interaction of bromadiolone with the plasma proteins bovine serum albumin (BSA) and human serum albumin (HSA), using the intrinsic fluorescence emission properties of bromadiolone. Bromadiolone is weakly fluorescent in aqueous buffer medium, with an emission at 397 nm. Binding of bromadiolone with serum albumins (SA) leads to a marked enhancement in the fluorescence emission intensity and steady state fluorescence anisotropy (r(ss)), accompanied by a blueshift of 10 nm. In the serum albumin-bromadiolone complex, selective excitation of tryptophan (Trp) residue results in emission from bromadiolone, thereby indicating a Förster type energy transfer from Trp to BRD. This quenching of Trp fluorescence by BRD was used to estimate the binding constant of the SA-BRD complex. The binding constants for BRD with BSA and HSA were 7.5 x 10(4) and 3.7 x 10(5)L mol(-1), respectively. Based on this, a new method involving SA as fluorescence-enhancing reagent for estimation of BRD in aqueous samples has been suggested. The detection limits of bromadiolone under the optimum conditions were 0.77 and 0.19 microg mL(-1) in presence of BSA and HSA, respectively. PMID:15925260

  15. Lifetime number of mates interacts with female age to determine reproductive success in female guppies.

    PubMed

    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

  16. 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.

  17. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions.

    PubMed

    Bardwell, A Jane; Bardwell, Lee

    2015-10-30

    MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.

  18. Preparation of a new nanobiosensor for the determination of some biogenic polyamines and investigation of their interaction with DNA.

    PubMed

    Bagheryan, Zahra; Noori, Abolhassan; Zahra Bathaie, S; Yousef-Elahi, Mozhdeh; Mousavi, Mir F

    2016-03-15

    Biogenic polyamines are small organic polycations involving in a variety of biological processes. They form high affinity complexes with DNA. Here, we have followed two different novel approaches, either fabrication of an electrochemical nanobiosensor for determination of three of the most important biogenic polyamines; spermine (SPM), spermidine (SPD) and putrescine (PUT), or electrochemical investigation of their interaction with DNA. Strong binding of polyamines to DNA makes the DNA a suitable recognition element for construction of a sensitive biosensor. The fabricated biosensor responded to SPM, SPD and PUT over an extended dynamic range of 0.04-100 μM, 0.01-24 μM, and 0.08-100 μM respectively, with low detection limits of a few nM. We also studied the interaction of polyamines with three different DNA sequences with base composition of 100% AT, 80% AT and 100% GC in the presence of [Ru(NH3)6]3(+) as a redox probe. The highest kb values were obtained in the interaction of polyamines with 80% AT (mixed) DNA sequence. The kb values were 5.24 × 10(5), 4.17 × 10(5) and 1.46 × 10(5)M(-1) for SPM, SPD and PUT, respectively, which correlated well with their increasing number of amino groups. In addition, competition study showed the impotence of SPD to replace with histone H1 in histone H1-DNA complex, which indicates the more potent interaction of histone H1 with DNA. In this proof-of-principle study, we have proposed an approach for simple, cost-effective, miniaturizable, and direct-readout detection of polyamines, as well as the understanding of the modes of interaction between polyamines and DNA.

  19. Comparison Between Interactive Closest Point and Procrustes Analysis for Determining the Median Sagittal Plane of Three-Dimensional Facial Data

    PubMed Central

    Xiong, Yuxue; Zhao, Yijiao; Yang, Huifang; Sun, Yucun; Wang, Yong

    2016-01-01

    Objective: To compare 2 digital methods to determine median sagittal plane of three-dimensional facial data—the interactive closest point algorithm and Procrustes analysis. Methods: The three-dimensional facial data of the 30 volunteers were got by the Face Scan 3D optical sensor (3D-Shape GmbH, Erlangen, Germany), and then were input to the reverse engineering software Imageware 13.0 (Siemens, Plano, TX) and Geomagic 2012 (Cary, NC). Their mirrored data were acquired and superimposed with the original data by the methods of interactive closest points and Procrustes analysis. The median sagittal planes of the 2 methods were extracted from the original and mirrored facial data respectively, 3 asymmetry indices were measured for comparison. Differences between the facial asymmetry indices of the 2 methods were evaluated using the paired sample t-test. Results: In terms of the 3 asymmetry indices, there were no significant differences between interactive closest points and Procrustes analysis for extracting median sagittal plane from three-dimensional facial data.(t = 0.0.060, P = 0.953 for asymmetry index (AI) 1, t = −0.926, P = 0.362 for AI 2, t = 1.1172, P = 0.0.251 for AI 3). Conclusions: In this evaluation of 30 subjects, the Procrustes analysis and the interactive closest point median-sagittal planes were similar in terms of the 3 asymmetry indices. Thus, Procrustes analysis and interactive closest point can both be used to abstract median sagittal plane from three-dimensional facial data. PMID:26825747

  20. [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.

  1. 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. PMID:21691855

  2. Evolutionary history and novel biotic interactions determine plant responses to elevated CO2 and nitrogen fertilization.

    PubMed

    Wooliver, Rachel; Senior, John K; Schweitzer, Jennifer A; O'Reilly-Wapstra, Julianne M; Langley, J Adam; Chapman, Samantha K; Bailey, Joseph K

    2014-01-01

    A major frontier in global change research is predicting how multiple agents of global change will alter plant productivity, a critical component of the carbon cycle. Recent research has shown that plant responses to climate change are phylogenetically conserved such that species within some lineages are more productive than those within other lineages in changing environments. However, it remains unclear how phylogenetic patterns in plant responses to changing abiotic conditions may be altered by another agent of global change, the introduction of non-native species. Using a system of 28 native Tasmanian Eucalyptus species belonging to two subgenera, Symphyomyrtus and Eucalyptus, we hypothesized that productivity responses to abiotic agents of global change (elevated CO2 and increased soil N) are unique to lineages, but that novel interactions with a non-native species mediate these responses. We tested this hypothesis by examining productivity of 1) native species monocultures and 2) mixtures of native species with an introduced hardwood plantation species, Eucalyptus nitens, to experimentally manipulated soil N and atmospheric CO2. Consistent with past research, we found that N limits productivity overall, especially in elevated CO2 conditions. However, monocultures of species within the Symphyomyrtus subgenus showed the strongest response to N (gained 127% more total biomass) in elevated CO2 conditions, whereas those within the Eucalyptus subgenus did not respond to N. Root:shoot ratio (an indicator of resource use) was on average greater in species pairs containing Symphyomyrtus species, suggesting that functional traits important for resource uptake are phylogenetically conserved and explaining the phylogenetic pattern in plant response to changing environmental conditions. Yet, native species mixtures with E. nitens exhibited responses to CO2 and N that differed from those of monocultures, supporting our hypothesis and highlighting that both plant

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Selective determination of thiram residues in fruit and vegetables by hydrophilic interaction LC-MS.

    PubMed

    Ringli, Daniela; Schwack, Wolfgang

    2013-01-01

    Thiram belongs to the most important class of dithiocarbamate (DTC) fungicides including dimethyldithiocarbamates (DMDs), ethylenebis(dithiocarbamtes) (EBDs) and propylenebis(dithiocarbamates) (PBDs). During the surface extraction of fruit and vegetables for the LC-MS determination of residues of DMDs, EBDs and PBDs, thiram is reduced by the penicillamine buffer to the DMD anion, thus resulting in false-positive findings of DMD fungicides like ziram. Therefore, an alkaline sulfite buffer was applied for surface extraction, quantitatively transforming thiram into the DMD anion and a stable DMD-sulfite adduct that was used as a selective marker for thiram. Separation was performed isocratically on a ZIC-pHILIC column with acetonitrile-10 mM ammonium hydroxide solution (85/15). Mass selective detection was carried out on a single-quadrupole mass spectrometer coupled to an electrospray ionisation interface operating in negative mode. Using d12-thiram as the internal standard, recoveries of 80-108% were obtained from apples, tomatoes, grapes and sweet peppers, spiked in the range of 0.02-1 mg kg(-1). Limits of detection and quantification were 0.6 and 2 µg kg(-1), respectively.

  10. Genetic Determinants of Cardio-Metabolic Risk: A Proposed Model for Phenotype Association and Interaction

    PubMed Central

    Blackett, Piers R; Sanghera, Dharambir K

    2012-01-01

    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 non-alcoholic fatty liver (NAFLD) 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, pharmacological 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. PMID:23351585

  11. Selective determination of thiram residues in fruit and vegetables by hydrophilic interaction LC-MS.

    PubMed

    Ringli, Daniela; Schwack, Wolfgang

    2013-01-01

    Thiram belongs to the most important class of dithiocarbamate (DTC) fungicides including dimethyldithiocarbamates (DMDs), ethylenebis(dithiocarbamtes) (EBDs) and propylenebis(dithiocarbamates) (PBDs). During the surface extraction of fruit and vegetables for the LC-MS determination of residues of DMDs, EBDs and PBDs, thiram is reduced by the penicillamine buffer to the DMD anion, thus resulting in false-positive findings of DMD fungicides like ziram. Therefore, an alkaline sulfite buffer was applied for surface extraction, quantitatively transforming thiram into the DMD anion and a stable DMD-sulfite adduct that was used as a selective marker for thiram. Separation was performed isocratically on a ZIC-pHILIC column with acetonitrile-10 mM ammonium hydroxide solution (85/15). Mass selective detection was carried out on a single-quadrupole mass spectrometer coupled to an electrospray ionisation interface operating in negative mode. Using d12-thiram as the internal standard, recoveries of 80-108% were obtained from apples, tomatoes, grapes and sweet peppers, spiked in the range of 0.02-1 mg kg(-1). Limits of detection and quantification were 0.6 and 2 µg kg(-1), respectively. PMID:24070320

  12. 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.

  13. 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.

  14. RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes.

    PubMed

    Mekler, Vladimir; Minakhin, Leonid; Kuznedelov, Konstantin; Mukhamedyarov, Damir; Severinov, Konstantin

    2012-12-01

    Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are considerably less stable than Escherichia coli RNAP promoter complexes, particularly at temperatures below 37°C. Here, we used a fluorometric RNAP molecular beacon assay to discern partial RNAP-promoter interactions. We quantitatively compared the strength of E. coli and Taq RNAPs partial interactions with the -10, -35 and UP promoter elements; the TG motif of the extended -10 element; the discriminator and the downstream duplex promoter segments. We found that compared with Taq RNAP, E. coli RNAP has much higher affinity only to the UP element and the downstream promoter duplex. This result indicates that the difference in stability between E. coli and Taq promoter complexes is mainly determined by the differential strength of core RNAP-DNA contacts. We suggest that the relative weakness of Taq RNAP interactions with DNA downstream of the transcription start point is the major reason of low stability and temperature sensitivity of promoter complexes formed by this enzyme.

  15. Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor

    PubMed Central

    Chitranshi, Nitin; Gupta, Vivek; Dheer, Yogita; Gupta, Veer; Vander Wall, Roshana; Graham, Stuart

    2016-01-01

    TrkB is a high affinity receptor for the brain derived neurotrophic factor (BDNF) and its phosphorylation stimulates activation of several intracellular signalling pathways linked to cellular growth, differentiation and maintenance. Identification of various activators and inhibitors of the TrkB receptor and greater understanding their binding mechanisms is critical to elucidate the biochemical and pharmacological pathways and analyse various protein crystallization studies. The data presented here is related to the research article entitled “Brain Derived neurotrophic factor is involved in the regulation of glycogen synthase kinase 3β (GSK3β) signalling” [1]. Cyclotraxin B (CTXB) is a disulphide bridge linked cyclic peptide molecule that interacts with TrkB receptor and inhibits the BDNF/TrkB downstream signalling. This article reports for the first time binding mechanism and interaction parameters of CTXB with the TrkB receptor. The molecular model of CTXB has been generated and it’s docking with TrkB domain carried out to determine the critical residues involved in the protein peptide interaction. PMID:26909388

  16. Simultaneous determination of 16 nucleosides and nucleobases by hydrophilic interaction chromatography and its application to the quality evaluation of Ganoderma.

    PubMed

    Chen, Yi; Bicker, Wolfgang; Wu, Junyan; Xie, Mingyong; Lindner, Wolfgang

    2012-05-01

    In order to develop a simple, efficient, and sensitive method for comprehensive analysis of the nucleosides and nucleobases in natural products, a zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) method for the simultaneous determination of 16 nucleosides and nucleobases has been studied. A mechanistic study confirmed that ZIC-HILIC separation showed a mixed-mode effect of both hydrophilic and electrostatic interactions. This method was validated to be precise, accurate, and sensitive with overall precision (intra- and interday) less than 1.8% (RSD), and LOD and LOQ was in the range of 0.005-0.029 μg/mL and 0.018-0.096 μg/mL, respectively. With this method, the nucleosides and nucleobases in Ganoderma of different species (G. atrum, G. lucidum, and G. sinense) and origins were quantified. The results showed that the contents varied with the species and origins. With the aid of hierarchical cluster analysis (HCA), cultivated Ganoderma from different origins and species were successfully discriminated. It is for the first time that the content of nucleosides and nucleobases in G. atrum is reported and compared. Our data showed that HILIC had advantages as a useful and potential tool for the study of the bioactive components in Ganoderma as well as their quality control, and could therefore be used for the determination of the analytes in other natural products.

  17. Intramitochondrial positions of cytochrome haem groups determined by dipolar interactions with paramagnetic cations.

    PubMed Central

    Case, G D; Leigh, J S

    1976-01-01

    E.p.r.(electron-paramagnetic-resonance) spectra of the ferricytochromes were studied in normal and 'nickel-plated' pigeon heart mitochondria and pigeon heart submitochondrial particles. NiCL2 added to either mitochondria or particles was bound completely to the membranes, but none was transported across the vesicles. Hence, any perturbations of the haem e.p.r. spectra by Ni(II) should occur only for those cytochromes in close proximity to the exterior surface. Whenever Ni(II) can approach to within 1 nm of cytochrome haem. the consequent acceleration of the haem e.p.r. relaxation kinetics should elicit dipolar line broadening. Relaxation acceleration should also increase the incident power level required to saturate the haem e.p.r. signal. In pigeon heart mitochondria, at least three e.p.r. resonances, attributable in part to cytochromes c1, bK and br, are observed at gz=3.3 resonance. In these submitochondrial particles, the peak at gz=3.5 is missing, and the resonance at gz=3.6 resolves into two components, neither of which is sensitive to added Ni(ii). Addition of free haemin (ferric, a paramagnetic anion) to intact mitochondria elicits the same e.p.r. signal changes as does a preparation of submitochondrial particles. Saturation curves for cytochrome oxidase obtained for e.p.r. spectra of the high-spin form (g = 6) and the low-spin form (gz=3.1) also reveal no effect of Ni(II) on the haem e.p.r. relaxation in either mitochondria or inverted submitochondrial particles. Further, Ni(II) fails to alter the spectra or saturation properties of cytochrome c in either mitochondria or submitochondrial particles therefrom. Only with a 50-fold molar excess of Ni(II) can one accelerate the e.p.r. relaxation of cytochrome c in aqueous solution, although other more subtle types of magnetic interactions may occur between the cytochrome and either Ni(II) or ferricyanide. Addition of haemin to mitochondria likewise failed to alter the e.p.r. characteristics of either cytochrome

  18. Spectroscopic and functional determination of the interaction of Pb2+ with GATA proteins.

    PubMed

    Ghering, Amy B; Jenkins, Lisa M Miller; Schenck, Brandy L; Deo, Sandhya; Mayer, R Aeryn; Pikaart, Michael J; Omichinski, James G; Godwin, Hilary A

    2005-03-23

    GATA proteins are transcription factors that bind GATA DNA elements through Cys4 structural zinc-binding domains and play critical regulatory roles in neurological and urogenital development and the development of cardiac disease. To evaluate GATA proteins as potential targets for lead, spectroscopically monitored metal-binding titrations were used to measure the affinity of Pb2+ for the C-terminal zinc-binding domain from chicken GATA-1 (CF) and the double-finger domain from human GATA-1 (DF). Using this method, Pb2+ coordinating to CF and DF was directly observed through the appearance of intense bands in the near-ultraviolet region of the spectrum (250-380 nm). Absorption data collected from these experiments were best fit to a 1:1 Pb2+ -CF model and a 2:1 Pb2+ -DF model. Competition experiments using Zn2+ were used to determine the absolute affinities of Pb2+ for these proteins. These studies reveal that Pb2+ forms tight complexes with cysteine residues in the zinc-binding sites in GATA proteins, beta1Pb = 6.4 (+/- 2.0) x 10(9) M(-1) for CF and beta2 = 6.3 (+/- 6.3) x 10(19) M(-2) for Pb(2+)2-DF, and within an order of magnitude of the affinity of Zn2+ for these proteins. Furthermore, Pb2+ was able to displace bound Zn2+ from CF and DF. Upon addition of Pb2+, GATA shows a decreased ability to bind to DNA and subsequently activate transcription. Therefore, the DNA binding and transcriptional activity of GATA proteins are most likely to be targeted by Pb2+ in cells and tissues that sequester Pb2+ in vivo, which include the brain and the heart. PMID:15771509

  19. 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

  20. Using Multiple-viewpoint Observations to Determine the Interaction of Three Coronal Mass Ejections Observed on 2012 March 5

    NASA Astrophysics Data System (ADS)

    Colaninno, Robin C.; Vourlidas, Angelos

    2015-12-01

    We examine the interaction of three coronal mass ejections (CMEs) that took place on 2012 March 5 at heights less than 20 R ⊙ 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-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.

  1. 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.

  2. Jacalin interaction with human immunoglobulin A1 and bovine immunoglobulin G1: affinity constant determined by piezoelectric biosensoring.

    PubMed

    Pedroso, Mariele M; Pesquero, Naira C; Thomaz, Sandra M O; Roque-Barreira, Maria C; Faria, Ronaldo C; Bueno, Paulo R

    2012-03-01

    The affinity of the D-galactose-binding lectin from Artocarpus heterophyllus lectin, known as jacalin, with immonuglobulins (Igs) was determined by biofunctionalization of a piezoelectric transducer. This piezoelectric biofunctionalized transducer was used as a mass-sensitive analytical tool, allowing the real-time binding analysis of jacalin-human immunoglobulin A1 (IgA(1)) and jacalin-bovine IgG(1) interactions from which the apparent affinity constant was calculated. The strategy was centered in immobilizing jacalin on the gold electrode's surface of the piezoelectric crystal resonator using appropriate procedures based on self-assembling of 11-mercaptoundecanoic acid and 2-mercaptoethanol thiol's mixture, a particular immobilization strategy by which it was possible to avoid cross-interaction between the proteins over electrode's surface. The apparent affinity constants obtained between jacalin-human IgA(1) and jacalin-bovine IgG(1) differed by 1 order of magnitude [(8.0 ± 0.9) 10(5) vs (8.3 ± 0.1) 10(6) L mol(-1)]. On the other hand, the difference found between human IgA(1) and human IgA(2) interaction with jacalin, eight times higher for IgA(1), was attributed to the presence of O-linked glycans in the IgA(1) hinge region, which is absent in IgA(2). Specific interaction of jacalin with O-glycans, proved to be present in the human IgA(1) and hypothetically present in bovine IgG(1) structures, is discussed as responsible for the obtained affinity values.

  3. BECN1 and BIM interactions with MCL-1 determine fludarabine resistance in leukemic B cells.

    PubMed

    Sharma, A; Singh, K; Mazumder, S; Hill, B T; Kalaycio, M; Almasan, A

    2013-01-01

    The purine analog fludarabine (Fd) is an essential therapeutic for chronic lymphocytic leukemia (CLL). Innate or acquired resistance to Fd is a significant clinical problem and is largely mediated by increased expression of BCL-2 family members. The antiapoptotic BCL-2 family proteins inhibit both apoptosis and autophagy, therefore, downregulation of antiapoptotic BCL-2 family proteins and enhanced autophagy must coexist in cells dying in response to an apoptosis inducing therapeutic. However, in the drug-resistant cells that have an increased dependence on antiapoptotic proteins, whether autophagy is also inhibited remains unclear. Here, we examined the role of the BCL-2 family in regulating cell death and autophagy in leukemic cell lines and their derivative isogenic Fd-resistant (FdR) cells. MCL-1 degradation following Fd treatment freed the proapoptotic effectors BIM and BECN1, thus leading to cell death-associated autophagy in Fd-sensitive cells. However, in FdR cells, low BIM expression and BECN1 sequestration by MCL-1 prevented cell death. Consistently, in sensitive cells inhibition of apoptosis using siBIM and of both the early-phase autophagy nucleation steps by siBECN1, shATG7 or 3-methyladenine and the late-phase autophagy by shLAMP2, significantly reduced Fd-induced cell death. Paradoxically, FdR cells were addicted to basal autophagy, which was dependent on AMP-activated protein kinase (AMPK) but not BECN1. Moreover, in FdR cells, inhibition of autophagy by shLAMP2, but not siBECN1, enhanced cell death. The BH3-mimetic obatoclax released BIM and BECN1 from MCL-1 in Fd-sensitive and BECN1 from MCL-1 in FdR cells, and was effective at killing both Fd-sensitive and - resistant leukemic cells, including primary CLL cells. Therefore, a differential regulation of autophagy through BECN1 and AMPK signaling in Fd-sensitive and - resistant cells determines the different possible outcomes of autophagy inhibition. These findings suggest effective means to

  4. 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'.

  5. 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.

  6. Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes.

    PubMed

    Diehl, Carl; Wisniewska, Magdalena; Frick, Inga-Maria; Streicher, Werner; Björck, Lars; Malmström, Johan; Wikström, Mats

    2016-01-01

    Streptococcus pyogenes is one of the most significant bacterial pathogens in the human population mostly causing superficial and uncomplicated infections (pharyngitis and impetigo) but also invasive and life-threatening disease. We have previously identified a virulence determinant, protein sHIP, which is secreted at higher levels by an invasive compared to a non-invasive strain of S. pyogenes. The present work presents a further characterization of the structural and functional properties of this bacterial protein. Biophysical and structural studies have shown that protein sHIP forms stable tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We identified three residues at the tetramer interface (Leu84, Leu88, Tyr95), which due to largely non-polar side-chains, could be important determinants for protein oligomerization. Based on these observations, we produced a sHIP variant in which these residues were mutated to alanines. Biophysical experiments clearly indicated that the sHIP mutant appear only as dimers in solution confirming the importance of the interfacial residues for protein oligomerisation. Furthermore, we could show that the sHIP mutant interacts with intact histidine-rich glycoprotein (HRG) and the histidine-rich repeats in HRG, and inhibits their antibacterial activity to the same or even higher extent as compared to the wild type protein sHIP. We determined the crystal structure of the sHIP mutant, which, as a result of the high quality of the data, allowed us to improve the existing structural model of the protein. Finally, by employing NMR spectroscopy in solution, we generated a model for the complex between the sHIP mutant and an HRG-derived heparin-binding peptide, providing further molecular

  7. Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes

    PubMed Central

    Diehl, Carl; Wisniewska, Magdalena; Frick, Inga-Maria; Streicher, Werner; Björck, Lars; Malmström, Johan; Wikström, Mats

    2016-01-01

    Streptococcus pyogenes is one of the most significant bacterial pathogens in the human population mostly causing superficial and uncomplicated infections (pharyngitis and impetigo) but also invasive and life-threatening disease. We have previously identified a virulence determinant, protein sHIP, which is secreted at higher levels by an invasive compared to a non-invasive strain of S. pyogenes. The present work presents a further characterization of the structural and functional properties of this bacterial protein. Biophysical and structural studies have shown that protein sHIP forms stable tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We identified three residues at the tetramer interface (Leu84, Leu88, Tyr95), which due to largely non-polar side-chains, could be important determinants for protein oligomerization. Based on these observations, we produced a sHIP variant in which these residues were mutated to alanines. Biophysical experiments clearly indicated that the sHIP mutant appear only as dimers in solution confirming the importance of the interfacial residues for protein oligomerisation. Furthermore, we could show that the sHIP mutant interacts with intact histidine-rich glycoprotein (HRG) and the histidine-rich repeats in HRG, and inhibits their antibacterial activity to the same or even higher extent as compared to the wild type protein sHIP. We determined the crystal structure of the sHIP mutant, which, as a result of the high quality of the data, allowed us to improve the existing structural model of the protein. Finally, by employing NMR spectroscopy in solution, we generated a model for the complex between the sHIP mutant and an HRG-derived heparin-binding peptide, providing further molecular

  8. Interaction between PNPLA3 I148M Variant and Age at Infection in Determining Fibrosis Progression in Chronic Hepatitis C

    PubMed Central

    Aghemo, Alessio; Cheroni, Cristina; D'Ambrosio, Roberta; Pedrazzini, Michele; Marabita, Francesco; Donnici, Lorena; Maggioni, Marco; Fargion, Silvia; Colombo, Massimo; De Francesco, Raffaele; Valenti, Luca

    2014-01-01

    Background and Aims The PNPLA3 I148M sequence variant favors hepatic lipid accumulation and confers susceptibility to hepatic fibrosis and hepatocellular carcinoma. The aim of this study was to estimate the effect size of homozygosity for the PNPLA3 I148M variant (148M/M) on the fibrosis progression rate (FPR) and the interaction with age at infection in chronic hepatitis C (CHC). Methods FPR was estimated in a prospective cohort of 247 CHC patients without alcohol intake and diabetes, with careful estimation of age at infection and determination of fibrosis stage by Ishak score. Results Older age at infection was the strongest determinant of FPR (p<0.0001). PNPLA3 148M/M was associated with faster FPR in individuals infected at older age (above the median, 21 years; −0.64±0.2, n = 8 vs. −0.95±0.3, n = 166 log10 FPR respectively; p = 0.001; confirmed for lower age thresholds, p<0.05), but not in those infected at younger age (p = ns). The negative impact of PNPLA3 148M/M on fibrosis progression was more marked in subjects at risk of altered hepatic lipid metabolism (those with grade 2–3 steatosis, genotype 3, and overweight; p<0.05). At multivariate analysis, PNPLA3 148M/M was associated with FPR (incremental effect 0.08±0.03 log10 fibrosis unit per year; p = 0.022), independently of several confounders, and there was a significant interaction between 148M/M and older age at infection (p = 0.025). The association between 148M/M and FPR remained significant even after adjustment for steatosis severity (p = 0.032). Conclusions We observed an interaction between homozygosity for the PNPLA3 I148M variant and age at infection in determining fibrosis progression in CHC patients. PMID:25171251

  9. Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes.

    PubMed

    Diehl, Carl; Wisniewska, Magdalena; Frick, Inga-Maria; Streicher, Werner; Björck, Lars; Malmström, Johan; Wikström, Mats

    2016-01-01

    Streptococcus pyogenes is one of the most significant bacterial pathogens in the human population mostly causing superficial and uncomplicated infections (pharyngitis and impetigo) but also invasive and life-threatening disease. We have previously identified a virulence determinant, protein sHIP, which is secreted at higher levels by an invasive compared to a non-invasive strain of S. pyogenes. The present work presents a further characterization of the structural and functional properties of this bacterial protein. Biophysical and structural studies have shown that protein sHIP forms stable tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We identified three residues at the tetramer interface (Leu84, Leu88, Tyr95), which due to largely non-polar side-chains, could be important determinants for protein oligomerization. Based on these observations, we produced a sHIP variant in which these residues were mutated to alanines. Biophysical experiments clearly indicated that the sHIP mutant appear only as dimers in solution confirming the importance of the interfacial residues for protein oligomerisation. Furthermore, we could show that the sHIP mutant interacts with intact histidine-rich glycoprotein (HRG) and the histidine-rich repeats in HRG, and inhibits their antibacterial activity to the same or even higher extent as compared to the wild type protein sHIP. We determined the crystal structure of the sHIP mutant, which, as a result of the high quality of the data, allowed us to improve the existing structural model of the protein. Finally, by employing NMR spectroscopy in solution, we generated a model for the complex between the sHIP mutant and an HRG-derived heparin-binding peptide, providing further molecular

  10. 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

  11. 3-Hydroxy-4-pyridinone derivatives designed for fluorescence studies to determine interaction with amyloid protein as well as cell permeability.

    PubMed

    Telpoukhovskaia, Maria A; Cawthray, Jacqueline F; Rodríguez-Rodríguez, Cristina; Scott, Lauren E; Page, Brent D G; Patrick, Brian O; Orvig, Chris

    2015-09-01

    Finding a cure for Alzheimer's disease is an urgent goal. Multifunctional metal binders are used to elucidate its pathological features and investigated as potential therapeutics. The use of physicochemical and TD-DFT calculations constituted successful strategy in the design of 1-(4-(benzo[d]oxazol-2-yl)phenyl)-3-hydroxy-2-methylpyridin-4(1H)-one (HL21) and 1-(4-(benzo[d]thiazol-2-yl)phenyl)-3-hydroxy-2-methylpyridin-4(1H)-one (HL22). We report the synthesis and full characterization of these compounds, including X-ray crystallography. Using fluorescent signal as the readout, it was determined that HL22 interacts with amyloid-beta protein fibrils, and permeates into bEnd.3 cells used as a mimic of the blood-brain barrier. This provides the first example of direct investigation of our hydroxypyridinone compounds within a biological setting. PMID:26141772

  12. 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.

  13. Analytical determination of the reflection coefficient by the evanescent modes model during the wave-current-horizontal plate interaction

    NASA Astrophysics Data System (ADS)

    Errifaiy, Meriem; Naasse, Smail; Chahine, Chakib

    2016-07-01

    Our work presents an analytical study of the determination of the reflection coefficient during the interaction between the regular wave current and a horizontal plate. This study was done using the linearized potential flow theory with the evanescent modes model, while searching for complex solutions to the dispersion equation that are neither real pure nor imaginary pure. To validate the established model, it has been confronted with the experimental results of V. Rey and J. Touboul, in a first phase, and then compared to those of the numerical study by H.-X. Lin et al. Then, this model was used to study the effect of current on the reflection coefficient. xml:lang="fr"

  14. 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.

  15. 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. PMID:25383921

  16. 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".

  17. 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.

  18. 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. PMID:22073655

  19. Determinants of cue interactions.

    PubMed

    Wheeler, Daniel S; Miller, Ralph R

    2008-06-01

    In a Pavlovian conditioning situation, there are many training variables that may affect responding to a conditioned stimulus (CS), such as contiguity, contingency, and the presence of other CSs. This review describes recent experiments that show that some manipulations that usually decrease responding to a CS may have the opposite effect when they are combined with other normally pernicious manipulations. A theoretical framework that explains these so-called counteraction effects is provided. The apparent boundary conditions on the effects and limitations of the theory are discussed.

  20. 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.

  1. Solution structure of mouse hepatitis virus (MHV) nsp3a and determinants of the interaction with MHV nucleocapsid (N) protein.

    PubMed

    Keane, Sarah C; Giedroc, David P

    2013-03-01

    Coronaviruses (CoVs) are positive-sense, single-stranded, enveloped RNA viruses that infect a variety of vertebrate hosts. The CoV nucleocapsid (N) protein contains two structurally independent RNA binding domains, designated the N-terminal domain (NTD) and the dimeric C-terminal domain (CTD), joined by a charged linker region rich in serine and arginine residues (SR-rich linker). An important goal in unraveling N function is to molecularly characterize N-protein interactions. Recent genetic evidence suggests that N interacts with nsp3a, a component of the viral replicase. Here we present the solution nuclear magnetic resonance (NMR) structure of mouse hepatitis virus (MHV) nsp3a and show, using isothermal titration calorimetry, that MHV N219, an N construct that extends into the SR-rich linker (residues 60 to 219), binds cognate nsp3a with high affinity (equilibrium association constant [K(a)], [1.4 ± 0.3] × 10(6) M(-1)). In contrast, neither N197, an N construct containing only the folded NTD (residues 60 to 197), nor the CTD dimer (residues 260 to 380) binds nsp3a with detectable affinity. This indicates that the key nsp3a binding determinants localize to the SR-rich linker, a finding consistent with those of reverse genetics studies. NMR chemical shift perturbation analysis reveals that the N-terminal region of an MHV N SR-rich linker peptide (residues 198 to 230) binds to the acidic face of MHV nsp3a containing the acidic α2 helix with an affinity (expressed as K(a)) of 8.1 × 10(3) M(-1). These studies reveal that the SR-rich linker of MHV N is necessary but not sufficient to maintain this high-affinity binding to N.

  2. 22 Protein-Protein Interactions Determine IgE Reactivity to Polygalacturonase From Cupressus sempervirens Pollen

    PubMed Central

    Shahali, Youcef; Sutra, Jean-Pierre; Chollet-Martin, Sylvie; Haddad, Iman; Vinh, Joëlle; Mari, Adriano; Charpin, Denis; Sénéchal, Hélène; Poncet, Pascal

    2012-01-01

    study demonstrates that the sensitization to the Cups pollen PG is mainly due to CCD bromelain-type epitopes and directly associated with an increased prevalence of IgE reactivity to cypress pollen extracts due to CCD interference. However, the Cups pollen PG and its carbohydrate-specific determinants seem to play a key role in the dynamics of protein-protein interaction in cypress pollen and may confer to protein complexes a higher allergenicity.

  3. 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. PMID:23326392

  4. 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.

  5. 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. PMID:23861863

  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. PMID:23065931

  7. Arsenic bioaccessibility upon gastrointestinal digestion is highly determined by its speciation and lipid-bile salt interactions.

    PubMed

    Alava, Pradeep; Du Laing, Gijs; Odhiambo, Moses; Verliefde, Arne; Tack, Filip; Van de Wiele, Tom R

    2013-01-01

    The release of arsenic (As) from a contaminated food matrix during gastrointestinal digestion, i.e., its bioaccessibility, is an important estimator of its bioavailability, and therefore also its health risk. In addition, As toxicity is primarily determined by its speciation and it is not clear how different As species behave during digestion in the upper digestive tract. Here, we evaluated to what extent digestive parameters like gastric pH and bile concentration, but also food matrix constituents affect the bioaccessibility of 8 As species (As(III), As(V), MMA(V), DMA(V), MMA(III), DMA(III), MMMTA(V), DMMTA(V)). Bioaccessibility of all As standards ranged between 85% and 90% under pH 1.8. Bioaccessibility of methylated and thiolated arsenicals was decreased from 85% to 50% with increasing gastric pH to 4, yet an increasing bile salts concentration up to 30 g/L lowered the bioaccessibility of inorganic species from 83% to 70% due to interaction with Fe present in bile salts. With respect to food matrices, we noted that the fiber content did not affect As bioaccessibility, yet the presence of fat resulted in an increased bioaccessibility of both inorganic and organic arsenicals in the presence of bile salts. With respect to inorganic arsenic, the intestinal presence of trivalent Fe appeared to be the predominant factor for bioaccessibility of iAs. These data demonstrate that species dependent bioaccessibility must be considered upon ingestion and gastrointestinal digestion. PMID:23442116

  8. Rapid determination of amino acids in foods by hydrophilic interaction liquid chromatography coupled to high-resolution mass spectrometry.

    PubMed

    Gökmen, Vural; Serpen, Arda; Mogol, Burçe Ataç

    2012-07-01

    This study describes a rapid and sensitive analytical method for the determination of amino acids in foods and drinks. The method entailed dilution or extraction of amino acids from foods using the mixture of acetonitrile and 0.1% aqueous formic acid (50:50, v/v). Chromatographic separation of underivatized amino acids was performed using a hydrophilic interaction liquid chromatography within a runtime of 6 min. Both hydrophobicity and charge of the side chain played important roles on the elution order of amino acids under the chromatographic conditions. High-resolution mass spectrometry allowed qualitative and quantitative detection of amino acids in complex food matrices. Its response was found linear over a concentration range of 0.25-10 μg/ml. The method could be successfully applied to various foods and drinks to profile individual amino acids. Mean percentage recoveries of amino acids from different matrices were 88.5% or higher with residual standard deviation of less than 5.0%.

  9. 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. PMID:23609802

  10. 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

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

    Yan, Yangqian; Blume, D

    2016-06-10

    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 b_{4} 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 b_{4}, our b_{4} 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. PMID:27341213

  15. Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein

    NASA Astrophysics Data System (ADS)

    Li, Jun-Wei; Xiao, Shao-Ying; Xie, Xiao-Xiao; Yu, Hui; Zhang, Hai-Lin; Zhan, Yong; An, Hai-Long

    2015-02-01

    We find that a conserved mutation residue Glu to residue Asp (E303D), which both have the same polar and charged properties, makes Kir2.1 protein lose its function. To understand the mechanism, we identify three interactions which control the conformation change and maintain the function of the Kir2.1 protein by combining homology modeling and molecular dynamics with targeted molecular dynamics. We find that the E303D mutation weakens these interactions and results in the loss of the related function. Our data indicate that not only the amino residues but also the interactions determine the function of proteins.

  16. Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using biofilter, and gene-environment interactions using the Phenx Toolkit*.

    PubMed

    Pendergrass, Sarah A; Verma, Shefali S; Hall, Molly A; Holzinger, Emily R; Moore, Carrie B; Wallace, John R; Dudek, Scott M; Huggins, Wayne; Kitchner, Terrie; Waudby, Carol; Berg, Richard; Mccarty, Catherine A; Ritchie, Marylyn D

    2015-01-01

    Investigating the association between biobank derived genomic data and the information of linked electronic health records (EHRs) is an emerging area of research for dissecting the architecture of complex human traits, where cases and controls for study are defined through the use of electronic phenotyping algorithms deployed in large EHR systems. For our study, cataract cases and controls were identified within the Marshfield Personalized Medicine Research Project (PMRP) biobank and linked EHR, which is a member of the NHGRI-funded electronic Medical Records and Genomics (eMERGE) Network. Our goal was to explore potential gene-gene and gene-environment interactions within these data for 527,953 and 527,936 single nucleotide polymorphisms (SNPs) for gene-gene and gene-environment analyses, respectively, with minor allele frequency > 1%, in order to explore higher level associations with cataract risk beyond investigations of single SNP-phenotype associations. To build our SNP-SNP interaction models we utilized a prior-knowledge driven filtering method called Biofilter to minimize the multiple testing burden of exploring the vast array of interaction models possible from our extensive number of SNPs. Using Biofilter, we developed 57,376 prior-knowledge directed SNP-SNP models to test for association with cataract status. We selected models that required 6 sources of external domain knowledge. We identified 13 statistically significant SNP-SNP models with an interaction with p-value < 1 × 10(-4), as well as an overall model with p-value < 0.01 associated with cataract status. We also conducted gene-environment interaction analyses for all GWAS SNPs and a set of environmental factors from the PhenX Toolkit: smoking, UV exposure, and alcohol use;these environmental factors have been previously associated with the formation of cataracts. We found a total of 782 gene-environment models that exhibit an interaction with a p-value < 1 × 10(-4) associatedwith cataract

  17. 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. PMID:25428455

  18. 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.

  19. 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.

  20. 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

  1. 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. PMID:27061175

  2. Fast HPLC method using ion-pair and hydrophilic interaction liquid chromatography for determination of phenylephrine in pharmaceutical formulations.

    PubMed

    Dousa, Michal; Gibala, Petr

    2010-01-01

    A rapid procedure based on a direct extraction and HPLC determination with fluorescence detection of phenylephrine in pharmaceutical sachets that include a large excess of paracetamol (65 + 1, w/w), ascorbic acid (5 + 1, w/w), and other excipients (aspartame and sucrose) was developed and validated. The final optimized chromatographic method for ion-pair chromatography used an XTerra RP18 column, 3 microm particle size, 50 x 3.0 mm id. The mobile phase consisted of a mixture of acetonitrile and buffer (10 mM sodium octane-1-sulfonate, adjusted with H3PO4 to pH 2.2; 200 + 800, v/v), with a constant flow rate of 0.3 mL/min. The separation was carried out at 30 degrees C, and the injection volume was 3 microL. Fluorescence detection was performed at excitation and emission wavelengths of 275 and 310 nm, respectively. The mobile phase parameters, such as the organic solvent fraction (acetonitrile) in mobile phase as an organic modifier, the concentration of sodium octane-1-sulfonate as a counter-ion, temperature, and pH of mobile phase, were studied. As an alternative to ion-pair chromatography, hydrophilic interaction liquid chromatography (HILIC) was investigated using a Luna HILIC column, 3 microm, 100 x 4.6 mm id. The mobile phase consisted of acetonitrile and buffer (5 mM potassium dihydrogen phosphate, adjusted with H3PO4 to pH 2.5; 750 + 250, v/v) at a flow rate of 0.8 mL/min. The separation was carried out at 25 degrees C, and the injection volume was 5 microL. The proposed method has an advantage of a very simple sample pretreatment, and is much faster than the currently utilized HPLC methods using gradient elution and UV detection. Commercial samples of sachets were successfully analyzed by the proposed HPLC method.

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

    PubMed Central

    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.

    2013-01-01

    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. PMID:24151981

  4. 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.

  5. X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions

    NASA Astrophysics Data System (ADS)

    Kelly, S. D.; Kemner, K. M.; Fein, J. B.; Fowle, D. A.; Boyanov, M. I.; Bunker, B. A.; Yee, N.

    2002-11-01

    X-ray absorption fine structure (XAFS) measurements was used at the U L3-edge to directly determine the pH dependence of the cell wall functional groups responsible for the absorption of aqueous UO 22+ to Bacillus subtilis from pH 1.67 to 4.80. Surface complexation modeling can be used to predict metal distributions in water-rock systems, and it has been used to quantify bacterial adsorption of metal cations. However, successful application of these models requires a detailed knowledge not only of the type of bacterial surface site involved in metal adsorption/desorption, but also of the binding geometry. Previous acid-base titrations of B. subtilis cells suggested that three surface functional group types are important on the cell wall; these groups have been postulated to correspond to carboxyl, phosphoryl, and hydroxyl sites. When the U(VI) adsorption to B. subtilis is measured, observed is a significant pH-independent absorption at low pH values (<3.0), ascribed to an interaction between the uranyl cation and a neutrally charged phosphoryl group on the cell wall. The present study provides independent quantitative constraints on the types of sites involved in uranyl binding to B. subtilis from pH 1.67 to 4.80. The XAFS results indicate that at extremely low pH (pH 1.67) UO 22+ binds exclusively to phosphoryl functional groups on the cell wall, with an average distance between the U atom and the P atom of 3.64 ± 0.01 Å. This U-P distance indicates an inner-sphere complex with an oxygen atom shared between the UO 22+ and the phosphoryl ligand. The P signal at extremely low pH value is consistent with the UO 22+ binding to a protonated phosphoryl group, as previously ascribed. With increasing pH (3.22 and 4.80), UO 22+ binds increasingly to bacterial surface carboxyl functional groups, with an average distance between the U atom and the C atom of 2.89 ± 0.02 Å. This U-C distance indicates an inner-sphere complex with two oxygen atoms shared between the UO 22

  6. The Interaction between the Fiber Knob Domain and the Cellular Attachment Receptor Determines the Intracellular Trafficking Route of Adenoviruses

    PubMed Central

    Shayakhmetov, Dmitry M.; Li, Zong-Yi; Ternovoi, Vladimir; Gaggar, Anuj; Gharwan, Helen; Lieber, André

    2003-01-01

    Most of the presently used adenovirus (Ad) vectors are based on serotype 5. However, the application of these vectors is limited by the native tropism of Ad5. To address this problem, a series of fiber chimeric vectors were produced to take advantage of the different cellular receptors used by Ad of different subgroups. In this study we utilize an Ad5-based chimeric vector containing sequences encoding the Ad35 fiber knob domain instead of the Ad5 knob (Ad5/35L) to analyze factors responsible for selection of intracellular trafficking routes by Ads. By competition analysis with recombinant Ad5 and Ad35 knobs we showed that the Ad5/35L vector infected cells through a receptor different from the Ad5 receptor. Intracellular trafficking of Ad5 and Ad5/35L viruses was analyzed in HeLa cells by tracking fluorophore-conjugated Ad particles, by immunostaining for capsid hexon protein, by electron microscopy, and by Southern blotting for viral DNA. These studies showed that the interaction with the Ad35 receptor(s) predestines Ad5/35L vector to intracellular trafficking pathways different from those of Ad5. Ad5 efficiently escaped from the endosomes early after infection. In contrast, Ad5/35L remained longer in late endosomal/lysosomal compartments and used them to achieve localization to the nucleus. However, a significant portion of Ad5/35L particles appeared to be recycled back to the cell surface. This phenomenon resulted in significantly less efficient Ad5/35L-mediated gene transfer compared to that of Ad5. We also demonstrated that the selection of intracellular trafficking routes was determined by the fiber knob domain and did not depend on the length of the fiber shaft. This study contributes to a better understanding of the mechanisms that govern the infection of retargeted, capsid-modified vectors which have potential application for hematopoietic stem cell and tumor gene therapy. PMID:12610146

  7. 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. PMID:27154684

  8. 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.

  9. 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.

  10. [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.

  11. Interactions among lactose, β-lactoglobulin and starch in co-lyophilized mixtures as determined by Fourier Transform Infrared Spectroscopy.

    PubMed

    Hajihashemi, Zohreh; Nasirpour, Ali; Scher, Joël; Desobry, Stéphane

    2014-11-01

    Processing and storage change food powders containing a large quantity of lactose due to lactose crystallization and interactions among components. Model food systems were prepared by co-lyophilization of lactose, β-lactoglobulin (BLG), and gelatinized starch. A mixture design was used to define the percentage of each mixture component to simulate a wide range of food powders. Interactions among lactose, BLG and starch were studied using Fourier Transform Infrared (FT-IR) at different relative humidities (RH), before and after 3 months storage. Results showed the presence of hydrogen bonds among these components. Moreover, interactions or formation of hydrogen bonds among lactose, starch and BLG preserved BLG against freezing and freeze-drying shocks. Lactose crystallization could be identified by comparing infrared spectra of amorphous and crystallized lactose at O - H and C - H stretching vibration bands. PMID:26396334

  12. 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.

  13. The Interaction between Cyclin B1 and Cytomegalovirus Protein Kinase pUL97 is Determined by an Active Kinase Domain.

    PubMed

    Steingruber, Mirjam; Socher, Eileen; Hutterer, Corina; Webel, Rike; Bergbrede, Tim; Lenac, Tihana; Sticht, Heinrich; Marschall, Manfred

    2015-08-11

    Replication of human cytomegalovirus (HCMV) is characterized by a tight virus-host cell interaction. Cyclin-dependent protein kinases (CDKs) are functionally integrated into viral gene expression and protein modification. The HCMV-encoded protein kinase pUL97 acts as a CDK ortholog showing structural and functional similarities. Recently, we reported an interaction between pUL97 kinase with a subset of host cyclins, in particular with cyclin T1. Here, we describe an interaction of pUL97 at an even higher affinity with cyclin B1. As a striking feature, the interaction between pUL97 and cyclin B1 proved to be strictly dependent on pUL97 activity, as interaction could be abrogated by treatment with pUL97 inhibitors or by inserting mutations into the conserved kinase domain or the nonconserved C-terminus of pUL97, both producing loss of activity. Thus, we postulate that the mechanism of pUL97-cyclin B1 interaction is determined by an active pUL97 kinase domain.

  14. 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.

  15. 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.

  16. 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.

  17. Student Aptitudes and Methods of Teaching Beginning Reading: A Predictive Instrument for Determining Interaction Patterns. Final Report.

    ERIC Educational Resources Information Center

    Stallings, Jane A.; Keepes, Bruce D.

    The question of whether reading methods interact differentially with student sequencing abilities was investigated. One hundred and thirty-one children from three schools in Palo Alto, California, were given reading instruction using a linguistic approach (Palo Alto Reading Program), and 115 children from three Palo Alto schools used a whole-word…

  18. 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.

  19. 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.

  20. Inelastic Neutron Scattering and Molecular Dynamics Determination of the Interaction Potential in Liquid CD{sub 4}

    SciTech Connect

    Guarini, E.; Barocchi, F.

    2007-10-19

    Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.

  1. 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.

  2. Linear 3d-4f compounds: synthesis, structure, and determination of the d-f magnetic interaction.

    PubMed

    Wu, Jianfeng; Zhao, Lang; Zhang, Peng; Zhang, Li; Guo, Mei; Tang, Jinkui

    2015-07-14

    A family of [RE2M2L2(BA)6] (RE = Gd, Tb, Dy, Y; M = Co, Ni, Cu, Zn; L = 1,2-bis(2-hydroxy-3-methoxybenzylidene)hydrazine; BA = benzoic acid) complexes were synthesized and structurally and magnetically characterized. The magnetic interactions between spin centers were systematically investigated. The interactions of M-M (M = Co, Ni and Cu) and Gd-Ni/Cu were extracted from the fitting of the experimental data of Y2M2 (M = Co, Ni and Cu) and Gd2M2 (M = Ni and Cu) derivatives, respectively. Furthermore, the Ln-M interactions were qualitatively analyzed by deducting the M-M coupling and the contribution of the crystal-field effects of the Ln(III) ion from the total magnetic susceptibility of Ln2M2 (Ln = Dy and Tb) compounds. In addition, complex [Dy2Zn2L2(BA)6] shows field induced single molecular magnet behavior profiting from the isolated anisotropic dysprosium ions. PMID:26066788

  3. SiO2 nanoparticles modified CPE as a biosensor for determination of i-motif DNA/Tamoxifen interaction.

    PubMed

    Heydari, Elham; Raoof, Jahan Bakhsh; Ojani, Reza; Bagheryan, Zahra

    2016-08-01

    Cytosine-rich DNA sequences can form a highly ordered structure known as i-motif in slightly acidic solutions. The stability of the folded i-motif structure is a good strategy to inhibit the telomerase reaction in cancer cells. The electrochemical biosensor was prepared by modifying carbon paste electrode with SiO2 nanoparticles to investigate drugs which can stabilize this structure. Tamoxifen (Tam), an antiestrogen hormonal agent for treatment of breast cancer, was chosen as the model ligand and its interaction with i-motif structure was examined. The interaction between i-motif DNA and Tam was studied in PBS buffer and [Fe(CN)6](3-) through the cyclic voltammetry and square wave voltammetry methods. The oxidation peak of Tam, due to the i-motif DNA/Tam interaction, was observed after i-motif immobilized on the surface of the electrode. The i-motif formation was investigated by circular dichroism spectroscopy and the results showed that this structure can certainly be made with pH around 4.5, but its stability reduced by going to the more alkaline pH. The selectivity which was studied in the presence of complementary strand demonstrated that i-motif structure could be stabilized in acidic pH even in the presence of its complementary strand. PMID:27151665

  4. 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. PMID:24054328

  5. Acquired type III secretion system determines environmental fitness of epidemic Vibrio parahaemolyticus in the interaction with bacterivorous protists.

    PubMed

    Matz, Carsten; Nouri, Bianka; McCarter, Linda; Martinez-Urtaza, Jaime

    2011-01-01

    Genome analyses of marine microbial communities have revealed the widespread occurrence of genomic islands (GIs), many of which encode for protein secretion machineries described in the context of bacteria-eukaryote interactions. Yet experimental support for the specific roles of such GIs in aquatic community interactions remains scarce. Here, we test for the contribution of type III secretion systems (T3SS) to the environmental fitness of epidemic Vibrio parahaemolyticus. Comparisons of V. parahaemolyticus wild types and T3SS-defective mutants demonstrate that the T3SS encoded on genome island VPaI-7 (T3SS-2) promotes survival of V. parahaemolyticus in the interaction with diverse protist taxa. Enhanced persistence was found to be due to T3SS-2 mediated cytotoxicity and facultative parasitism of V. parahaemolyticus on coexisting protists. Growth in the presence of bacterivorous protists and the T3SS-2 genotype showed a strong correlation across environmental and clinical isolates of V. parahaemolyticus. Short-term microcosm experiments provide evidence that protistan hosts facilitate the invasion of T3SS-2 positive V. parahaemolyticus into a coastal plankton community, and that water temperature and productivity further promote enhanced survival of T3SS-2 positive V. parahaemolyticus. This study is the first to describe the fitness advantage of GI-encoded functions in a microbial food web, which may provide a mechanistic explanation for the global spread and the seasonal dynamics of V. parahaemolyticus pathotypes, including the pandemic serotype cluster O3:K6, in aquatic environments.

  6. Rubrene: The Interplay between Intramolecular and Intermolecular Interactions Determines the Planarization of Its Tetracene Core in the Solid State.

    PubMed

    Sutton, Christopher; Marshall, Michael S; Sherrill, C David; Risko, Chad; Brédas, Jean-Luc

    2015-07-15

    Rubrene is one of the most studied molecular semiconductors; its chemical structure consists of a tetracene backbone with four phenyl rings appended to the two central fused rings. Derivatization of these phenyl rings can lead to two very different solid-state molecular conformations and packings: One in which the tetracene core is planar and there exists substantive overlap among neighboring π-conjugated backbones; and another where the tetracene core is twisted and the overlap of neighboring π-conjugated backbones is completely disrupted. State-of-the-art electronic structure calculations show for all isolated rubrene derivatives that the twisted conformation is more favorable (by -1.7 to -4.1 kcal mol(-1)), which is a consequence of energetically unfavorable exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned through well-chosen functionalization of the phenyl side groups and lead to improved intermolecular electronic couplings. Understanding the interplay of these intramolecular and intermolecular interactions provides insight into how to chemically modify rubrene and similar molecular semiconductors to improve the intrinsic materials electronic properties. PMID:26075966

  7. Determination and comparison of how the chain number and chain length of a lipid affects its interactions with a phospholipid at an air/water interface.

    PubMed

    Ngyugen, Hang; McNamee, Cathy E

    2014-06-01

    We determined how the number of chains in a lipid and its chain length affects its interactions with a phospholipid model membrane, and whether the number of chains or the chain length of lipids affects their interactions with the phospholipids more. This was achieved by using a Langmuir trough and a fluorescence microscope to study the interactions of mono-, di-, and triglycerides with a phospholipid monolayer at an air/water interface. The effect of the number of chains in a lipid on its interactions with phospholipids at air/water interfaces was shown by surface pressure-area per molecule isotherms and their thermodynamic analysis to worsen as the number of alkyl chains was increased to be greater than one. An increase in the packing density decreased the mixing ability of the lipids with the phospholipids, resulting in the formation of aggregates in the mixed monolayer. The aggregation was explained by the intermolecular hydrophobic and van der Waals attractions between the lipid molecules. Fluorescence microscopy revealed partial mixing without aggregation for monoglycerides, but the presence of lipid aggregation for diglycerides and triglycerides. The effect of decreasing the chain length of triglycerides from a long chain to a medium chain caused the interactions of the lipids with the phospholipid molecules at the air/water interface to significantly improve. Decreasing the chain length of monoglycerides from a long chain to a medium chain worsened their interaction with the phospholipid molecules. The effect of decreasing the triglyceride chain length on their interactions with phospholipids was much greater than the effect of decreasing the number of alkyl chains in the lipid.

  8. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions.

    PubMed

    Glasfeld, A; Koehler, A N; Schumacher, M A; Brennan, R G

    1999-08-13

    The interaction of the dimeric Escherichia coli purine repressor (PurR) with its cognate sequences leads to a 45 degrees to 50 degrees kink at a central CpG base step towards the major groove, as dyad-related leucine side-chains interdigitate between these bases from the minor groove. The resulting broadening of the minor groove increases the accessibility of the six central base-pairs towards minor groove interactions with residues from PurR. It has been shown that lysine 55 of PurR makes a direct contact with the adenine base (Ade8) directly 5' to the central CpG base-pair step in the high-affinity purF operator sequence. We have investigated the importance of this interaction in the specificity and affinity of wild-type PurR (WT) for its operators and we have studied a mutant of PurR in which Lys55 is replaced with alanine (K55A). Complexes of WT and K55A with duplex DNA containing pur operator sequences varied at position 8 were investigated crystallographically, and binding studies were performed using fluorescence anisotropy. The structures of the protein-DNA complexes reveal a relatively unperturbed global conformation regardless of the identity of the base-pair at position 8 or residue 55. In all structures the combination of higher resolution and a palindromic purF operator site allowed several new PurR.DNA interactions to be observed, including contacts by Thr15, Thr16 and His20. The side-chain of Lys55 makes productive, though varying, interactions with the adenine, thymine or cytosine base at position 8 that result in equilibrium dissociation constants of 2.6 nM, 10 nM and 35 nM, respectively. However, the bulk of the lysine side-chain apparently blocks high-affinity binding of operators with guanine at position 8 (Kd620 nM). Also, the high-affinity binding conformation appears blocked, as crystals of WT bound to DNA with guanine at position 8 could not be grown. In complexes containing K55A, the alanine side-chain is too far removed to engage in van

  9. Role of Directed van der Waals Bonded Interactions in the Determination of the Structures of Molecular Arsenate Solids

    SciTech Connect

    Gibbs, Gerald V.; Wallace, Adam F.; Cox, David F.; Dove, Patricia M; Downs, R. T.; Ross, Nancy L.; Rosso, Kevin M.

    2009-01-05

    Bond paths, local energy density properties, and Laplacian, L(r) = -2ρ(r), composite isosurfaces of the electron density distributions were calculated for the intramolecular and intermolecular bonded interactions for molecular solids of As2O3 and AsO2 composition, an As2O5 crystal, a number of arsenate molecules, and the arsenic metalloid, arsenolamprite. The directed intermolecular van der Waals As-O, O-O, and As-As bonded interactions are believed to serve as mainstays between the individual molecules in each of the molecular solids. As-O bond paths between the bonded atoms connect Lewis base charge concentrations and Lewis acid charge depletion domains, whereas the O-O and As-As paths connect Lewis base pair and Lewis acid pair domains, respectively, giving rise to sets of intermolecular directed bond paths. The alignment of the directed bond paths results in the periodic structures adopted by the arsenates. The arrangements of the As atoms in the claudetite polymorphs of As2O3 and the As atoms in arsenolamprite are similar. Like the As2O3 polymorphs, arsenolamprite is a molecular solid connected by relatively weak As-As intermolecular directed van der Waals bond paths between the layers of stronger As-As intramolecular bonded interactions. The bond critical point and local energy density properties of the intermolecular As-As bonded interactions in arsenolamprite are comparable with the As-As interactions in claudetite I. As such, the structure of claudetite I can be viewed as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure. The cubic structure adopted by the arsenolite polymorph can be understood in terms of sets of directed acid-base As-O and base-base O-O pair domains and bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face key

  10. Interaction mechanisms between organic UV filters and bovine serum albumin as determined by comprehensive spectroscopy exploration and molecular docking.

    PubMed

    Ao, Junjie; Gao, Li; Yuan, Tao; Jiang, Gaofeng

    2015-01-01

    Organic UV filters are a group of emerging PPCP (pharmaceuticals and personal care products) contaminants. Current information is insufficient to understand the in vivo processes and health risks of organic UV filters in humans. The interaction mechanism of UV filters with serum albumin provides critical information for the health risk assessment of these active ingredients in sunscreen products. This study investigates the interaction mechanisms of five commonly used UV filters (2-hydroxy-4-methoxybenzophenone, BP-3; 2-ethylhexyl 4-methoxycinnamate, EHMC; 4-methylbenzylidene camphor, 4-MBC; methoxydibenzoylmethane, BDM; homosalate, HMS) with bovine serum albumin (BSA) by spectroscopic measurements of fluorescence, circular dichroism (CD), competitive binding experiments and molecular docking. Our results indicated that the fluorescence of BSA was quenched by these UV filters through a static quenching mechanism. The values of the binding constant (Ka) ranged from (0.78±0.02)×10(3) to (1.29±0.01)×10(5) L mol(-1). Further exploration by synchronous fluorescence and CD showed that the conformation of BSA was demonstrably changed in the presence of these organic UV filters. It was confirmed that the UV filters can disrupt the α-helical stability of BSA. Moreover, the results of molecular docking revealed that the UV filter molecule is located in site II (sub-domain IIIA) of BSA, which was further confirmed by the results of competitive binding experiments. In addition, binding occurred mainly through hydrogen bonding and hydrophobic interaction. This study raises critical concerns regarding the transportation, distribution and toxicity effects of organic UV filters in human body.

  11. A major determinant for membrane protein interaction localizes to the carboxy-terminal domain of the mouse coronavirus nucleocapsid protein.

    PubMed

    Hurst, Kelley R; Kuo, Lili; Koetzner, Cheri A; Ye, Rong; Hsue, Bilan; Masters, Paul S

    2005-11-01

    The two major constituents of coronavirus virions are the membrane (M) and nucleocapsid (N) proteins. The M protein is anchored in the viral envelope by three transmembrane segments flanked by a short amino-terminal ectodomain and a large carboxy-terminal endodomain. The M endodomain interacts with the viral nucleocapsid, which consists of the positive-strand RNA genome helically encapsidated by N protein monomers. In previous work with the coronavirus mouse hepatitis virus (MHV), a highly defective M protein mutant, MDelta2, was constructed. This mutant contained a 2-amino-acid carboxy-terminal truncation of the M protein. Analysis of second-site revertants of MDelta2 revealed mutations in the carboxy-terminal region of the N protein that compensated for the defect in the M protein. To seek further genetic evidence corroborating this interaction, we generated a comprehensive set of clustered charged-to-alanine mutants in the carboxy-terminal domain 3 of N protein. One of these mutants, CCA4, had a highly defective phenotype similar to that of MDelta2. Transfer of the CCA4 mutation into a partially diploid MHV genome showed that CCA4 was a loss-of-function mutation rather than a dominant-negative mutation. Analysis of multiple second-site revertants of CCA4 revealed mutations in both the M protein and the N protein that could compensate for the original lesion in N. These data more precisely define the region of the N protein that interacts with the M protein. Further, we found that fusion of domain 3 of the N protein to the carboxy terminus of a heterologous protein caused it to be incorporated into MHV virions.

  12. 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

  13. Determining the mode of interaction of calf thymus DNA with the drug sumatriptan using voltammetric and spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Moghadam, Neda Hosseinpour

    2012-12-01

    The interaction of native calf thymus DNA with sumatriptan(1-[3-(2-dimethylaminoethyl)-1H-indol-5-yl]-N-methyl-methanesulfonamide) at physiological pH was studied by spectrophotometry, circular dichroism, voltammetry and viscosimetric techniques. Sumatriptan molecule intercalated between base pairs of DNA, showed by a sharp increase in specific viscosity of DNA. In cyclic voltammetry, decrease of the peak current and positive shift indicated that this drug is able to intercalate between the DNA base pairs. In addition, the drug induced changes in the CD spectrum of CT-DNA, as well as hypochromism changes in its UV-vis spectrum.

  14. Role of Structure and Entropy in Determining Differences in Dynamics for Glass Formers with Different Interaction Potentials

    NASA Astrophysics Data System (ADS)

    Banerjee, Atreyee; Sengupta, Shiladitya; Sastry, Srikanth; Bhattacharyya, Sarika Maitra

    2014-11-01

    We present a study of two model liquids with different interaction potentials, exhibiting similar structure but significantly different dynamics at low temperatures. By evaluating the configurational entropy, we show that the differences in the dynamics of these systems can be understood in terms of their thermodynamic differences. Analyzing their structure, we demonstrate that differences in pair correlation functions between the two systems, through their contribution to the entropy, dominate the differences in their dynamics, and indeed overestimate the differences. Including the contribution of higher order structural correlations to the entropy leads to smaller estimates for the relaxation times, as well as smaller differences between the two studied systems.

  15. FIT: Computer Program that Interactively Determines Polynomial Equations for Data which are a Function of Two Independent Variables

    NASA Technical Reports Server (NTRS)

    Arbuckle, P. D.; Sliwa, S. M.; Roy, M. L.; Tiffany, S. H.

    1985-01-01

    A computer program for interactively developing least-squares polynomial equations to fit user-supplied data is described. The program is characterized by the ability to compute the polynomial equations of a surface fit through data that are a function of two independent variables. The program utilizes the Langley Research Center graphics packages to display polynomial equation curves and data points, facilitating a qualitative evaluation of the effectiveness of the fit. An explanation of the fundamental principles and features of the program, as well as sample input and corresponding output, are included.

  16. 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.

  17. 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.

  18. Determination of pharmacological interactions of uliginosin B, a natural phloroglucinol derivative, with amitriptyline, clonidine and morphine by isobolographic analysis.

    PubMed

    Stolz, Eveline D; Müller, Liz G; Antonio, Camila B; da Costa, Paola F; von Poser, Gilsane L; Noël, François; Rates, Stela M K

    2014-10-15

    Uliginosin B is a natural phloroglucinol derivative, obtained from Hypericum species native to South America. Previous studies have shown that uliginosin B presents antidepressant-like and antinociceptive effects. Although its mechanism of action is still not completely elucidated, it is known that it involves the activation of monoaminergic neurotransmission. The aim of the current study was to further investigate the antinociceptive mechanism of action of uliginosin B by combining it with different drugs used for treating pain in clinical practice. The intraperitoneal administration of uliginosin B, morphine, amitriptyline and clonidine, alone or in mixture, produced a dose-dependent antinociceptive effect in the hot-plate assay in mice. The effect of the mixtures of drugs was studied using an adapted isobologram analysis at the effect level of 50% of the maximal effect observed. The analysis showed that the interactions between uliginosin B and morphine was synergistic, while the interactions between uliginosin B and amitriptyline or clonidine were additive. These findings point to uliginosin B as a potential adjuvant for pain pharmacotherapy, especially for opioid analgesia.

  19. Combining Steady-State and Dynamic Methods for Determining Absolute Signs of Hyperfine Interactions: Pulsed ENDOR Saturation and Recovery (PESTRE)

    PubMed Central

    Doan, Peter E.

    2010-01-01

    The underlying causes of asymmetric intensities in Davies pulsed ENDOR spectra that are associated with the signs of the hyperfine interaction are reinvestigated. The intensity variations in these asymmetric ENDOR patterns are best described as shifts in an apparent baseline intensity that occurs dynamically following on-resonance ENDOR transitions. We have developed an extremely straightforward multi-sequence protocol that is capable of giving the sign of the hyperfine interaction by probing a single ENDOR transition, without reference to its partner transition. This technique, Pulsed ENDOR Saturatation and Recovery (PESTRE) monitors dynamic shifts in the ‘baseline’ following measurements at a single RF frequency (single ENDOR peak), rather than observing anomalous ENDOR intensity differences between the two branches of an ENDOR response. These baseline shifts, referred to as dynamic reference levels (DRLs), can be directly tied to the electron spin manifold from which that ENDOR transition arises. The application of this protocol is demonstrated on 57Fe ENDOR of a 2Fe-2S ferredoxin. We use the 14N ENDOR transitions of the S = 3/2 [Fe(II)NO]2+ center of the non-heme iron enzyme, anthranilate dioxygenase (AntDO) to examine the details of the relaxation model using PESTRE. PMID:21075026

  20. 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.

  1. The Microphthalmia-Associated Transcription Factor Mitf Interacts with β-Catenin To Determine Target Gene Expression▿

    PubMed Central

    Schepsky, Alexander; Bruser, Katja; Gunnarsson, Gunnar J.; Goodall, Jane; Hallsson, Jón H.; Goding, Colin R.; Steingrimsson, Eirikur; Hecht, Andreas

    2006-01-01

    Commitment to the melanocyte lineage is characterized by the onset of expression of the microphthalmia-associated transcription factor (Mitf). This transcription factor plays a fundamental role in melanocyte development and maintenance and seems to be crucial for the survival of malignant melanocytes. Furthermore, Mitf has been shown to be involved in cell cycle regulation and to play important functions in self-renewal and maintenance of melanocyte stem cells. Although little is known about how Mitf regulates these various processes, one possibility is that Mitf interacts with other regulators. Here we show that Mitf can interact directly with β-catenin, the key mediator of the canonical Wnt signaling pathway. The Wnt signaling pathway plays a critical role in melanocyte development and is intimately involved in triggering melanocyte stem cell proliferation. Significantly, constitutive activation of this pathway is a feature of a number of cancers including malignant melanoma. Here we show that Mitf can redirect β-catenin transcriptional activity away from canonical Wnt signaling-regulated genes toward Mitf-specific target promoters to activate transcription. Thus, by a feedback mechanism, Mitf can diversify the output of canonical Wnt signaling to enhance the repertoire of genes regulated by β-catenin. Our results reveal a novel mechanism by which Wnt signaling and β-catenin activate gene expression, with significant implications for our understanding of both melanocyte development and melanoma. PMID:17000761

  2. 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...

  3. 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

  4. Interaction of maize zein with wheat gluten in composite dough and bread as determined by confocal laser scanning microscopy.

    PubMed

    Bugusu, Betry A; Rajwa, Bartlomiej; Hamaker, Bruce R

    2002-01-01

    Protein body-free maize zein, when mixed at 35 degrees C (above its glass transition temperature range), significantly (p < 0.01) improved the rheological and leavening properties of sorghum-wheat composite flour dough, resulting in improved loaf volume. Confocal laser scanning microscopy was used to observe the structure of zein fibrils and the interaction between zein and gluten proteins in the composite dough and bread systems. Autofluorescence and immunolocalization techniques were used to locate gluten and zein, respectively. Optical sections were collected every 0.4 microm through the samples and digitally processed to produce reconstructed three-dimensional images. Results showed that zein fibrils form an outer layer that intermittently coats the gluten networks, thereby strengthening them. This type of microstructure is able to withstand the pressure exerted by gas cell expansion during yeast fermentation to increase loaf volume.

  5. The interaction of two groups of murine genes determines the persistence of Theiler's virus in the central nervous system.

    PubMed Central

    Bureau, J F; Montagutelli, X; Lefebvre, S; Guénet, J L; Pla, M; Brahic, M

    1992-01-01

    Theiler's murine encephalomyelitis virus is responsible for a chronic inflammatory demyelinating disease of the central nervous system of the mouse. The disease is associated with persistent viral infection of the spinal cord. Some strains of mice are susceptible to viral infection, and other strains are resistant. The effect of the genetic background of the host on viral persistence has not been thoroughly investigated. We studied the amount of viral RNA in the spinal cords of 17 inbred strains of mice and their F1 crosses with the SJL/J strain and observed a large degree of variability among strains. The pattern of viral persistence among mouse strains could be explained by the interaction of two loci. One locus is localized in the H-2D region of the major histocompatibility complex, whereas the other locus is outside this complex and is not linked to the Tcrb locus on chromosome 6. Images PMID:1378508

  6. The interaction of two groups of murine genes determines the persistence of Theiler's virus in the central nervous system.

    PubMed

    Bureau, J F; Montagutelli, X; Lefebvre, S; Guénet, J L; Pla, M; Brahic, M

    1992-08-01

    Theiler's murine encephalomyelitis virus is responsible for a chronic inflammatory demyelinating disease of the central nervous system of the mouse. The disease is associated with persistent viral infection of the spinal cord. Some strains of mice are susceptible to viral infection, and other strains are resistant. The effect of the genetic background of the host on viral persistence has not been thoroughly investigated. We studied the amount of viral RNA in the spinal cords of 17 inbred strains of mice and their F1 crosses with the SJL/J strain and observed a large degree of variability among strains. The pattern of viral persistence among mouse strains could be explained by the interaction of two loci. One locus is localized in the H-2D region of the major histocompatibility complex, whereas the other locus is outside this complex and is not linked to the Tcrb locus on chromosome 6.

  7. The importance of charge-transfer interactions in determining chromophoric dissolved organic matter (CDOM) optical and photochemical properties.

    PubMed

    Sharpless, Charles M; Blough, Neil V

    2014-04-01

    Absorption of sunlight by chromophoric dissolved natural organic matter (CDOM) is environmentally significant because it controls photic zone depth and causes photochemistry that affects elemental cycling and contaminant fate. Both the optics (absorbance and fluorescence) and photochemistry of CDOM display unusual properties that cannot easily be ascribed to a superposition of individual chromophores. These include (i) broad, unstructured absorbance that decreases monotonically well into the visible and near IR, (ii) fluorescence emission spectra that all fall into a single envelope regardless of the excitation wavelength, and (iii) photobleaching and photochemical quantum yields that decrease monotonically with increasing wavelength. In contrast to a simple superposition model, these phenomena and others can be reasonably well explained by a physical model in which charge-transfer interactions between electron donating and accepting chromophores within the CDOM control the optical and photophysical properties. This review summarizes current understanding of the processes underlying CDOM photophysics and photochemistry as well as their physical basis.

  8. Chlamydial virulence determinants in atherogenesis: the role of chlamydial lipopolysaccharide and heat shock protein 60 in macrophage-lipoprotein interactions.

    PubMed

    Kalayoglu, M V; Indrawati; Morrison, R P; Morrison, S G; Yuan, Y; Byrne, G I

    2000-06-01

    Data from a spectrum of epidemiologic, pathologic, and animal model studies show that Chlamydia pneumoniae infection is associated with coronary artery disease, but it is not clear how the organism may initiate or promote atherosclerosis. It is postulated that C. pneumoniae triggers key atherogenic events through specific virulence determinants. C. pneumoniae induces mononuclear phagocyte foam cell formation by chlamydial lipopolysaccharide (cLPS) and low-density lipoprotein oxidation by chlamydial hsp60 (chsp60). Thus, different chlamydial components may promote distinct events implicated in the development of atherosclerosis. Data implicating cLPS and chsp60 in the pathogenesis of atherosclerosis are discussed and novel approaches are presented for attempting to elucidate how these putative virulence determinants signal mononuclear phagocytes to modulate lipoprotein influx and modification.

  9. 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

  10. CO2 and vitamin B12 interactions determine bioactive trace metal requirements of a subarctic Pacific diatom

    PubMed Central

    King, Andrew L; Sañudo-Wilhelmy, Sergio A; Leblanc, Karine; Hutchins, David A; Fu, Feixue

    2011-01-01

    Phytoplankton growth can be limited by numerous inorganic nutrients and organic growth factors. Using the subarctic diatom Attheya sp. in culture studies, we examined how the availability of vitamin B12 and carbon dioxide partial pressure (pCO2) influences growth rate, primary productivity, cellular iron (Fe), cobalt (Co), zinc (Zn) and cadmium (Cd) quotas, and the net use efficiencies (NUEs) of these bioactive trace metals (mol C fixed per mol cellular trace metal per day). Under B12-replete conditions, cells grown at high pCO2 had lower Fe, Zn and Cd quotas, and used those trace metals more efficiently in comparison with cells grown at low pCO2. At high pCO2, B12-limited cells had ∼50% lower specific growth and carbon fixation rates, and used Fe ∼15-fold less efficiently, and Zn and Cd ∼3-fold less efficiently, in comparison with B12-replete cells. The observed higher Fe, Zn and Cd NUE under high pCO2/B12-replete conditions are consistent with predicted downregulation of carbon-concentrating mechanisms. Co quotas of B12-replete cells were ∼5- to 14-fold higher in comparison with B12-limited cells, suggesting that >80% of cellular Co of B12-limited cells was likely from B12. Our results demonstrate that CO2 and vitamin B12 interactively influence growth, carbon fixation, trace metal requirements and trace metal NUE of this diatom. This suggests the need to consider complex feedback interactions between multiple environmental factors for this biogeochemically critical group of phytoplankton in the last glacial maximum as well as the current and future changing ocean. PMID:21248860

  11. Structural determinants of Rab and Rab Escort Protein interaction: Rab family motifs define a conserved binding surface.

    PubMed

    Pereira-Leal, José B; Strom, Molly; Godfrey, Richard F; Seabra, Miguel C

    2003-01-31

    Rab proteins are a large family of monomeric GTPases with 60 members identified in the human genome. Rab GTPases require an isoprenyl modification to their C-terminus for membrane association and function in the regulation of vesicular trafficking pathways. This reaction is catalysed by Rab geranylgeranyl transferase, which recognises as protein substrate any given Rab in a 1:1 complex with Rab Escort Protein (REP). REP is therefore able to bind many distinct Rab proteins but the molecular basis for this activity is still unclear. We recently identified conserved motifs in Rabs termed RabF motifs, which we proposed to mediate a conserved mode of interaction between Rabs and REPs. Here, we tested this hypothesis. We first used REP1 as a bait in the yeast two-hybrid system and isolated strictly full-length Rabs, suggesting that REP recognises multiple regions within and properly folded Rabs. We introduced point mutations in Rab3a as a model Rab and assessed the ability of the mutants to interact with REP using the yeast two-hybrid system and an in vitro prenylation assay. We identified several residues that affect REP:Rab binding in the RabF1, RabF3, and RabF4 regions (which include parts of the switch I and II regions), but not other RabF regions. These results support the hypothesis that Rabs bind REP via conserved RabF motifs and provide a molecular explanation for the preferential recognition of the GDP-bound conformation of Rab by REP. PMID:12535645

  12. NMR determines transient structure and dynamics in the disordered C-terminal domain of WASp interacting protein.

    PubMed

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

    2013-07-16

    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 WIP(C), 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 WIP(C) and the high occurrence (25%) of proline residues, we employed 5D-NMR(13)C-detected NMR experiments with nonuniform sampling to accomplish full resonance assignment. Secondary chemical-shift analysis, (15)N 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 (13)C-detected approach allows chemical-shift assignment in the WIP(C) 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 WIP(C). Thus, we conclude that the disordered WIP(C) fragment is comprised of regions with latent structure connected by flexible loops, an architecture with implications for binding affinity and function.

  13. Understanding the interaction determinants of CAPN1 inhibition by CAST4 from bovines using molecular modeling techniques.

    PubMed

    Chai, Han-Ha; Lim, Dajeong; Jung, Eunkyoung; Choi, Bong-Hwan; Cho, Yong-Min

    2014-01-01

    HCV-induced CAPN activation and its effects on virus-infected cells in a host-immune system have been studied recently. It has been shown that the HCV-nonstructural 5A protein acts as both an inducer and a substrate for host CAPN protease; it participates in suppressing the TNF-α-induced apoptosis response and downstream IFN-induced antiviral processes. However, little is known regarding the disturbance of antiviral responses generated by bovine CAPN activation by BVDV, which is a surrogate model of HCV and is one of the most destructive diseases leading to great economic losses in cattle herds worldwide. This is also thought to be associated with the effects of either small CAPN inhibitors or the natural inhibitor CAST. They mainly bind to the binding site of CAPN substrate proteins and competitively inhibit the binding of the enzyme substrates to possibly defend against the two viruses (HCV and BVDV) for anti-viral immunity. To devise a new stratagem to discover lead candidates for an anti-BVDV drug, we first attempted to understand the bovine CAPN-CAST interaction sites and the interaction constraints of local binding architectures, were well reflected in the geometry between the pharmacophore features and its shape constraints identified using our modeled bovine CAPN1/CAST4 complex structures. We propose a computer-aided molecular design of an anti-BVDV drug as a mimetic CAST inhibitor to develop a rule-based screening function for adjusting the puzzle of relationship between bovine CAPN1 and the BVDV nonstructural proteins from all of the data obtained in the study. PMID:25215589

  14. Molecular Determinants for Targeting Heterochromatin Protein 1-Mediated Gene Silencing: Direct Chromoshadow Domain–KAP-1 Corepressor Interaction Is Essential

    PubMed Central

    Lechner, Mark S.; Begg, Gillian E.; Speicher, David W.; Rauscher, Frank J.

    2000-01-01

    The KRAB domain is a highly conserved transcription repression module commonly found in eukaryotic zinc finger proteins. KRAB-mediated repression requires binding to the KAP-1 corepressor, which in turn recruits members of the heterochromatin protein 1 (HP1) family. The HP1 proteins are nonhistone chromosomal proteins, although it is unclear how they are targeted to unique chromosomal domains or promoters. In this report, we have reconstituted and characterized the HP1–KAP-1 interaction using purified proteins and have compared KAP-1 to three other known HP1 binding proteins: SP100, lamin B receptor (LBR), and the p150 subunit from chromatin assembly factor (CAF-1 p150). We show that the chromoshadow domain (CSD) of HP1 is a potent repression domain that binds directly to all four previously described proteins. For KAP-1, we have mapped the CSD interaction region to a 15-amino-acid segment, termed the HP1BD, which is also present in CAF-1 p150 but not SP100 or LBR. The region of KAP-1 harboring the HP1BD binds as a monomer to a dimer of the CSD, as revealed by gel filtration, analytical ultracentrifugation, and optical biosensor analyses. The use of a spectrum of amino acid substitutions in the human HP1α CSD revealed a strong correlation between CSD-mediated repression and binding to KAP-1, CAF-1 p150, and SP100 but not LBR. Differences among the HP1 binding partners could also be discerned by fusion to a heterologous DNA binding domain and by the potential to act as dominant negative molecules. Together, these results strongly suggest that KAP-1 is a physiologically relevant target for HP1 function. PMID:10938122

  15. Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii.

    PubMed

    Moens, Frédéric; Weckx, Stefan; De Vuyst, Luc

    2016-08-16

    Prebiotic inulin-type fructans (ITF) display a bifidogenic and butyrogenic effect. Four bifidobacterial strains (Bifidobacterium breve Yakult, Bifidobacterium adolescentis LMG 10734, Bifidobacterium angulatum LMG 11039(T), and Bifidobacterium longum subsp. longum LMG 11047), displaying different ITF degradation capacities, were each grown in cocultivation with Faecalibacterium prausnitzii DSM 17677(T), an ITF-degrading butyrate-producing colon bacterium, as to unravel their cross-feeding interactions. These coculture fermentations were performed in a medium for colon bacteria, whether or not including acetate (necessary for the growth of F. prausnitzii DSM 17677(T) and whether or not provided through cross-feeding), supplemented with oligofructose or inulin as the sole energy source. Bifidobacterium breve Yakult did not degrade oligofructose, resulting in the production of high concentrations of butyrate by F. prausnitzii DSM 17677(T) through oligofructose degradation. The degradation of oligofructose by B. adolescentis LMG 10734 and of oligofructose and inulin by B. angulatum LMG 11039(T) and B. longum LMG 11047 resulted in the production of acetate, which was cross-fed to F. prausnitzii DSM 17677(T), enabling the latter strain to degrade oligofructose and inulin. Slow preferential degradation of the short chain length fractions of oligofructose (intracellularly) by B. adolescentis LMG 10734 enabled substantial oligofructose degradation by F. prausnitzii DSM 17677(T). However, fast non-preferential degradation of all chain length fractions of oligofructose (extracellularly) and efficient degradation of the short chain length fractions of inulin by B. angulatum LMG 11039(T) and B. longum LMG 11047 made it impossible for F. prausnitzii DSM 17677(T) to compete for the available substrate. These results indicate that cross-feeding interactions between bifidobacteria and acetate-depending, butyrate-producing colon bacteria can be either a pure commensal or beneficial

  16. Three principles for determining the relevancy of store-and-forward and live interactive telemedicine: reinterpreting two telemedicine research reviews and other research.

    PubMed

    Locatis, Craig; Ackerman, Michael

    2013-01-01

    The Agency for Healthcare Research and Quality sponsored two telemedicine research reviews. The latest review concluded that telemedicine is most relevant to specialties, such as psychiatry and neurology, where high levels of patient interaction are crucial to assessment. Telemedicine research studies cited in the reviews having positive findings in the specialties of ophthalmology, otolaryngology, obstetrics and gynecology, gastroenterology, and cardiology and more recent research in these areas are reviewed to identify criteria other than degree of interaction for determining the appropriateness of telemedicine interventions. These criteria include congruity or the extent that procedures used in telemedicine are similar to those of in-person examination, fidelity or the degree to which the information used for assessment in remote examinations is of similar quality to that used in-person, and reliability or the consistency with which information can be gathered and transmitted.

  17. Three principles for determining the relevancy of store-and-forward and live interactive telemedicine: reinterpreting two telemedicine research reviews and other research.

    PubMed

    Locatis, Craig; Ackerman, Michael

    2013-01-01

    The Agency for Healthcare Research and Quality sponsored two telemedicine research reviews. The latest review concluded that telemedicine is most relevant to specialties, such as psychiatry and neurology, where high levels of patient interaction are crucial to assessment. Telemedicine research studies cited in the reviews having positive findings in the specialties of ophthalmology, otolaryngology, obstetrics and gynecology, gastroenterology, and cardiology and more recent research in these areas are reviewed to identify criteria other than degree of interaction for determining the appropriateness of telemedicine interventions. These criteria include congruity or the extent that procedures used in telemedicine are similar to those of in-person examination, fidelity or the degree to which the information used for assessment in remote examinations is of similar quality to that used in-person, and reliability or the consistency with which information can be gathered and transmitted. PMID:23186085

  18. 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.

  19. 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.

  20. 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

  1. Determination of ligand-MurB interactions by isothermal denaturation: application as a secondary assay to complement high throughput screening.

    PubMed

    Sarver, Ronald W; Rogers, Joseph M; Epps, Dennis E

    2002-02-01

    We used a temperature-jump isothermal denaturation procedure with various methods of detection to evaluate the quality of putative inhibitors of MurB discovered by high-throughput screening. Three optical methods of detection-ultraviolet hyperchromicity of absorbance, fluorescence of bound dyes, and circular dichroism-as well as differential scanning calorimetry were used to dissect the effects of two chemical compounds and a natural substrate on the enzyme. The kinetics of the denaturation process and binding of the compounds detected by quenching of flavin fluorescence were used to quantitate the dose dependencies of the ligand effects. We found that the first step in the denaturation of MurB is the rapid loss of flavin from the active site and that the two chemical inhibitors appeared to destabilize the interaction of the cofactor with the enzyme but stabilize the global unfolding. The kinetics of the denaturation process as well as the loss of flavin fluorescence on binding established that both compounds had nanomolar affinities for the enzyme. We showed that coupling of the various detection methods with isothermal denaturation yields a powerful regimen to provide analytical data for assessing inhibitor specificity for a protein target. PMID:11897052

  2. Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions.

    PubMed

    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

    2016-06-15

    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

  3. 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

    2016-06-01

    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.

  4. Epistatic interactions between Tgfb1 and genetic loci, Tgfbm2 and Tgfbm3, determine susceptibility to an asthmatic stimulus.

    PubMed

    Freimuth, Julia; Clermont, Frederic F; Huang, Xiaozhu; DeSapio, Angela; Tokuyasu, Taku A; Sheppard, Dean; Akhurst, Rosemary J

    2012-10-30

    TGFβ activation and signaling have been extensively studied in experimental models of allergen-induced asthma as potential therapeutic targets during chronic or acute phases of the disease. Outcomes of experimental manipulation of TGFβ activity have been variable, in part due to use of different model systems. Using an ovalbumin (OVA)-induced mouse model of asthma, we here show that innate variation within TGFβ1 genetic modifier loci, Tgfbm2 and Tgfbm3, alters disease susceptibility. Specifically, Tgfbm2(129) and Tgfbm3(C57) synergize to reverse accentuated airway hyperresponsiveness (AHR) caused by low TGFβ1 levels in Tgfb1(+/-) mice of the NIH/OlaHsd strain. Moreover, epistatic interaction between Tgfbm2(129) and Tgfbm3(C57) uncouples the inflammatory response to ovalbumin from those of airway remodeling and airway hyperresponsiveness, illustrating independent genetic control of these responses. We conclude that differential inheritance of genetic variants of Tgfbm genes alters biological responses to reduced TGFβ1 signaling in an experimental asthma model. TGFβ antagonists for treatment of lung diseases might therefore give diverse outcomes, dependent on genetic variation. PMID:23064636

  5. Determination of creatinine, uric and ascorbic acid in bovine milk and orange juice by hydrophilic interaction HPLC.

    PubMed

    Zuo, Ruiting; Zhou, Si; Zuo, Yuegang; Deng, Yiwei

    2015-09-01

    Creatinine (Cr), uric (UA) and ascorbic acid (AA) are common constituents in human fluids. Their abnormal concentrations in human fluids are associated with various diseases. Thus, apart from the endogenous formation in human body, it is also important to examine their sources from food products. In this study, a rapid and accurate HILIC method was developed for simultaneous determination of Cr, UA and AA in bovine milk and orange juice. Milk samples were pretreated by protein precipitation, centrifugation and filtration, followed by HPLC separation and quantification using a Waters Spherisorb S5NH2 column. The developed method has been successfully applied to determine the concentration of UA, AA and Cr in milk and fruit juice samples. The milk samples tested were found to contain UA and creatinine in the concentration range of 24.1-86.0 and 5.07-11.2 μg mL(-1), respectively. The orange juices contain AA over 212 μg mL(-1).

  6. 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.

  7. Determinants of Human Immunodeficiency Virus Type 1 Baseline Susceptibility to the Fusion Inhibitors Enfuvirtide and T-649 Reside outside the Peptide Interaction Site

    PubMed Central

    Heil, Marintha L.; Decker, Julie M.; Sfakianos, Jeffrey N.; Shaw, George M.; Hunter, Eric; Derdeyn, Cynthia A.

    2004-01-01

    The peptide fusion inhibitor (PFI) enfuvirtide is the first of a new class of entry inhibitors to receive FDA approval. We previously determined the susceptibility of 55 PFI-naïve-patient isolates to enfuvirtide and a second peptide inhibitor, T-649. Seven of the 55 viral isolates were insusceptible to enfuvirtide, T-649, or both inhibitors in the absence of prior exposure. To determine the molecular basis of the insusceptible phenotypes, we PCR amplified and cloned five PFI-insusceptible and one PFI-susceptible, full-length, biologically functional env genes and characterized viruses pseudotyped with the Env proteins in a single-round drug sensitivity assay. Overall, the mean 50% inhibitory concentrations of enfuvirtide and T-649 for the PFI-insusceptible Env pseudotypes were 1.4 to 1.7 log10 and 1.2 to 1.8 log10 greater, respectively, than those for a PFI-susceptible lab strain, NLHX; however, all of the PFI-insusceptible Env proteins conserved the sequence of a critical enfuvirtide interaction site (residues 36 to 38 of gp41, GIV) in HR-1. In contrast, multiple amino acid changes were observed C-terminal to HR-1, many of which were located in regions of HR-2 corresponding to the PFI. Nevertheless, peptides based on patient-derived HR-2 sequences were not more potent inhibitors than enfuvirtide or T-649, arguing that the basis of PFI susceptibility is not a higher-affinity, competitive HR-1/HR-2 interaction. These results demonstrate that regions of Env outside the enfuvirtide interaction site can significantly impact the PFI susceptibility of patient-derived Env, even prior to drug exposure. We hypothesize that both gp120 gene- and gp41 gene-encoded determinants that minimize the window of opportunity for PFI to bind provide a growth advantage and possibly a predisposition to resistance to this new class of drugs in vivo. PMID:15220433

  8. Structural determinants of interaction, trafficking and function in the ClC-2/MLC1 subunit GlialCAM involved in leukodystrophy

    PubMed Central

    Capdevila-Nortes, Xavier; Jeworutzki, Elena; Elorza-Vidal, Xabier; Barrallo-Gimeno, Alejandro; Pusch, Michael; Estévez, Raúl

    2015-01-01

    Abstract Mutations in the genes encoding the astrocytic protein MLC1, the cell adhesion molecule GlialCAM or the Cl− channel ClC-2 underlie human leukodystrophies. GlialCAM binds to itself, to MLC1 and to ClC-2, and directs these proteins to cell–cell contacts. In addition, GlialCAM dramatically activates ClC-2 mediated currents. In the present study, we used mutagenesis studies combined with functional and biochemical analyses to determine which parts of GlialCAM are required to perform these cellular functions. We found that the extracellular domain of GlialCAM is necessary for cell junction targeting and for mediating interactions with itself or with MLC1 and ClC-2. The C-terminus is also necessary for proper targeting to cell–cell junctions but is not required for the biochemical interaction. Finally, we identified the first three amino acids of the transmembrane segment of GlialCAM as being essential for the activation of ClC-2 currents but not for targeting or biochemical interaction. Our results provide new mechanistic insights concerning the regulation of the cell biology and function of MLC1 and ClC-2 by GlialCAM. Key points The extracellular domain of GlialCAM is necessary for its targeting to cell junctions, as well as for interactions with itself and MLC1 and ClC-2. The C-terminus of GlialCAM is not necessary for interaction but is required for targeting to cell junctions. The first three residues of the transmembrane segment of GlialCAM are required for GlialCAM-mediated ClC-2 activation. PMID:26033718

  9. Sequence determination of a new parrot bornavirus-5 strain in Japan: implications of clade-specific sequence diversity in the regions interacting with host factors.

    PubMed

    Komorizono, Ryo; Makino, Akiko; Horie, Masayuki; Honda, Tomoyuki; Tomonaga, Keizo

    2016-06-01

    In this study, the genome sequence of a new parrot bornavirus-5 (PaBV-5) detected in Eclectus roratus was determined. Phylogenetic analysis showed that the genus Bornavirus is divided into three major clades and that PaBV-5 belongs to clade 2, which contains avian viruses that exhibit infectivity to mammalian cells. Sequence comparisons of the regions known to interact with host factors indicated that the clade 2 avian viruses possess sequences intermediate between the clade 1 mammalian viruses and the clade 3 avian viruses, suggesting that the identified regions might contribute to the differences in virological properties between the three clades. PMID:27166599

  10. Theoretical determination of spin Hamiltonians with isotropic and anisotropic magnetic interactions in transition metal and lanthanide complexes.

    PubMed

    Maurice, Rémi; Graaf, Coen de; Guihéry, Nathalie

    2013-11-21

    The determination of anisotropic magnetic parameters is a task of both experimental and theoretical interest. The added value of theoretical calculations can be crucial for analyzing experimental data by (i) allowing assessment of the validity of the phenomenological spin Hamiltonians, (ii) allowing discussion of the values of parameters extracted from experiments, and (iii) proposing rationalizations and magneto-structural correlations to better understand the relations between geometry, electronic structure, and properties. In this review, we discuss the model Hamiltonians that are used to describe magnetic properties, the computational approaches that can be used to compute magnetic parameters, and review their applications to transition metal and (to a lesser extent) lanthanide based complexes. Perspectives concerning current methodological challenges will then be presented, and finally the need for further joint experimental/theoretical efforts will be underlined.

  11. Side-chain interactions in the regulatory domain of human glutamate dehydrogenase determine basal activity and regulation.

    PubMed

    Mastorodemos, Vasileios; Kanavouras, Konstantinos; Sundaram, Shobana; Providaki, Maria; Petraki, Zoe; Kokkinidis, Michael; Zaganas, Ioannis; Logothetis, Diomedes E; Plaitakis, Andreas

    2015-04-01

    Glutamate Dehydrogenase (GDH) is central to the metabolism of glutamate, a major excitatory transmitter in mammalian central nervous system (CNS). hGDH1 is activated by ADP and L-leucine and powerfully inhibited by GTP. Besides this housekeeping hGDH1, duplication led to an hGDH2 isoform that is expressed in the human brain dissociating its function from GTP control. The novel enzyme has reduced basal activity (4-6% of capacity) while remaining remarkably responsive to ADP/L-leucine activation. While the molecular basis of this evolutionary adaptation remains unclear, substitution of Ser for Arg443 in hGDH1 is shown to diminish basal activity (< 2% of capacity) and abrogate L-leucine activation. To explore whether the Arg443Ser mutation disrupts hydrogen bonding between Arg443 and Ser409 of adjacent monomers in the regulatory domain ('antenna'), we replaced Ser409 by Arg or Asp in hGDH1. The Ser409Arg-1 change essentially replicated the Arg443Ser-1 mutation effects. Molecular dynamics simulation predicted that Ser409 and Arg443 of neighboring monomers come in close proximity in the open conformation and that introduction of Ser443-1 or Arg409-1 causes them to separate with the swap mutation (Arg409/Ser443) reinstating their proximity. A swapped Ser409Arg/Arg443Ser-1 mutant protein, obtained in recombinant form, regained most of the wild-type hGDH1 properties. Also, when Ser443 was replaced by Arg443 in hGDH2 (as occurs in hGDH1), the Ser443Arg-2 mutant acquired most of the hGDH1 properties. Hence, side-chain interactions between 409 and 443 positions in the 'antenna' region of hGDHs are crucial for basal catalytic activity, allosteric regulation, and relative resistance to thermal inactivation. PMID:25620628

  12. 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

  13. Development of hyperbranched polymers with non-covalent interactions for extraction and determination of aflatoxins in cereal samples.

    PubMed

    Liu, Xiaoyan; Li, Huihui; Xu, Zhigang; Peng, Jialin; Zhu, Shuqiang; Zhang, Haixia

    2013-10-01

    A novel approach for assembling homogeneous hyperbranched polymers based on non-covalent interactions with aflatoxins was developed; the polymers were used to evaluate the extraction of aflatoxins B1, B2, G1 and G2 (AFB1, AFB2, AFG1 and AFG2) in simulant solutions. The results showed that the extraction efficiencies of three kinds of synthesized polymers for the investigated analytes were not statistically different; as a consequence, one of the representative polymers (polymer I) was used as the solid-phase extraction (SPE) sorbent to evaluate the influences of various parameters, such as desorption conditions, pH, ionic strength, concentration of methanol in sample solutions, and the mass of the sorbent on the extraction efficiency. In addition, the extraction efficiencies for these aflatoxins were compared between the investigated polymer and the traditional sorbent C18. The results showed that the investigated polymer had superior extraction efficiencies. Subsequently, the proposed polymer for the SPE packing material was employed to enrich and analyze four aflatoxins in the cereal powder samples. The limits of detection (LODs) at a signal-to-noise (S/N) ratio of 3 were in the range of 0.012-0.120 ng g(-1) for four aflatoxins, and the limits of quantification (LOQs) calculated at S/N=10 were from 0.04 to 0.40 ng g(-1) for four aflatoxins. The recoveries of four aflatoxins from cereal powder samples were in the range of 82.7-103% with relative standard deviations (RSDs) lower than 10%. The results demonstrate the suitability of the SPE approach for the analysis of trace aflatoxins in cereal powder samples.

  14. 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.

  15. 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

    2014-02-01

    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.

  16. 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. PMID:26851087

  17. 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

  18. 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.

  19. In Vitro Interaction between Alginate Lyase and Amphotericin B against Aspergillus fumigatus Biofilm Determined by Different Methods

    PubMed Central

    Bugli, Francesca; Posteraro, Brunella; Papi, Massimiliano; Torelli, Riccardo; Maiorana, Alessandro; Paroni Sterbini, Francesco; Posteraro, Patrizia; De Spirito, Marco

    2013-01-01

    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

  20. Virulence determinants in enteroaggregative Escherichia coli from North India and their interaction in in vitro organ culture system.

    PubMed

    Gupta, Deepika; Sharma, Monica; Sarkar, Subendu; Thapa, B R; Chakraborti, Anuradha

    2016-09-01

    Enteroaggregative Escherichia coli (EAEC) is an important diarrhoeal pathogen causing diseases in multiple epidemiological and clinical settings. In developing countries like India, diarrhoeal diseases are one of the major killers among paediatric population and oddly, few studies are available from Indian paediatric population on the variability of EAEC virulence genes. In this study, we examined the distribution of plasmid and chromosomal-encoded virulence determinants in EAEC isolates, and analysed cytokines response generated against EAEC with specific aggregative adherence fimbriae (AAF) type in duodenal biopsies using in vitro organ culture (IVOC) mimicking in vivo conditions. Different virulence marker combinations among strains were reflected as a function of specific adhesins signifying EAEC heterogeneity. fis gene emerged as an important genetic marker apart from aggA and aap Further, EAEC infection in IVOC showed upregulation of IL-8, IL-1β, IL-6, TNF-α and TLR-5 expression. EAEC with AAFII induced significant TLR-5 and IL-8 response, conceivably owing to more pathogenicity markers. This study sheds light on the pattern of EAEC pathotypes prevalent in North Indian paediatric population and highlights the presence of unique virulence combinations in pathogenic strains. Thus, evident diversity in EAEC virulence and multifaceted bacteria-host crosstalk can provide useful insights for the strategic management of diarrhoeal diseases in India, where diarrhoeal outbreaks are more frequent. PMID:27493010

  1. Optimization of o-phtaldialdehyde/2-mercaptoethanol postcolumn reaction for the hydrophilic interaction liquid chromatography determination of memantine utilizing a silica hydride stationary phase.

    PubMed

    Douša, Michal; Pivoňková, Veronika; Sýkora, David

    2016-08-01

    A rapid procedure for the determination of memantine based on hydrophilic interaction chromatography with fluorescence detection was developed. Fluorescence detection after postcolumn derivatization with o-phtaldialdehyde/2-mercaptoethanol was performed at excitation and emission wavelengths of 345 and 450 nm, respectively. The postcolumn reaction conditions such as reaction temperature, derivatization reagent flow rate, and reagents concentration were studied due to steric hindrance of amino group of memantine. The derivatization reaction was applied for the hydrophilic interaction liquid chromatography method which was based on Cogent Silica-C stationary phase with a mobile phase consisting of a mixture of 10 mmol/L citric acid and 10 mmol/L o-phosphoric acid (pH 6.0) with acetonitrile using an isocratic composition of 2:8 v/v. The benefit of the reported approach consists in a simple sample pretreatment and a quick and sensitive hydrophilic interaction chromatography method. The developed method was validated in terms of linearity, accuracy, precision, and selectivity according to the International Conference on Harmonisation guidelines. The developed method was successfully applied for the analysis of commercial memantine tablets.

  2. Identification of a Skp1-Like Protein Interacting with SFB, the Pollen S Determinant of the Gametophytic Self-Incompatibility in Prunus1[W

    PubMed Central

    Matsumoto, Daiki; Yamane, Hisayo; Abe, Kazuyuki; Tao, Ryutaro

    2012-01-01

    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 SCFSLF 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. PMID:22548785

  3. 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. PMID:22548785

  4. 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.

  5. 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.

  6. 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

  7. Competing Lipid-Protein and Protein-Protein Interactions Determine Clustering and Gating Patterns in the Potassium Channel from Streptomyces lividans (KcsA).

    PubMed

    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

    2015-10-16

    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 Trp(67)-Glu(71)-Asp(80) inactivation triad within the channel structure and its bearing on the selectivity filter.

  8. 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

  9. The interactions between plant life form and fungal traits of arbuscular mycorrhizal fungi determine the symbiotic community.

    PubMed

    López-García, Álvaro; Azcón-Aguilar, Concepción; Barea, José M

    2014-12-01

    Arbuscular mycorrhizal (AM) fungi have traditionally been considered generalist symbionts. However, an increasing number of studies are pointing out the selectivity potential of plant hosts. Plant life form, determined by plant life history traits, seems to drive the AM fungal community composition. The AM fungi also exhibit a wide diversity of functional traits known to be responsible for their distribution in natural ecosystems. However, little is known about the role of plant and fungal traits driving the resultant symbiotic assemblages. With the aim of testing the feedback relationship between plant and fungal traits on the resulting AM fungal community, we inoculated three different plant life forms, i.e. annual herbs, perennial herbs and perennial semi-woody plants, with AM fungal communities sampled in different seasons. We hypothesized that the annual climate variation will induce changes in the mean traits of the AM fungal communities present in the soil throughout the year. Furthermore, the association of plants with different life forms with AM fungi with contrasting life history traits will show certain preferences according to reciprocal traits of the plants and fungi. We found changes in the AM fungal community throughout the year, which were differentially disrupted by disturbance and altered by plant growth form and plant biomass. Both plant and fungal traits clearly contributed to the resultant AM fungal communities. The revealed process can have implications for the functioning of ecosystems since changes in dominant plant life forms or climatic variables could influence the traits of AM fungal communities in soil and hence ecosystem processes.

  10. 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

  11. Non-linear interactions between consumers and flow determine the probability of plant community dominance on Maine rocky shores.

    PubMed

    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

  12. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots.

    PubMed

    Wang, Yan; Yao, Huili; Cheng, Yuan; Lovell, Scott; Battaile, Kevin P; Midaugh, C Russell; Rivera, Mario

    2015-10-13

    Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe−2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the Pseudomonas aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe−2S] cluster of each Bfd immediately above a heme group in BfrB [Yao, H., et al. (2012) J. Am. Chem. Soc., 134, 13470−13481]. We report here study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance and isothermal titration calorimetry as well as determining the binding energy hot spots at the protein−protein interaction interface. The results show that the 12 Bfd-binding sites on BfrB are equivalent and independent and that the protein−protein association at each of these sites is driven entropically and is characterized by a dissociation constant (Kd) of approximately 3 μM. Determination of the binding energy hot spots was carried out by replacing certain residues that comprise the protein−protein interface with alanine and by evaluating the effect of the mutation on Kd and on the efficiency of core iron mobilization from BfrB. The results identified hot spot residues in both proteins [LB 68, EA 81, and EA 85 in BfrB (superscript for residue number and subscript for chain) and Y2 and L5 in Bfd] that network at the interface to produce a highly complementary hot region for the interaction. The hot spot residues are conserved in the amino acid sequences of Bfr and Bfd proteins from a number of Gram-negative pathogens, indicating that the BfrB:Bfd interaction is of widespread significance in bacterial iron metabolism.

  13. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein–Protein Interaction in Solution and Determination of Binding Energy Hot Spots

    PubMed Central

    2015-01-01

    Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe–2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the Pseudomonas aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe–2S] cluster of each Bfd immediately above a heme group in BfrB [Yao, H., et al. (2012) J. Am. Chem. Soc., 134, 13470–13481]. We report here a study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance and isothermal titration calorimetry as well as determining the binding energy hot spots at the protein–protein interaction interface. The results show that the 12 Bfd-binding sites on BfrB are equivalent and independent and that the protein–protein association at each of these sites is driven entropically and is characterized by a dissociation constant (Kd) of approximately 3 μM. Determination of the binding energy hot spots was carried out by replacing certain residues that comprise the protein–protein interface with alanine and by evaluating the effect of the mutation on Kd and on the efficiency of core iron mobilization from BfrB. The results identified hot spot residues in both proteins [LB68, EA81, and EA85 in BfrB (superscript for residue number and subscript for chain) and Y2 and L5 in Bfd] that network at the interface to produce a highly complementary hot region for the interaction. The hot spot residues are conserved in the amino acid sequences of Bfr and Bfd proteins from a number of Gram-negative pathogens, indicating that the BfrB:Bfd interaction is of widespread significance in bacterial iron metabolism. PMID:26368531

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

    PubMed

    Sundlov, Jesse A; Gulick, Andrew M

    2013-08-01

    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.

  15. The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering.

    PubMed

    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 microg ml(-1) for herring sperm DNA (hsDNA), 0.02-10.0 microg ml(-1) for calf thymus DNA (ctDNA), 0.02-20.0 microg 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 x 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. PMID:14670501

  16. Loose Plant Architecture1 (LPA1) determines lamina joint bending by suppressing auxin signalling that interacts with C-22-hydroxylated and 6-deoxo brassinosteroids in rice

    PubMed Central

    Liu, Jing Miao; Park, Soon Ju; Huang, Jin; Lee, Eun Jin; Xuan, Yuan Hu; Je, Byoung Il; Kumar, Vikranth; Priatama, Ryza A.; Raj K, Vimal; Kim, Sung Hoon; Min, Myung Ki; Cho, Jun Hyeon; Kim, Tae Ho; Chandran, Anil Kumar Nalini; Jung, Ki Hong; Takatsuto, Suguru; Fujioka, Shozo; Han, Chang-deok

    2016-01-01

    Lamina inclination is a key agronomical character that determines plant architecture and is sensitive to auxin and brassinosteroids (BRs). Loose Plant Architecture1 (LPA1) in rice (Oryza sativa) and its Arabidopsis homologues (SGR5/AtIDD15) have been reported to control plant architecture and auxin homeostasis. This study explores the role of LPA1 in determining lamina inclination in rice. LPA1 acts as a positive regulator to suppress lamina bending. Genetic and biochemical data indicate that LPA1 suppresses the auxin signalling that interacts with C-22-hydroxylated and 6-deoxo BRs, which regulates lamina inclination independently of OsBRI1. Mutant lpa1 plants are hypersensitive to indole-3-acetic acid (IAA) during the lamina inclination response, which is suppressed by the brassinazole (Brz) inhibitor of C-22 hydroxylase involved in BR synthesis. A strong synergic effect is detected between lpa1 and d2 (the defective mutant for catalysis of C-23-hydroxylated BRs) during IAA-mediated lamina inclination. No significant interaction between LPA1 and OsBRI1 was identified. The lpa1 mutant is sensitive to C-22-hydroxylated and 6-deoxo BRs in the d61-1 (rice BRI1 mutant) background. We present evidence verifying that two independent pathways function via either BRs or BRI1 to determine IAA-mediated lamina inclination in rice. RNA sequencing analysis and qRT-PCR indicate that LPA1 influences the expression of three OsPIN genes (OsPIN1a, OsPIN1c and OsPIN3a), which suggests that auxin flux might be an important factor in LPA1-mediated lamina inclination in rice. PMID:26826218

  17. Loose Plant Architecture1 (LPA1) determines lamina joint bending by suppressing auxin signalling that interacts with C-22-hydroxylated and 6-deoxo brassinosteroids in rice.

    PubMed

    Liu, Jing Miao; Park, Soon Ju; Huang, Jin; Lee, Eun Jin; Xuan, Yuan Hu; Je, Byoung Il; Kumar, Vikranth; Priatama, Ryza A; Raj K, Vimal; Kim, Sung Hoon; Min, Myung Ki; Cho, Jun Hyeon; Kim, Tae Ho; Chandran, Anil Kumar Nalini; Jung, Ki Hong; Takatsuto, Suguru; Fujioka, Shozo; Han, Chang-Deok

    2016-03-01

    Lamina inclination is a key agronomical character that determines plant architecture and is sensitive to auxin and brassinosteroids (BRs). Loose Plant Architecture1 (LPA1) in rice (Oryza sativa) and its Arabidopsis homologues (SGR5/AtIDD15) have been reported to control plant architecture and auxin homeostasis. This study explores the role of LPA1 in determining lamina inclination in rice. LPA1 acts as a positive regulator to suppress lamina bending. Genetic and biochemical data indicate that LPA1 suppresses the auxin signalling that interacts with C-22-hydroxylated and 6-deoxo BRs, which regulates lamina inclination independently of OsBRI1. Mutant lpa1 plants are hypersensitive to indole-3-acetic acid (IAA) during the lamina inclination response, which is suppressed by the brassinazole (Brz) inhibitor of C-22 hydroxylase involved in BR synthesis. A strong synergic effect is detected between lpa1 and d2 (the defective mutant for catalysis of C-23-hydroxylated BRs) during IAA-mediated lamina inclination. No significant interaction between LPA1 and OsBRI1 was identified. The lpa1 mutant is sensitive to C-22-hydroxylated and 6-deoxo BRs in the d61-1 (rice BRI1 mutant) background. We present evidence verifying that two independent pathways function via either BRs or BRI1 to determine IAA-mediated lamina inclination in rice. RNA sequencing analysis and qRT-PCR indicate that LPA1 influences the expression of three OsPIN genes (OsPIN1a, OsPIN1c and OsPIN3a), which suggests that auxin flux might be an important factor in LPA1-mediated lamina inclination in rice.

  18. Structural Determinants of the Interaction between the TpsA and TpsB Proteins in the Haemophilus influenzae HMW1 Two-Partner Secretion System

    PubMed Central

    Grass, Susan; Rempe, Katherine A.

    2015-01-01

    ABSTRACT The two-partner secretion (TPS) pathway in Gram-negative bacteria consists of a TpsA exoprotein and a cognate TpsB outer membrane pore-forming translocator protein. Previous work has demonstrated that the TpsA protein contains an N-terminal TPS domain that plays an important role in targeting the TpsB protein and is required for secretion. The nontypeable Haemophilus influenzae HMW1 and HMW2 adhesins are homologous proteins that are prototype TpsA proteins and are secreted by the HMW1B and HMW2B TpsB proteins. In the present study, we sought to define the structural determinants of HMW1 interaction with HMW1B during the transport process and while anchored to the bacterial surface. Modeling of HMW1B revealed an N-terminal periplasmic region that contains two polypeptide transport-associated (POTRA) domains and a C-terminal membrane-localized region that forms a pore. Biochemical studies demonstrated that HMW1 engages HMW1B via interaction between the HMW1 TPS domain and the HMW1B periplasmic region, specifically, the predicted POTRA1 and POTRA2 domains. Subsequently, HMW1 is shuttled to the HMW1B pore, facilitated by the N-terminal region, the middle region, and the NPNG motif in the HMW1 TPS domain. Additional analysis revealed that the interaction between HMW1 and HMW1B is highly specific and is dependent upon the POTRA domains and the pore-forming domain of HMW1B. Further studies established that tethering of HMW1 to the surface-exposed region of HMW1B is dependent upon the external loops of HMW1B formed by residues 267 to 283 and residues 324 to 330. These observations may have broad relevance to proteins secreted by the TPS pathway. IMPORTANCE Secretion of HMW1 involves a recognition event between the extended form of the HMW1 propiece and the HMW1B POTRA domains. Our results identify specific interactions between the HMW1 propiece and the periplasmic HMW1B POTRA domains. The results also suggest that the process of HMW1 translocation involves at

  19. Ab initio determination of spin Hamiltonians with anisotropic exchange interactions: The case of the pyrochlore ferromagnet Lu2V2O7

    NASA Astrophysics Data System (ADS)

    Riedl, Kira; Guterding, Daniel; Jeschke, Harald O.; Gingras, Michel J. P.; Valentí, Roser

    2016-07-01

    We present a general framework for deriving effective spin Hamiltonians of correlated magnetic systems based on a combination of relativistic ab initio density functional theory calculations, exact diagonalization of a generalized Hubbard Hamiltonian on finite clusters, and spin projections onto the low-energy subspace. A key motivation is to determine anisotropic bilinear exchange couplings in materials of interest. As an example, we apply this method to the pyrochlore Lu2V2O7 where the vanadium ions form a lattice of corner-sharing spin-1/2 tetrahedra. In this compound, anisotropic Dzyaloshinskii-Moriya interactions (DMIs) play an essential role in inducing a magnon Hall effect. We obtain quantitative estimates of the nearest-neighbor Heisenberg exchange, the DMI, and the symmetric part of the anisotropic exchange tensor. Finally, we compare our results with experimental ones on the Lu2V2O7 compound.

  20. 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. PMID:27283702

  1. Structure determination of human Fas apoptosis inhibitory molecule and identification of the critical residues linking the interdomain interaction to the anti-apoptotic activity.

    PubMed

    Li, Guoming; Qu, Linglong; Ma, Shuaipeng; Wu, Yujie; Jin, Changwen; Zheng, Xiaofeng

    2014-07-01

    Fas apoptosis inhibitory molecule (FAIM) is a highly conserved anti-apoptotic protein which plays important roles in cells. There are two isoforms of FAIM, of which the short isoform FAIM-S is broadly expressed in all tissues, whereas the long isoform FAIM-L is exclusively expressed in the nervous system. No structure of human FAIM has been reported to date and the detailed molecular mechanisms underlying the anti-apoptotic function of FAIM remain unknown. Here, the crystal structure of the human FAIM-S N-terminal domain (NTD) and the NMR solution structure of the human FAIM-S C-terminal domain (CTD) were determined. The structures revealed that the NTD and CTD adopt a similar protein fold containing eight antiparallel β-strands which form two sheets. Both structural and biochemical analyses implied that the NTD exists as a dimer and the CTD as a monomer and that they can interact with each other. Several critical residues were identified to be involved in this interaction. Moreover, mutations of these critical residues also interfered in the anti-apoptotic activity of FAIM-S. Thus, the structural and functional data presented here will provide insight into the anti-apoptotic mechanism of FAIM-S.

  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. 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

  4. [Determination of the interaction kinetics between meloxicam and β-cyclodextrin using the quantitative high-performance affinity chromatography coupled with mass spectrometry].

    PubMed

    Wang, Cai-fen; Li, Zhuo; Wang, Xiao-bo; Li, Hai-yan; Zhang, Ji-wen; Sun, Li-xin

    2015-09-01

    The association rate constant and dissociation rate constant are important parameters of the drug-cyclodextrin supermolecule systems, which determine the dissociation of drugs from the complex and the further in vivo absorption of drugs. However, the current studies of drug-cyclodextrin interactions mostly focus on the thermodynamic parameter of equilibrium constants (K). In this paper, a method based on quantitative high performance affinity chromatography coupled with mass spectrometry was developed to determine the apparent dissociation rate constant (k(off,app)) of drug-cyclodextrin supermolecule systems. This method was employed to measure the k(off,app) of meloxicam and acetaminophen. Firstly, chromatographic peaks of drugs and non-retained solute (uracil) on β-cyclodextrin column at different flow rates were acquired, and the retention time and variance values were obtained via the fitting the peaks. Then, the plate heights of drugs (H(R)) and uracil (H(M,C)) were calculated. The plate height of theoretical non-retained solute (H(M,T)) was calculated based on the differences of diffusion coefficient and the stagnant mobile phase mass transfer between drugs and uracil. Finally, the k(off,app) was calculated from the slope of the regression equation between (H(R)-H(M,T)) and uk/(1+k)2, (0.13 ± 0.00) s(-1) and (4.83 ± 0.10) s(-1) for meloxicam and acetaminophen (control drug), respectively. In addition, the apparent association rate constant (k(on,app)) was also calculated through the product of K (12.53 L x mol(-1)) and k(off,app). In summary, it has been proved that the method established in our study was simple, efficiently fast and reproducible for investigation on the kinetics of drug-cyclodextrin interactions. PMID:26757555

  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

    2013-01-01

    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. Spectrofluorimetric study on the inclusion interaction between vitamin K 3 with p-( p-sulfonated benzeneazo)calix[6]arene and determination of VK 3

    NASA Astrophysics Data System (ADS)

    Zhou, Yunyou; Xu, Hongwei; Wu, Lian; Liu, Chun; Lu, Qin; Wang, Lun

    2008-11-01

    The characteristics of host-guest complexation between p-( p-sulfonated benzeneazo) calix[6]arene (SBC6A) and vitamin K 3 (VK 3) were investigated by fluorescence spectrometry. A 1:1 stoichiometry for the complexation was established and was verified by Job's plot. An association constant of 4.95 × 10 3 L mol -1 at 20 °C was calculated by applying a deduced equation. The interaction mechanism of the inclusion complex was discussed. It was found that the fluorescence of SBC6A could be remarkably quenched by an appropriate amount of VK 3 especially when non-ionic surfactant Triton X-100 existed. According to the obtained results, a novel sensitive spectrofluorimetric method for the determination of VK 3 based on supramolecular complex was developed with a linear range of 5.0 × 10 -7-3.0 × 10 -5 mol L -1 and a detection limit of 2.0 × 10 -7 mol L -1. The proposed method was used to determine VK 3 in commercial preparations with satisfactory results.

  7. Fabrication of an electrochemical sensor based on carbon nanotubes modified with gold nanoparticles for determination of valrubicin as a chemotherapy drug: valrubicin-DNA interaction.

    PubMed

    Hajian, R; Mehrayin, Z; Mohagheghian, M; Zafari, M; Hosseini, P; Shams, N

    2015-04-01

    In this study, an electrochemical sensor was fabricated based on gold nanoparticles/ ethylenediamine/ multi-wall carbon-nanotubes modified gold electrode (AuNPs/en/MWCNTs/AuE) for determination of valrubicin in biological samples. Valrubicin was effectively accumulated on the surface of AuNPs/en/MWCNTs/AuE and produced a pair of redox peaks at around 0.662 and 0.578V (vs. Ag/AgCl) in citrate buffer (pH4.0). The electrochemical parameters including pH, buffer, ionic strength, scan rate and size of AuNPs have been optimized. There was a good linear correlation between cathodic peak current and concentration of valrubicin in the range of 0.5 to 80.0μmolL(-1) with the detection limit of 0.018μmolL(-1) in citrate buffer (pH4.0) and 0.1molL(-1) KCl. Finally, the constructed sensor was successfully applied for determination of valrubicin in human urine and blood serum. In further studies, the different sequences of single stranded DNA probes have been immobilized on the surface of AuNPs decorated on MWCNTs to study the interaction of oligonucleotides with valrubicin.

  8. Determination of polar pesticides in olive oil and olives by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry and high resolution mass spectrometry.

    PubMed

    Nortes-Méndez, Rocío; Robles-Molina, José; López-Blanco, Rafael; Vass, Andrea; Molina-Díaz, Antonio; Garcia-Reyes, Juan F

    2016-09-01

    This article reports the development of two HPLC-MS methods for the determination of polar pesticides in olive oil and olive samples by hydrophilic interaction liquid chromatography (HILIC) separation followed by mass spectrometry detection with tandem mass spectrometry using a triple quadrupole instrument operated in multiple reaction monitoring mode (HILIC-MS/MS) or electrospray time-of-flight mass spectrometry (HILIC-TOFMS). The selected polar pesticides included in the study were: amitrol, cyromazine, diquat, paraquat, mepiquat, trimethylsulfonium (trimesium, glyphosate counterion) and fosetyl aluminium. The simple sample treatment procedure was based on liquid partitioning with methanol. The performance of the sample extraction was evaluated in terms of recovery rates and matrix effects in both olive oil and olives matrices. The results obtained for olive oil were satisfactory while, due to the high complexity of olives, poor recovery rates were obtained for the extraction of diquat, paraquat and amitrol, although with a reasonable precision enabling its use in routine analysis. Similarly, matrix effects were minor in the case of olive oil (ca. 20% suppression average), while significantly higher suppression was observed for olives (30-50% suppression average). The studied approaches were found to be useful for the determination of the pesticides studied in olive oil and olives with limits of quantitation below 5µgkg(-1) in most cases when tandem mass spectrometry was used, thus being in compliance with MRLs set by current EU regulation.

  9. 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.

  10. 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.

  11. Determination of polar pesticides in olive oil and olives by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry and high resolution mass spectrometry.

    PubMed

    Nortes-Méndez, Rocío; Robles-Molina, José; López-Blanco, Rafael; Vass, Andrea; Molina-Díaz, Antonio; Garcia-Reyes, Juan F

    2016-09-01

    This article reports the development of two HPLC-MS methods for the determination of polar pesticides in olive oil and olive samples by hydrophilic interaction liquid chromatography (HILIC) separation followed by mass spectrometry detection with tandem mass spectrometry using a triple quadrupole instrument operated in multiple reaction monitoring mode (HILIC-MS/MS) or electrospray time-of-flight mass spectrometry (HILIC-TOFMS). The selected polar pesticides included in the study were: amitrol, cyromazine, diquat, paraquat, mepiquat, trimethylsulfonium (trimesium, glyphosate counterion) and fosetyl aluminium. The simple sample treatment procedure was based on liquid partitioning with methanol. The performance of the sample extraction was evaluated in terms of recovery rates and matrix effects in both olive oil and olives matrices. The results obtained for olive oil were satisfactory while, due to the high complexity of olives, poor recovery rates were obtained for the extraction of diquat, paraquat and amitrol, although with a reasonable precision enabling its use in routine analysis. Similarly, matrix effects were minor in the case of olive oil (ca. 20% suppression average), while significantly higher suppression was observed for olives (30-50% suppression average). The studied approaches were found to be useful for the determination of the pesticides studied in olive oil and olives with limits of quantitation below 5µgkg(-1) in most cases when tandem mass spectrometry was used, thus being in compliance with MRLs set by current EU regulation. PMID:27343599

  12. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms

    PubMed Central

    van Opijnen, Tim; Lazinski, David W.; Camilli, Andrew

    2015-01-01

    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 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. PMID:25641100

  13. 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. PMID:27240760

  14. 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. PMID:27473511

  15. 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. PMID:27085018

  16. 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

  17. 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.

  18. 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. PMID:27272319

  19. Endoplasmic reticulum protein quality control is determined by cooperative interactions between Hsp/c70 protein and the CHIP E3 ligase.

    PubMed

    Matsumura, Yoshihiro; Sakai, Juro; Skach, William R

    2013-10-25

    The C terminus of Hsp70 interacting protein (CHIP) E3 ligase functions as a key regulator of protein quality control by binding the C-terminal (M/I)EEVD peptide motif of Hsp/c70(90) with its N-terminal tetratricopeptide repeat (TPR) domain and facilitating polyubiquitination of misfolded client proteins via its C-terminal catalytic U-box. Using CFTR as a model client, we recently showed that the duration of the Hsc70-client binding cycle is a primary determinant of stability. However, molecular features that control CHIP recruitment to Hsp/c70, and hence the fate of the Hsp/c70 client, remain unknown. To understand how CHIP recognizes Hsp/c70, we utilized a dominant negative mutant in which loss of a conserved proline in the U-box domain (P269A) eliminates E3 ligase activity. In a cell-free reconstituted ER-associated degradation system, P269A CHIP inhibited Hsc70-dependent CFTR ubiquitination and degradation in a dose-dependent manner. Optimal inhibition required both the TPR and the U-box, indicating cooperativity between the two domains. Neither the wild type nor the P269A mutant changed the extent of Hsc70 association with CFTR nor the dissociation rate of the Hsc70-CFTR complex. However, the U-box mutation stimulated CHIP binding to Hsc70 while promoting CHIP oligomerization. CHIP binding to Hsc70 binding was also stimulated by the presence of an Hsc70 client with a preference for the ADP-bound state. Thus, the Hsp/c70 (M/I)EEVD motif is not a simple anchor for the TPR domain. Rather CHIP recruitment involves reciprocal allosteric interactions between its TPR and U-box domains and the substrate-binding and C-terminal domains of Hsp/c70.

  20. 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

  1. Pulsed electron spin nutation spectroscopy of weakly exchange-coupled biradicals: a general theoretical approach and determination of the spin dipolar interaction.

    PubMed

    Ayabe, Kazuki; Sato, Kazunobu; Nishida, Shinsuke; Ise, Tomoaki; Nakazawa, Shigeaki; Sugisaki, Kenji; Morita, Yasushi; Toyota, Kazuo; Shiomi, Daisuke; Kitagawa, Masahiro; Takui, Takeji

    2012-07-01

    Weakly exchange-coupled biradicals have attracted much attention in terms of their DNP application in NMR spectroscopy for biological systems or the use of synthetic electron-spin qubits. Pulse-ESR based electron spin nutation (ESN) spectroscopy applied to biradicals is generally treated as transition moment spectroscopy from the theoretical side, illustrating that it is a powerful and facile tool to determine relatively short distances between weakly exchange-coupled electron spins. The nutation frequency as a function of the microwave irradiation strength ω(1) (angular frequency) for any cases of weakly exchange-coupled systems can be classified into three categories; D(12) (spin dipolar interaction)-driven, Δg-driven and ω(1)-driven nutation behaviour with the increasing strength of ω(1). For hetero-spin biradicals, Δg effects can be a dominating characteristic in the biradical nutation spectroscopy. Two-dimensional pulse-based electron spin nutation (2D-ESN) spectroscopy operating at the X-band can afford to determine small values of D(12) in weakly exchange-coupled biradicals in rigid glasses. The analytical expressions derived here for ω(1)-dependent nutation frequencies are based on only four electronic spin states relevant to the biradicals, while real biradical systems often have sizable hyperfine interactions. Thus, we have evaluated nuclear hyperfine effects on the nutation frequencies to check the validity of the present theoretical treatment. The experimental spin dipolar coupling of a typical TEMPO-based biradical 1, (2,2,6,6-tetra[((2)H(3))methyl]-[3,3-(2)H(2),4-(2)H(1),5,5-(2)H(2)]piperidin-N-oxyl-4-yl)(2,2,6,6-tetra[((2)H(3))methyl]-[3,3-(2)H(2),4-(2)H(1),5,5-(2)H(2),(15)N]piperidin-(15)N-oxyl-4-yl) terephthalate in a toluene glass, with a distance of 1.69 nm between the two spin sites is D(12) = -32 MHz (the effect of the exchange coupling J(12) is vanishing due to the homo-spin sites of 1, i.e.Δg = 0), while 0 < |J(12)|≦ 1.0 MHz as

  2. The motion of Hurricane-like vortices determined by multi-scale interactions between the mesoscale vortex flow and its large-scale environment: a theoretical model

    NASA Astrophysics Data System (ADS)

    Päschke, E.; Klein, R.

    2009-04-01

    Research in recent years have shown that multi-scale processes play a nontrivial role in tropical cyclone development, motion and structure. For example, important multi-scale processes that determine these vortex features arise from interactions between the vortex flow itself, its environmental flow, the Coriolis force due to the earth's rotation and diabatic effects as a consequence of moisture conversion processes occuring in convective cloud systems. Concerning the vortex motion it is well known that the large-scale environmental flow acts as a steering flow. Beta-gyres arising from interactions between the vortex flow and the earth's vorticity field contribute to a deviation of the storm track from the steering flow. Interactions between mesoscale vortices and small scale convective systems are assumed to be responsible for the tendency of tropical cyclones to meander about a mean path, which can be seen in long-range observations based on modern satellite techniques. The structure and intensity changes of tropical cyclones strongly depend from both diabatic effects and the environmental flow. For instance, it is observed that an unfavourable condition for a hurricane to develop or survive is given by a strong vertical shear in the environmental flow. One common explanation for this is that the dispersion of heat as a consequence of disruption of organized pattern of convection by strong winds aloft is responsible for a weakening or limiting of the development of mature storms. We present a threedimensional model to describe the motion and structure of Hurricane strength H1/H2 vortices. From a theoretical point of view this model gives deeper insight how the mesoscale structure of the vortex itself affects the synoptic scale vortex motion and vice versa, while taking the influence of a vertically sheared environmental flow and diabatic effects due to moisture conversion processes into account. The derivation of the model equations is based on matched

  3. Quantitative pharmacological analyses of the interaction between flumazenil and midazolam in monkeys discriminating midazolam: Determination of the functional half life of flumazenil.

    PubMed

    Zanettini, Claudio; France, Charles P; Gerak, Lisa R

    2014-01-15

    The duration of action of a drug is commonly estimated using plasma concentration, which is not always practical to obtain or an accurate estimate of functional half life. For example, flumazenil is used clinically to reverse the effects of benzodiazepines like midazolam; however, its elimination can be altered by other drugs, including some benzodiazepines, thereby altering its half life. This study used Schild analyses to characterize antagonism of midazolam by flumazenil and determine the functional half life of flumazenil. Four monkeys discriminated 0.178mg/kg midazolam while responding under a fixed-ratio 10 schedule of stimulus-shock termination; flumazenil was given at various times before determination of a midazolam dose-effect curve. There was a time-related decrease in the magnitude of shift of the midazolam dose-effect curve as the interval between flumazenil and midazolam increased. The potency of flumazenil, estimated by apparent pA2 values (95% CI), was 7.30 (7.12, 7.49), 7.17 (7.03, 7.31), 6.91 (6.72, 7.10) and 6.80 (6.67, 6.92) at 15, 30, 60 and 120min after flumazenil administration, respectively. The functional half life of flumazenil, derived from potency estimates, was 57±13min. Thus, increasing the interval between flumazenil and midazolam causes orderly decreases in flumazenil potency; however, across a broad range of conditions, the qualitative nature of the interaction does not change, as indicated by slopes of Schild plots at all time points that are not different from unity. Differences in potency of flumazenil are therefore due to elimination of flumazenil and not due to pharmacodynamic changes over time.

  4. 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. PMID:26948581

  5. 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.

  6. A new hydrophilic interaction liquid chromatographic (HILIC) procedure for the simultaneous determination of pseudoephedrine hydrochloride (PSH), diphenhydramine hydrochloride (DPH) and dextromethorphan hydrobromide (DXH) in cough-cold formulations.

    PubMed

    Ali, Mohammed Shahid; Ghori, Mohsin; Rafiuddin, Syed; Khatri, Aamer Roshanali

    2007-01-01

    A new HILIC method has been developed for the simultaneous determination of pseudoephedrine hydrochloride (PSH), diphenhydramine hydrochloride (DPH) and dextromethorphan hydrobromide (DXH) in cough-cold syrup. Mobile phase consists of methanol:water (containing 6.0 g of ammonium acetate and 10 mL of triethylamine per liter, pH adjusted to 5.2 with orthophosphoric acid), 95:5 (v/v). Column containing porous silica particles (Supelcosil LC-Si, 25 cm x 4.6 mm, 5 microm) is used as stationary phase. Detection is carried out using a variable wavelength UV-vis detector at 254 nm for PSH and DPH, and at 280 nm for DXH. Solutions are injected into the chromatograph under isocratic condition at constant flow rate of 1.2 mL/min. Linearity range and percent recoveries for PSH, DPH and DXH were 150-600, 62.5-250, 75-300 microg/mL and 100.7%, 100.1% and 100.8%, respectively. Method is stability indicating and excipients like saccharin sodium, sodium citrate, flavour and sodium benzoate did not interfere in the analysis. Compounds elute in order of increasing ionization degree caused by cation-exchange mechanism in a run time of less than 15 min. Mobile phase pH is manipulated to regulate ionization and ion-exchange interaction and thereby retention of compounds. PMID:16887317

  7. Validation of a Stability-Indicating Hydrophilic Interaction Liquid Chromatographic Method for the Quantitative Determination of Vitamin K3 (Menadione Sodium Bisulfite) in Injectable Solution Formulation

    PubMed Central

    Ghanem, Mashhour M.; Abu-Lafi, Saleh A.; Hallak, Hussein O.

    2013-01-01

    A simple, specific, accurate, and stability-indicating method was developed and validated for the quantitative determination of menadione sodium bisulfite in the injectable solution formulation. The method is based on zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) coupled with a photodiode array detector. The desired separation was achieved on the ZIC-HILIC column (250 mm × 4.6 mm, 5 μm) at 25°C temperature. The optimized mobile phase consisted of an isocratic solvent mixture of 200mM ammonium acetate (NH4AC) solution and acetonitrile (ACN) (20:80; v/v) pH-adjusted to 5.7 by glacial acetic acid. The mobile phase was fixed at 0.5 ml/min and the analytes were monitored at 261 nm using a photodiode array detector. The effects of the chromatographic conditions on the peak retention, peak USP tailing factor, and column efficiency were systematically optimized. Forced degradation experiments were carried out by exposing menadione sodium bisulfite standard and the injectable solution formulation to thermal, photolytic, oxidative, and acid-base hydrolytic stress conditions. The degradation products were well-resolved from the main peak and the excipients, thus proving that the method is a reliable, stability-indicating tool. The method was validated as per ICH and USP guidelines (USP34/NF29) and found to be adequate for the routine quantitative estimation of menadione sodium bisulfite in commercially available menadione sodium bisulfite injectable solution dosage forms. PMID:24106670

  8. 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.

  9. Optical properties and London dispersion interaction of amorphous and crystalline SiO2 determined by vacuum ultraviolet spectroscopy and spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Tan, G. L.; Lemon, M. F.; Jones, D. J.; French, R. H.

    2005-11-01

    two layers of c-SiO2 or a-SiO2 separated by an interlayer film have been determined, using full spectral methods, from the interband transition strength. The London dispersion interaction is appreciably larger in c-SiO2 than a-SiO2 due to the increased physical density, index of refraction, transition strengths, and oscillator strengths in quartz.

  10. The effect of drought and interspecific interactions on depth of water uptake in deep- and shallow-rooting grassland species as determined by δ18O natural abundance

    NASA Astrophysics Data System (ADS)

    Hoekstra, N. J.; Finn, J. A.; Hofer, D.; Lüscher, A.

    2014-08-01

    . pratense decrease under drought conditions. In line with hypothesis (2), in monoculture, the PCWU0-10 of shallow-rooting species L. perenne and T. repens was 0.53 averaged over the two drought treatments, compared to 0.16 for the deep-rooting C. intybus. Surprisingly, in monoculture, water uptake by T. pratense was shallower than for the shallow-rooting species (PCWU0-10 = 0.68). Interspecific interactions in mixtures resulted in a shift in the depth of water uptake by the different species. As hypothesised, the shallow-rooting species L. perenne and T. repens tended to become shallower, and the deep-rooting T. pratense made a dramatic shift to deeper soil layers (reduction in PCWU0-10 of 58% on average) in mixture compared to monoculture. However, these shifts did not result in a reduction in the proportional similarity of the proportional water uptake from different soil depth intervals (niche overlap) in mixtures compared to monocultures. There was no clear link between interspecific differences in depth of water uptake and the reduction of biomass production under drought compared to control conditions (drought resistance). Cichorium intybus, the species with water uptake from the deepest soil layers was one of the species most affected by drought. Interestingly, T. pratense, which was least affected by drought, also had the greatest plasticity in depth of water uptake. This suggests that there may be an indirect effect of rooting depth on drought resistance, as it determines the potential plasticity in the depth of water uptake.

  11. 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

  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

    2016-08-01

    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. PMID:26782293

  13. Determination of glycine in biofluid by hydrophilic interaction chromatography coupled with tandem mass spectrometry and its application to the quantification of glycine released by embryonal carcinoma stem cells.

    PubMed

    Tang, Ya-Bin; Teng, Lin; Sun, Fan; Wang, Xiao-Lin; Peng, Liang; Cui, Yong-Yao; Hu, Jin-Jia; Luan, Xin; Zhu, Liang; Chen, Hong-Zhuan

    2012-09-15

    Because glycine plays a prominent role in living creatures, an accurate and precise quantitative analysis method for the compound is needed. Herein, a new approach to analyze glycine by hydrophilic interaction chromatography (HILIC) coupled with electrospray ionization tandem mass spectrometry (ESI-MS/MS) was developed. This method avoids the use of derivatization and/or ion-pairing reagents. N-methyl-D-aspartate (NMDA) is used as the internal standard (IS). The mobile phase for the isocratic elution consisted of 10 mM ammonium formate in acetonitrile-water (70:30, v/v, adjusted to pH 2.8 with formic acid), and a flow rate of 250 μL/min was used. Two microliters of sample was injected for analysis. The signal was monitored in the positive multiple reaction monitoring (MRM) mode. The total run time was 5 min. The dynamic range was 40-2000 ng/mL for glycine in the biological matrix. The LLOQ (lower limit of quantification) of this method was 40 ng/mL (80 pg on column). The validated method was applied to determine the dynamic release of glycine from P19 embryonal carcinoma stem cells (ECSCs). Glycine spontaneously released from the ECSCs into the intercellular space gradually increased from 331.02±60.36 ng/mL at 2 min in the beginning to 963.52±283.80 ng/mL at 60 min and 948.27±235.09 ng/mL at 120 min, finally reaching a plateau, indicating that ECSCs consecutively release glycine until achieving equilibration between the release and the reuptake of the compound; on the contrary, the negative control NIH/3T3 embryonic fibroblast cells did not release glycine. This finding will help to improve our understanding of the novel effects of neurotransmitters, including glycine, on non-neural systems. PMID:22906796

  14. 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

  15. Interactions between Copper-binding Sites Determine the Redox Status and Conformation of the Regulatory N-terminal Domain of ATP7B*

    PubMed Central

    LeShane, Erik S.; Shinde, Ujwal; Walker, Joel M.; Barry, Amanda N.; Blackburn, Ninian J.; Ralle, Martina; Lutsenko, Svetlana

    2010-01-01

    Copper-transporting ATPase ATP7B is essential for human copper homeostasis and normal liver function. ATP7B has six N-terminal metal-binding domains (MBDs) that sense cytosolic copper levels and regulate ATP7B. The mechanism of copper sensing and signal integration from multiple MBDs is poorly understood. We show that MBDs communicate and that this communication determines the oxidation state and conformation of the entire N-terminal domain of ATP7B (N-ATP7B). Mutations of copper-coordinating Cys to Ala in any MBD (2, 3, 4, or 6) change the N-ATP7B conformation and have distinct functional consequences. Mutating MBD2 or MBD3 causes Cys oxidation in other MBDs and loss of copper binding. In contrast, mutation of MBD4 and MBD6 does not alter the redox status and function of other sites. Our results suggest that MBD2 and MBD3 work together to regulate access to other metal-binding sites, whereas MBD4 and MBD6 receive copper independently, downstream of MBD2 and MBD3. Unlike Ala substitutions, the Cys-to-Ser mutation in MBD2 preserves the conformation and reduced state of N-ATP7B, suggesting that hydrogen bonds contribute to interdomain communications. Tight coupling between MBDs suggests a mechanism by which small changes in individual sites (induced by copper binding or mutation) result in stabilization of distinct conformations of the entire N-ATP7B and altered exposure of sites for interactions with regulatory proteins. PMID:20032459

  16. 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.

  17. 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. PMID:26747690

  18. 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

    2016-08-01

    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.

  19. 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…

  20. "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…

  1. Membrane interactions in nerve myelin. I. Determination of surface charge from effects of pH and ionic strength on period.

    PubMed Central

    Inouye, H.; Kirschner, D. A.

    1988-01-01

    We have used x-ray diffraction to study the interactions between myelin membranes in the sciatic nerve (PNS) and optic nerve (CNS) as a function of pH (2-10) and ionic strength (0-0.18). The period of myelin was found to change in a systematic manner with pH and ionic strength. PNS periods ranged from 165 to 250 A or more, while CNS periods ranged from 150 to 230 A. The native periods were observed only near physiological ionic strength at neutral or alkaline pH. The smallest periods were observed in the pH range 2.5-4 for PNS myelin and pH 2.5-5 for CNS myelin. The minimum period was also observed for PNS myelin after prolonged incubation in distilled water. At pH 4, within these acidic pH ranges, myelin period increased slightly with ionic strength; however, above these ranges, the period increased with pH and decreased with ionic strength. Electron density profiles calculated at different pH and ionic strength showed that the major structural alteration underlying the changes in period was in the width of the aqueous space at the extracellular apposition of membranes; the width of the cytoplasmic space was virtually constant. Assuming that the equilibrium myelin periods are determined by a balance of nonspecific forces/i.e., the electrostatic repulsion force and the van der Walls attractive force, as well as the short-range repulsion force (hydration force, or steric stabilization), then values in the period-dependency curve can be used to define the isoelectric pH and exclusion length of the membrane. The exclusion length, which is related to the minimum period at isoelectric pH, was used to calculate the electrostatic repulsion force given the other forces. The electrostatic repulsion was then used to calculate the surface potential, which in turn was used to calculate the surface charge density (at different pH and ionic strength). We found the negative surface charge increases with pH at constant ionic strength and with ionic strength at constant pH. We

  2. Solution structure of the two-iron rubredoxin of Pseudomonas oleovorans determined by NMR spectroscopy and solution X-ray scattering and interactions with rubredoxin reductase.

    PubMed

    Perry, Ashlee; Tambyrajah, Winston; Grossmann, J Günter; Lian, Lu-Yun; Scrutton, Nigel S

    2004-03-23

    Here we provide insights into the molecular structure of the two-iron 19-kDa rubredoxin (AlkG) of Pseudomonas oleovorans using solution-state nuclear magnetic resonance (NMR) and small-angle X-ray scattering studies. Sequence alignment and biochemical studies have suggested that AlkG comprises two rubredoxin folds connected by a linker region of approximately 70 amino acid residues. The C-terminal domain (C-Rb) of this unusual rubredoxin, together with approximately 35 amino acid residues of the predicted linker region, was expressed in Escherichia coli, purified in the one-iron form and the structure of the cadmium-substituted form determined at high-resolution by NMR spectroscopy. The structure shows that the C-Rb domain is similar in fold to the conventional one-iron rubredoxins from other organisms, whereas the linker region does not have any discernible structure. This tandem "flexible-folded" structure of the polypeptide chain derived for the C-Rb protein was confirmed using solution X-ray scattering methods. X-ray scattering studies of AlkG indicated that the 70-amino acid residue linker forms a structured, yet mobile, polypeptide segment connecting the globular N- and C-terminal domains. The X-ray scattering studies also showed that the N-terminal domain (N-Rb) has a molecular conformation similar to that of C-Rb. The restored molecular shape indicates that the folded N-Rb and C-Rb domains of AlkG are noticeably separated, suggesting some domain movement on complex formation with rubredoxin reductase to allow interdomain electron transfer between the metal centers in AlkG. This study demonstrates the advantage of combining X-ray scattering and NMR methods in structural studies of dynamic, multidomain proteins that are not suited to crystallographic analysis. The study forms a structural foundation for functional studies of the interaction and electron-transfer reactions of AlkG with rubredoxin reductase, also reported herein. PMID:15023067

  3. Putting the pieces into place: Properties of intact zinc metallothionein 1A determined from interaction of its isolated domains with carbonic anhydrase.

    PubMed

    Pinter, Tyler B J; Stillman, Martin J

    2015-11-01

    Mammalian metallothioneins (MTs) bind up to seven Zn(2+) using a large number of cysteine residues relative to their small size and can act as zinc-chaperones. In metal-saturated Zn7-MTs, the seven zinc ions are co-ordinated tetrahedrally into two distinct clusters separated by a linker; the N-terminal β-domain [(Zn3Cys9)(3-)] and C-terminal α-domain [(Zn4Cys11)(3-)]. We report on the competitive zinc metalation of apo-carbonic anhydrase [CA; metal-free CA (apo-CA)] in the presence of apo-metallothionein 1A domain fragments to identify domain specific determinants of zinc binding and zinc donation in the intact two-domain Znn-βαMT1A (human metallothionein 1A isoform; n=0-7). The apo-CA is shown to compete effectively only with Zn2-3-βMT and Zn4-αMT. Detailed modelling of the ESI mass spectral data have revealed the zinc-binding affinities of each of the zinc-binding sites in the two isolated fragments. The three calculated equilibrium zinc affinities [log(KF)] of the isolated β-domain were: 12.2, 11.7 and 11.4 and the four isolated α-domain affinities were: 13.5, 13.2, 12.7 and 12.6. These data provide guidance in identification of the location of the strongest-bound and weakest-bound zinc in the intact two-domain Zn7βαMT. The β-domain has the weakest zinc-binding site and this is where zinc ions are donated from in the Zn7-βαMT. The α-domain with the highest affinity binds the first zinc, which we propose leads to an unscrambling of the cysteine ligands from the apo-peptide bundle. We propose that stabilization of the intact Zn6-MT and Zn7-MT, relative to that of the sum of the separated fragments, is due to the availability of additional cysteine ligand orientations (through interdomain interactions) to support the clustered structures.

  4. Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization.

    PubMed

    Kindaichi, Tomonori; Ito, Tsukasa; Okabe, Satoshi

    2004-03-01

    Ecophysiological interactions between the community members (i.e., nitrifiers and heterotrophic bacteria) in a carbon-limited autotrophic nitrifying biofilm fed only NH(4)(+) as an energy source were investigated by using a full-cycle 16S rRNA approach followed by microautoradiography (MAR)-fluorescence in situ hybridization (FISH). Phylogenetic differentiation (identification) of heterotrophic bacteria was performed by 16S rRNA gene sequence analysis, and FISH probes were designed to determine the community structure and the spatial organization (i.e., niche differentiation) in the biofilm. FISH analysis showed that this autotrophic nitrifying biofilm was composed of 50% nitrifying bacteria (ammonia-oxidizing bacteria [AOB] and nitrite-oxidizing bacteria [NOB]) and 50% heterotrophic bacteria, and the distribution was as follows: members of the alpha subclass of the class Proteobacteria (alpha-Proteobacteria), 23%; gamma-Proteobacteria, 13%; green nonsulfur bacteria (GNSB), 9%; Cytophaga-Flavobacterium-Bacteroides (CFB) division, 2%; and unidentified (organisms that could not be hybridized with any probe except EUB338), 3%. These results indicated that a pair of nitrifiers (AOB and NOB) supported a heterotrophic bacterium via production of soluble microbial products (SMP). MAR-FISH revealed that the heterotrophic bacterial community was composed of bacteria that were phylogenetically and metabolically diverse and to some extent metabolically redundant, which ensured the stability of the ecosystem as a biofilm. alpha- and gamma-Proteobacteria dominated the utilization of [(14)C]acetic acid and (14)C-amino acids in this biofilm. Despite their low abundance (ca. 2%) in the biofilm community, members of the CFB cluster accounted for the largest fraction (ca. 64%) of the bacterial community consuming N-acetyl-D-[1-(14)C]glucosamine (NAG). The GNSB accounted for 9% of the (14)C-amino acid-consuming bacteria and 27% of the [(14)C]NAG-consuming bacteria but did not utilize

  5. Cytomegalovirus pUL50 is the multi-interacting determinant of the core nuclear egress complex (NEC) that recruits cellular accessory NEC components.

    PubMed

    Sonntag, Eric; Hamilton, Stuart T; Bahsi, Hanife; Wagner, Sabrina; Jonjic, Stipan; Rawlinson, William D; Marschall, Manfred; Milbradt, Jens

    2016-07-01

    Nuclear egress of herpesvirus capsids through the nuclear envelope is mediated by the multimeric nuclear egress complex (NEC). The human cytomegalovirus (HCMV) core NEC is defined by an interaction between the membrane-anchored pUL50 and its nuclear co-factor pUL53, tightly associated through heterodimeric corecruitment to the nuclear envelope. Cellular proteins, such as p32/gC1qR, emerin and protein kinase C (PKC), are recruited by direct interaction with pUL50 for the multimeric extension of the NEC. As a functionally important event, the recruitment of both viral and cellular protein kinases leads to site-specific lamin phosphorylation and nuclear lamina disassembly. In this study, interaction domains within pUL50 for its binding partners were defined by co-immunoprecipitation. The interaction domain for pUL53 is located within the pUL50 N-terminus (residues 10-169), interaction domains for p32/gC1qR (100-358) and PKC (100-280) overlap in the central part of pUL50, and the interaction domain for emerin is located in the C-terminus (265-397). Moreover, expression and formation of core NEC proteins at the nuclear rim were consistently detected in cells permissive for productive HCMV replication, including two trophoblast-cell lines. Importantly, regular nuclear-rim formation of the core NEC was blocked by inhibition of cyclin-dependent kinase (CDK) activity. In relation to the recently published crystal structure of the HCMV core NEC, our findings result in a refined view of NEC assembly. In particular, we suggest that CDKs may play an important regulatory role in NEC formation during HCMV replication.

  6. Cytomegalovirus pUL50 is the multi-interacting determinant of the core nuclear egress complex (NEC) that recruits cellular accessory NEC components.

    PubMed

    Sonntag, Eric; Hamilton, Stuart T; Bahsi, Hanife; Wagner, Sabrina; Jonjic, Stipan; Rawlinson, William D; Marschall, Manfred; Milbradt, Jens

    2016-07-01

    Nuclear egress of herpesvirus capsids through the nuclear envelope is mediated by the multimeric nuclear egress complex (NEC). The human cytomegalovirus (HCMV) core NEC is defined by an interaction between the membrane-anchored pUL50 and its nuclear co-factor pUL53, tightly associated through heterodimeric corecruitment to the nuclear envelope. Cellular proteins, such as p32/gC1qR, emerin and protein kinase C (PKC), are recruited by direct interaction with pUL50 for the multimeric extension of the NEC. As a functionally important event, the recruitment of both viral and cellular protein kinases leads to site-specific lamin phosphorylation and nuclear lamina disassembly. In this study, interaction domains within pUL50 for its binding partners were defined by co-immunoprecipitation. The interaction domain for pUL53 is located within the pUL50 N-terminus (residues 10-169), interaction domains for p32/gC1qR (100-358) and PKC (100-280) overlap in the central part of pUL50, and the interaction domain for emerin is located in the C-terminus (265-397). Moreover, expression and formation of core NEC proteins at the nuclear rim were consistently detected in cells permissive for productive HCMV replication, including two trophoblast-cell lines. Importantly, regular nuclear-rim formation of the core NEC was blocked by inhibition of cyclin-dependent kinase (CDK) activity. In relation to the recently published crystal structure of the HCMV core NEC, our findings result in a refined view of NEC assembly. In particular, we suggest that CDKs may play an important regulatory role in NEC formation during HCMV replication. PMID:27145986

  7. 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

  8. 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 ...

  9. Disparity between timed-kill and checkerboard methods for determination of in vitro bactericidal interactions of vancomycin plus rifampin versus methicillin-susceptible and -resistant Staphylococcus aureus.

    PubMed

    Bayer, A S; Morrison, J O

    1984-08-01

    The role of rifampin as an adjunctive agent to vancomycin in the therapy of serious systemic staphylococcal infections remains controversial. Several in vitro studies utilizing differing methodologies to define the bactericidal interactions of vancomycin plus rifampin versus Staphylococcus aureus have yielded markedly disparate results. The in vitro bactericidal synergistic activities of vancomycin plus rifampin were examined versus 48 clinical isolates of S. aureus, both methicillin susceptible and resistant. Each strain was tested simultaneously in timed-kill curve and checkerboard systems. By timed-kill curve, vancomycin plus rifampin usually had either an indifferent (67%) or synergistic (19 to 29%) effect, with a frequency dependent on sampling times; bactericidal antagonism was infrequently noted after 48 h of incubation (4%). Indifference was seen as a prevention of rifampin resistance by vancomycin. Synergy was more commonly noted at 48 than at 24 h of incubation. The bactericidal interaction results were similar for both methicillin-susceptible and -resistant strains. In contrast to the killing curve data, the checkerboard technique uniformly demonstrated bactericidal antagonism of vancomycin plus rifampin against all 48 staphylococci. We conclude that the nature of the in vitro bactericidal interactions of vancomycin plus rifampin against S. aureus is difficult to establish in vitro. This fact relates to the markedly disparate findings, which depended on both the synergy technique utilized and the test system conditions employed. In vivo studies are required to delineate the bactericidal interaction potentials of vancomycin plus rifampin versus S. aureus.

  10. ETTIN (ARF3) physically interacts with KANADI proteins to form a functional complex essential for integument development and polarity determination in Arabidopsis.

    PubMed

    Kelley, Dior R; Arreola, Alexandra; Gallagher, Thomas L; Gasser, Charles S

    2012-03-01

    KANADI (KAN) transcription factors promote abaxial cell fate throughout plant development and are required for organ formation during embryo, leaf, carpel and ovule development. ABERRANT TESTA SHAPE (ATS, or KAN4) is necessary during ovule development to maintain the boundary between the two ovule integuments and to promote inner integument growth. Yeast two-hybrid assays identified ETTIN (ETT, or AUXIN RESPONSE FACTOR 3) as a transcription factor that could physically interact with ATS. ATS and ETT were shown to physically interact in vivo in transiently transformed tobacco epidermal cells using bimolecular fluorescence complementation. ATS and ETT were found to share an overlapping expression pattern during Arabidopsis ovule development and loss of either gene resulted in congenital fusion of the integuments and altered seed morphology. We hypothesize that in wild-type ovules a physical interaction between ATS and ETT allows these proteins to act in concert to define the boundary between integument primordia. We further show protein-protein interaction in yeast between ETT and KAN1, a paralog of ATS. Thus, a direct physical association between ETT and KAN proteins underpins their previously described common role in polarity establishment and organogenesis. We propose that ETT-KAN protein complex(es) constitute part of an auxin-dependent regulatory module that plays a conserved role in a variety of developmental contexts. PMID:22296848

  11. Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects.

    PubMed

    Tse, A; Verkhivker, G M

    2015-07-01

    The human protein kinases play a fundamental regulatory role in orchestrating functional processes in complex cellular networks. Understanding how conformational equilibrium between functional kinase states can be modulated by ligand binding or mutations is critical for quantifying molecular basis of allosteric regulation and drug resistance. In this work, molecular dynamics simulations of the Abl kinase complexes with cancer drugs (Imatinib and Dasatinib) were combined with structure-based network modeling to characterize dynamics of the residue interaction networks in these systems. The results have demonstrated that structural architecture of kinase complexes can produce a small-world topology of the interaction networks. Our data have indicated that specific Imatinib binding to a small number of highly connected residues could lead to network-bridging effects and allow for efficient allosteric communication, which is mediated by a dominant pathway sensitive to the unphosphorylated Abl state. In contrast, Dasatinib binding to the active kinase form may activate a broader ensemble of allosteric pathways that are less dependent on the phosphorylation status of Abl and provide a better balance between the efficiency and resilience of signaling routes. Our results have unveiled how differences in the residue interaction networks and allosteric communications of the Abl kinase complexes can be directly related to drug resistance effects. This study offers a plausible perspective on how efficiency and robustness of the residue interaction networks and allosteric pathways in kinase structures may be associated with protein responses to drug binding.

  12. A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants

    PubMed Central

    Kong, Ling-Jie; Orozco, Beverly M.; Roe, Judith L.; Nagar, Steve; Ou, Sharon; Feiler, Heidi S.; Durfee, Tim; Miller, Ann B.; Gruissem, Wilhelm; Robertson, Dominique; Hanley-Bowdoin, Linda

    2000-01-01

    Geminiviruses replicate in nuclei of mature plant cells after inducing the accumulation of host DNA replication machinery. Earlier studies showed that the viral replication factor, AL1, is sufficient for host induction and interacts with the cell cycle regulator, retinoblastoma (pRb). Unlike other DNA virus proteins, AL1 does not contain the pRb binding consensus, LXCXE, and interacts with plant pRb homo logues (pRBR) through a novel amino acid sequence. We mapped the pRBR binding domain of AL1 between amino acids 101 and 180 and identified two mutants that are differentially impacted for AL1–pRBR interactions. Plants infected with the E-N140 mutant, which is wild-type for pRBR binding, developed wild-type symptoms and accumulated viral DNA and AL1 protein in epidermal, mesophyll and vascular cells of mature leaves. Plants inoculated with the KEE146 mutant, which retains 16% pRBR binding activity, only developed chlorosis along the veins, and viral DNA, AL1 protein and the host DNA synthesis factor, proliferating cell nuclear antigen, were localized to vascular tissue. These results established the importance of AL1–pRBR interactions during geminivirus infection of plants. PMID:10880461

  13. When Boy Meets Girl (Revisited): Gender, Gender Role Orientation, and Prospect of Future Interaction as Determinants of Self-Disclosure among Same- and Opposite-Sex Acquaintances.

    ERIC Educational Resources Information Center

    Shaffer, David R.; And Others

    1996-01-01

    Male and female research participants (n=254) self-disclosed to a male or female confederate with whom they anticipated or did not anticipate further interaction. Women disclosed more intimately, with increasing emotion, and displayed more topical responsiveness with female than with male targets. Only the highly masculine men reliably disclosed…

  14. Dual-polarization interferometry: an analytical technique to measure changes in protein structure in real time, to determine the stoichiometry of binding events, and to differentiate between specific and nonspecific interactions.

    PubMed

    Swann, Marcus J; Peel, Louise L; Carrington, Simon; Freeman, Neville J

    2004-06-15

    The study of solution-phase interactions between small molecules and immobilized proteins is of intense interest, especially to the pharmaceutical industry. An optical sensing technique, dual polarization interferometry, has been employed for the detailed study of a model protein system, namely, d-biotin interactions with streptavidin immobilized on a solid surface. Changes in thickness and density of an immobilized streptavidin layer as a result of the binding of d-biotin have been directly measured in solution and in real time. The results obtained from this approach are in excellent agreement with X-ray crystallographic data for the structural changes expected in the streptavidin-D-biotin system. The mass changes measured on binding d-biotin also agree closely with anticipated binding capacity values. Determination of the density changes occurring in the protein adlayer provides a means for differentiation between specific and nonspecific interactions. PMID:15158477

  15. BB0323 and Novel Virulence Determinant BB0238: Borrelia burgdorferi Proteins That Interact With and Stabilize Each Other and Are Critical for Infectivity

    PubMed Central

    Kariu, Toru; Sharma, Kavita; Singh, Preeti; Smith, Alexis A.; Backstedt, Brian; Buyuktanir, Ozlem; Pal, Utpal

    2015-01-01

    We have shown that Borrelia burgdorferi gene product BB0323 is essential for cell fission and pathogen persistence in vivo. Here we describe characterization of a conserved hypothetical protein annotated as BB0238, which specifically interacts with the N-terminal region of BB0323. We show that BB0238 is a subsurface protein, and similar to BB0323, exists in the periplasm and as a membrane-bound protein. Deletion of bb0238 in infectious B. burgdorferi did not affect microbial growth in vitro or survival in ticks, but the mutant was unable to persist in mice or transmit from ticks—defects that are restored on genetic complementation. Remarkably, BB0238 and BB0323 contribute to mutual posttranslational stability, because deletion of one causes dramatic reduction in the protein level of the other partner. Interference with the function of BB0238 or BB0323 and their interaction may provide novel strategies to combat B. burgdorferi infection. PMID:25139020

  16. The Role of CH···O Coulombic Interactions in Determining Rotameric Conformations of Phenyl Substituted 1,3-Dioxanes and Tetrahydropyrans.

    PubMed

    Wiberg, Kenneth B; Lambert, Kyle M; Bailey, William F

    2015-08-21

    The rotameric conformations of the phenyl ring in both the axial and the equatorial conformers of phenyl substituted 1,3-dioxanes and tetrahydropyrans are compared with those of the corresponding phenylcyclohexanes at the MP2/6-311+G* level. The compounds with an axial phenyl commonly adopt a conformation in which the plane of the aromatic ring is perpendicular to the benzylic C-H bond. However, axial 5-phenyl-1,3-dioxane adopts a "parallel" conformation that allows an ortho hydrogen to be proximate to the two ring oxygens, leading to attractive CH···O interactions. Stabilizing Coulombic interactions of this sort are found with many of the oxygen-containing six-membered rings that were investigated. PMID:26182246

  17. 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. PMID:26686922

  18. The number of responding CD4 T cells and the dose of antigen conjointly determine the TH1/TH2 phenotype by modulating B7/CD28 interactions.

    PubMed

    Rudulier, Christopher D; McKinstry, K Kai; Al-Yassin, Ghassan A; Kroeger, David R; Bretscher, Peter A

    2014-06-01

    Our previous in vivo studies show that both the amount of Ag and the number of available naive CD4 T cells affect the Th1/Th2 phenotype of the effector CD4 T cells generated. We examined how the number of OVA-specific CD4 TCR transgenic T cells affects the Th1/Th2 phenotype of anti-SRBC CD4 T cells generated in vivo upon immunization with different amounts of OVA-SRBC. Our observations show that a greater number of Ag-dependent CD4 T cell interactions are required to generate Th2 than Th1 cells. We established an in vitro system that recapitulates our main in vivo findings to more readily analyze the underlying mechanism. The in vitro generation of Th2 cells depends, as in vivo, upon both the number of responding CD4 T cells and the amount of Ag. We demonstrate, using agonostic/antagonistic Abs to various costimulatory molecules or their receptors, that the greater number of CD4 T cell interactions, required to generate Th2 over Th1 cells, does not involve CD40, OX40, or ICOS costimulation, but does involve B7/CD28 interactions. A comparison of the level of expression of B7 molecules by APC and CD4 T cells, under different conditions resulting in the substantial generation of Th1 and Th2 cells, leads us to propose that the critical CD28/B7 interactions, required to generate Th2 cells, may directly occur between CD4 T cells engaged with the same B cell acting as an APC.

  19. Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity.

    PubMed

    Cole, Daniel J; Rajendra, Eeson; Roberts-Thomson, Meredith; Hardwick, Bryn; McKenzie, Grahame J; Payne, Mike C; Venkitaraman, Ashok R; Skylaris, Chris-Kriton

    2011-07-01

    The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks. The primary mode of interaction between BRCA2 and RAD51 is through the BRC repeats, which are ∼35 residue peptide motifs that interact directly with RAD51 in vitro. Human BRCA2, like its mammalian orthologues, contains 8 BRC repeats whose sequence and spacing are evolutionarily conserved. Despite their sequence conservation, there is evidence that the different human BRC repeats have distinct capacities to bind RAD51. A previously published crystal structure reports the structural basis of the interaction between human BRC4 and the catalytic core domain of RAD51. However, no structural information is available regarding the binding of the remaining seven BRC repeats to RAD51, nor is it known why the BRC repeats show marked variation in binding affinity to RAD51 despite only subtle sequence variation. To address these issues, we have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass a range of techniques designed to link sequence variation with binding free energy. They include MM-PBSA and thermodynamic integration, which are based on classical force fields, and a recently developed approach to computing binding free energies from large-scale quantum mechanical first principles calculations with the linear-scaling density functional code onetep. Our findings not only reveal how sequence variation in the BRC repeats directly affects affinity with RAD51 and provide significant new insights into the control of RAD51 by human BRCA2, but also exemplify a palette of computational and experimental tools for the

  20. Determination of apical membrane polarity in mammary epithelial cell cultures: The role of cell-cell, cell-substratum, and membrane-cytoskeleton interactions

    SciTech Connect

    Parry, G.; Beck, J.C.; Moss, L.; Bartley, J. ); Ojakian, G.K. )

    1990-06-01

    The membrane glycoprotein, PAS-O, is a major differentiation antigen on mammary epithelial cells and is located exclusively in the apical domain of the plasma membrane. The authors have used 734B cultured human mammary carcinoma cells as a model system to study the role of tight junctions, cell-substratum contacts, and submembranous cytoskeletal elements in restricting PAS-O to the apical membrane. Immunofluorescence and immunoelectronmicroscopy experiments demonstrated that while tight junctions demarcate PAS-O distribution in confluent cultures, apical polarity could be established at low culture densities when cells could not form tight junctions with neighboring cells. They suggest, then, that interactions between vitronectin and its receptor, are responsible for establishment of membrane domains in the absence of tight junctions. The role of cytoskeletal elements in restricting PAS-O distribution was examined by treating cultures with cytochalasin D, colchicine, or acrylamide. Cytochalasin D led to a redistribution of PAS0O while colchicine and acrylamide did not. They hypothesize that PAS-O is restricted to the apical membrane by interactions with a microfilament network and that the cytoskeletal organization is dependent upon cell-cell and cell-substratum interactions.

  1. 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.

  2. 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

  3. Interaction of nickel with 4-(2'-benzothiazolylazo) salicylic acid (BTAS) and simultaneous first-derivative spectrophotometric determination of nickel(II) and iron(III)

    NASA Astrophysics Data System (ADS)

    Hashem, E. Y.; Abu-Bakr, M. S.; Hussain, S. M.

    2003-03-01

    The solution properties of nickel complex with 4-(2'-benzo-thiazolylazo) salicylic acid (BTAS) have been studied by zero-order absorption spectrophotometry in 40% (v/v) ethanol at 20 °C and an ionic strength of 0.1 mol dm -3 (KNO 3). The equilibria that exist in solution were established and the basic characteristics of complexes formed were determined. A new direct spectrophotometric method for the determination of trace amounts of the nickel is proposed based on the formation of the Ni (BTAS) complex at pH 7.0. The absorption maximum, molar absorbtivity, and Sandell's sensitivity of 1:1 (M:L) complex are 525 nm, 0.6×10 4 l mol -1 cm -1 and 2.824×10 -9 μg cm -2, respectively. The use of first-derivative spectrophotometry eliminates the interference of iron and enables the simultaneous determination of nickel and iron using BTAS. Quantitative determination of Ni(II) and Fe(III) is possible in the range (0.59-7.08) and (2.1-8.4) μg ml -1, respectively with a relative standard deviation of 0.5%. The proposed method has been successfully applied to the simultaneous spectrophotometric determination of nickel and iron in steel alloys and aluminum alloys.

  4. The interaction among age, thermal acclimation and growth rate in determining muscle metabolic capacities and tissue masses in the threespine stickleback, Gasterosteus aculeatus.

    PubMed

    Guderley, H; Lavoie, B A; Dubois, N

    1994-11-01

    Thermal acclimation may directly modify muscle metabolic capacities, or may modify them indirectly via effects upon physiological processes such as growth, reproduction or senescence. To evaluate these interacting effects, we examined the influence of thermal acclimation and acclimatization upon muscle metabolic capacities and tissue masses in 1 + stickleback, Gasterosteus aculeatus, in which confounding interactions between temperature and senescense should be absent. Furthermore, we examined the influence of thermal acclimation upon individual growth rate, muscle enzyme levels and tissue masses in 2 + stickleback sampled at the beginning of their final reproductive season. For 1 + stickleback, cold acclimation more than doubles mitochondrial enzyme levels in the axial muscle. Thermal acclimation did not change the condition of 1 + stickleback at feeding levels which could not maintain the condition of 2+ stickleback. Compensatory metabolic responses to temperature were not apparent in field acclimatized 1 + stickleback. The growth rate of 2 + stickleback was markedly affected by temperature: warm-acclimated fish generally lost mass even at very high levels of feeding (up to 78 enchytraid worms per day) while cold-acclimated fish gained mass. This suggests that warm temperatures accelerate the senescence of 2 + stickleback. Generally, muscle enzyme activities increased with growth rate. In axial muscle, the relationships between CS activity and growth rate differed with acclimation temperature. Independent of the influence of growth rate, CS activities were consistently higher in cold- than warm-acclimated 2 + stickleback, suggesting compensatory increases of CS activity with cold acclimation. PMID:24197078

  5. 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…

  6. Determination of metformin and other biguanides in forensic whole blood samples by hydrophilic interaction liquid chromatography-electrospray tandem mass spectrometry.

    PubMed

    Sørensen, Lambert K

    2012-01-01

    Metformin is an anti-diabetic drug in the biguanide class which also includes phenformin and buformin. Because of the potential adverse effects of the biguanides, a reliable liquid chromatography-tandem mass spectrometry method using pneumatically assisted electrospray ionization was developed for the quantification of the drugs in both live and post-mortem human whole blood. The blood proteins were precipitated by the addition of a mixture of methanol and acetonitrile, and the extract was cleaned up by cation-exchange solid-phase extraction to eliminate ion suppression effects. The separation was performed by hydrophilic interaction liquid chromatography. Matrix-matched calibrants combined with isotope dilution of metformin were used for calibration. The detection limits were 0.01 mg/L for metformin and phenformin and the relative intra-laboratory reproducibility standard deviations were less than 6% at concentrations of 1-10 mg/L. The mean true recoveries were greater than 86%.

  7. The determination of equilibrium constants, DeltaG, DeltaH and DeltaS for vapour interaction with a pharmaceutical drug, using gravimetric vapour sorption.

    PubMed

    Willson, Richard J; Beezer, Anthony E

    2003-06-01

    The application of gravimetric vapour sorption (GVS) to the characterisation of pharmaceutical drugs is often restricted to the study of gross behaviour such as a measure of hygroscopicity. Although useful in early development of a drug substance, for example, in salt selection screening exercises, such types of analysis may not contribute to a fundamental understanding of the properties of the material. This paper reports a new methodology for GVS experimentation that will allow specific sorption parameters to be calculated; equilibrium constant (K), van't Hoff enthalpy change (DeltaH(v)), Gibbs free energy for sorption (DeltaG) and the entropy change for sorption (DeltaS). Unlike other reports of such type of analysis that require the application of a specific model, this method is model free. The analysis does require that over the narrow temperature range of the study DeltaH(v) is constant and there is no change in interaction mechanism.

  8. Numerical solution of Bloch-Gruneisen function to determine the contribution of electron-phonon interaction in polycrystalline MgB 2 superconductor

    NASA Astrophysics Data System (ADS)

    Ansari, Intikhab A.

    2010-06-01

    Here, we report the efficient and feasible analytical method for the generalized Bloch-Gruneisen law in association with Debye temperature and various temperatures range in terms of incomplete gamma function. In addition, our results are in agreement with previous reports as shown in this letter. Bloch-Gruneisen function describes the contribution of electron-phonon interaction to the results of temperature dependence behavior of resistivity for integer and noninteger values of index m. In conclusion, the algorithm is constructed in Fortran 90 language for replicate the variation of temperature dependence of resistivity for pristine MgB 2 sample. Moreover, the comparison of numerical results with the proposed method reveals the validity and precision of the method.

  9. Kinetic Stability May Determine the Interaction Dynamics of the Bifunctional Protein DCoH1, the Dimerization Cofactor of the Transcription Factor HNF-1[alpha

    SciTech Connect

    Rho, H.; Jones, C.N.; Rose, R.B.

    2010-12-07

    The two disparate functions of DCoH1 (dimerization cofactor of HNF-1)/PCD (pterin-4a-carbinolamine dehydratase) are associated with a change in oligomeric state. DCoH dimers enhance the activity of the diabetes-associated transcription factor HNF-1{alpha} (hepatocyte nuclear factor-1{alpha}), while the PCD activity of DCoH1 homotetramers aids in aromatic amino acid metabolism. These complexes compete for the same interface of the DCoH dimer. Formation of the DCoH1/HNF-1{alpha} complex requires cofolding. The homotetramer of the DCoH1 paralogue, DCoH2, interacts with HNF-1{alpha} through simple mixing. To further investigate regulation of DCoH/HNF-1{alpha} complex formation, we measured the stability of the DCoH1 homotetramer through unfolding studies by intrinsic tryptophan fluorescence. DCoH2 unfolding is reversible. Surprisingly, the DCoH1 homotetramer is resistant to guanidine unfolding but refolds at a much lower guanidine concentration. We show that a point mutation at the DCoH1 tetramer interface, Thr 51 Ser, overcomes the dissociation barrier of the homotetramer and increases the interaction with HNF-1{alpha}. The 1.8 {angstrom} resolution crystal structure of DCoH1 T51S shows the presence of an ordered water molecule at the tetramer interface, as in DCoH2, which may destabilize the homotetramer. The equilibrium unfolding data were fit to a two-state model with no apparent intermediate. Folding intermediates were detectable by size exclusion chromatography. For wild-type DCoH1 the intermediates changed with time, suggesting a kinetic origin for the unfolding barrier of the homotetramer. We propose an unfolding pathway in which the tetramer unfolds slowly, but the dimer folds reversibly. Implications for regulation of DCoH1/HNF-1{alpha} complex formation are discussed.

  10. Simultaneous determination and pharmacokinetics of protein unbound aspirin and salicylic acid in rat blood and brain by microdialysis: an application to herbal-drug interaction.

    PubMed

    Shaw, Lee-Hsin; Tsai, Tung-Hu

    2012-05-01

    Aspirin is commonly used for the prevention of myocardial infarction and ischemic stroke; whereas the Chinese people employ the bu-yang-huan-wu-tang (BYHWT) as a routine herbal formulation for the treatment and prevention of transient ischemic stroke. The current study develops a microdialysis technique coupled to a validated liquid chromatography system to measure free-form aspirin and salicylic acid for herbal-drug interaction in rat blood and brain. The intra- and inter-day precisions in biological dialysates were within 0.1-9.4% in the concentration ranges of 0.1-50 μg/mL and the accuracies ranged from -4.7 to 6.1%. The pharmacokinetic data demonstrate that the area under the concentration time curve (AUC) of the aspirin was 2031 ± 266 min μg/mL after aspirin administration (100mg/kg, i.v.). The AUC of salicylic acid was 12660 ± 1799 min μg/mL, which suggests that aspirin is quickly hydrolyzed to salicylic acid in blood and the metabolite can also be detected within 15 min in brain dialysate. The herbal-drug pharmacokinetic interaction showed no significant effect in blood and brain. The results of pharmacodynamics for the bleeding time suggested that there were no significant differences between the aspirin alone group and the BYHWT pretreated group. However, the bleeding time has been prolonged when compared aspirin alone or the group pretreated with BYHWT to the blank control. The conclusion provides practical information for clinical practice for the herbal formulation BYHWT and aspirin used concurrently.

  11. 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

  12. 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

  13. Short-term solar pressure effect and GM uncertainty on TDRS orbital accuracy: A study of the interaction of modeling error with tracking and orbit determination

    NASA Technical Reports Server (NTRS)

    Fang, B. T.

    1979-01-01

    The TDRS was modeled as a combination of a sun-pointing solar panel and earth-pointing plate. Based on this model, explanations are given for the following orbit determination error characteristics: inherent limits in orbital accuracy, the variation of solar pressure induced orbital error with time of the day of epoch, the insensitivity of range-rate orbits to GM error, and optimum bilateration baseline.

  14. 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.

  15. 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

  16. Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence

    PubMed Central

    Houston, Kelly; McKim, Sarah M.; Comadran, Jordi; Bonar, Nicola; Druka, Ilze; Uzrek, Nicola; Cirillo, Elisa; Guzy-Wrobelska, Justyna; Collins, Nicholas C.; Halpin, Claire; Hansson, Mats; Dockter, Christoph; Druka, Arnis; Waugh, Robbie

    2013-01-01

    Within the cereal grasses, variation in inflorescence architecture results in a conspicuous morphological diversity that in crop species influences the yield of cereal grains. Although significant progress has been made in identifying some of the genes underlying this variation in maize and rice, in the temperate cereals, a group that includes wheat, barley, and rye, only the dosage-dependent and highly pleiotropic Q locus in hexaploid wheat has been molecularly characterized. Here we show that the characteristic variation in the density of grains along the inflorescence, or spike, of modern cultivated barley (Hordeum vulgare) is largely the consequence of a perturbed interaction between microRNA172 and its corresponding binding site in the mRNA of an APELATA2 (AP2)-like transcription factor, HvAP2. We used genome-wide association and biparental mapping to identify HvAP2. By comparing inflorescence development and HvAP2 transcript abundance in an extreme dense-spike mutant and its nearly isogenic WT line, we show that HvAP2 turnover driven by microRNA 172 regulates the length of a critical developmental window that is required for elongation of the inflorescence internodes. Our data indicate that this heterochronic change, an altered timing of developmental events caused by specific temporal variation in the efficiency of HvAP2 turnover, leads to the striking differences in the size and shape of the barley spike. PMID:24065816

  17. 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.

  18. 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.

  19. Dynamic determination of kinetic parameters for the interaction between polypeptide hormones and cell-surface receptors in the perfused rat liver by the multiple-indicator dilution method

    SciTech Connect

    Sato, H.; Sugiyama, Y.; Sawada, Y.; Iga, T.; Sakamoto, S.; Fuwa, T.; Hanano, M. )

    1988-11-01

    Hepatic elimination of epidermal growth factor (EGF) via receptor-mediated endocytosis was studied by a multiple-indicator dilution method in the isolated perfused rat liver, in which cell polarity and spatial organization are maintained. In this method EGF was given with inulin, an extracellular reference, as a bolus into the portal vein, and dilution curves of both compounds in the hepatic vein effluent were analyzed. Analysis of the dilution curve for EGF, compared with that for somatostatin, which showed no specific binding to isolated liver plasma membranes, resulted as follows: (i) both extraction ratio and distribution volume of {sup 125}I-labeled EGF decreased as the injected amount of unlabeled EGF increased; (ii) the ratio plot of the dilution curve for EGF exhibited an upward straight line initially for a short period of time, whereas the ratio plot of somatostatin gradually decreased. The multiple-indicator dilution method was used for other peptides also. Insulin and glucagon, known to have hepatocyte receptors, behaved similarly to EGF in shape of their ratio plots. The kinetic parameters calculated by this analysis were comparable with reported values obtained by in vitro direct binding measurements at equilibrium using liver homogenates. They conclude that the multiple-indicator dilution method is a good tool for analyzing the dynamics of peptide hormones-cell-surface receptor interaction under a condition in which spatial architecture of the liver is maintained.

  20. Determination of therapeutic γ-aminobutyric acid analogs in forensic whole blood by hydrophilic interaction liquid chromatography-electrospray tandem mass spectrometry.

    PubMed

    Sørensen, Lambert K; Hasselstrøm, Jørgen B

    2014-05-01

    Vigabatrin, pregabalin, gabapentin and baclofen are γ-aminobutyric acid analogs that are used in the treatment of epileptic seizures (vigabatrin, pregabalin and gabapentin) and spasticity (baclofen). The intake of these drugs may induce adverse reactions and impair the ability of an individual to drive a vehicle. There have also been reports of cases of intoxication and fatalities from overdoses. For rapid and accurate quantification of these drugs in forensic cases, an ultraperformance liquid chromatography tandem mass spectrometry method using pneumatically assisted electrospray ionization has been developed. The technique has been validated on both ante- and postmortem human whole blood. The protein in the blood samples was removed by the addition of a mixture of methanol and acetonitrile, and the extract was ultrafiltered and diluted with acetonitrile. The separation was performed by hydrophilic interaction liquid chromatography. Calibration of the system was achieved through use of matrix-matched calibrants combined with isotope dilution. The lower limits of quantification were 0.02-0.04 mg/L, and the relative intra-laboratory reproducibility standard deviations were <4 and 8% at concentrations of 10 and 1 mg/L, respectively. The mean true recoveries were >89%. The trueness expressed as the relative bias of the test results was within ±7% at concentrations of 1-40 mg/L for vigabatrin, pregabalin and gabapentin and of 0.1-4 mg/L for baclofen.

  1. Hydrophilic interaction liquid chromatography-tandem mass spectrometry methylphosponic and alkyl methylphosphonic acids determination in environmental samples after pre-column derivatization with p-bromophenacyl bromide.

    PubMed

    Baygildiev, T M; Rodin, I A; Stavrianidi, A N; Braun, A V; Lebedev, A T; Rybalchenko, I V; Shpigun, O A

    2016-04-15

    Once exposed to the environment organophosphate nerve agents readily degrade by rapid hydrolysis to the corresponding alkyl methylphosphonic acids which do not exist in nature. These alkyl methylphosphonic acids are finally slowly hydrolyzed to methylphosphonic acid. Methylphosphonic acid is the most stable hydrolysis product of organophosphate nerve agents, persisting in environment for a long time. A highly sensitive method of methylphosphonic acid and alkyl methylphosphonic acids detection in dust and ground mixed samples has been developed and validated. The fact that alkyl methylphosphonic acids unlike methylphosphonic acid did not react with p-bromophenacyl bromide under chosen conditions was discovered. This allowed simultaneous chromatographic separation and mass spectrometric detection of derivatized methylphosphonic acid and underivatized alkyl methylphosphonic acids using HILIC-MS/MS method. Very simple sample pretreatment with high recoveries for each analyte was developed. Methylphosphonic acid pre-column derivate and alkyl methylphosphonic acids were detected using tandem mass spectrometry with electrospray ionization after hydrophilic interaction liquid chromatography separation. The developed approach allows achieving ultra-low detection limits: 200 pg mL(-1) for methylphosphonic acid, 70 pg mL(-1) for ethyl methylphosphonic acid, 8 pg mL(-1) for i-propyl methylphosphonic acid, 8 pg mL(-1) for i-butyl methylphosphonic acid, 5 pg mL(-1) for pinacolyl methylphosphonic acid in the extracts of dust and ground mixed samples. This approach was successfully applied to the dust and ground mixed samples from decommissioned plant for the production of chemical weapons.

  2. Structure and DNA-Binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-Specific DNA Recognition

    SciTech Connect

    Kim, Suhkmann; Zhang, Ziming; Upchurch, Sean; Isern, Nancy G.; Chen, Yuan

    2004-04-16

    2 ARID is a homologous family of DNA-binding domains that occur in DNA binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We have solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized non-specific DNA-binding by the SWI1 ARID domain. Results from this study indicate that a flexible long internal loop in ARID motif is likely to be important for sequence specific DNA-recognition. The structure of human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that boundary of the DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies. Key Words: ARID, SWI1, NMR, structural genomics, protein-DNA interaction.

  3. Hydrophilic interaction liquid chromatography-tandem mass spectrometry methylphosponic and alkyl methylphosphonic acids determination in environmental samples after pre-column derivatization with p-bromophenacyl bromide.

    PubMed

    Baygildiev, T M; Rodin, I A; Stavrianidi, A N; Braun, A V; Lebedev, A T; Rybalchenko, I V; Shpigun, O A

    2016-04-15

    Once exposed to the environment organophosphate nerve agents readily degrade by rapid hydrolysis to the corresponding alkyl methylphosphonic acids which do not exist in nature. These alkyl methylphosphonic acids are finally slowly hydrolyzed to methylphosphonic acid. Methylphosphonic acid is the most stable hydrolysis product of organophosphate nerve agents, persisting in environment for a long time. A highly sensitive method of methylphosphonic acid and alkyl methylphosphonic acids detection in dust and ground mixed samples has been developed and validated. The fact that alkyl methylphosphonic acids unlike methylphosphonic acid did not react with p-bromophenacyl bromide under chosen conditions was discovered. This allowed simultaneous chromatographic separation and mass spectrometric detection of derivatized methylphosphonic acid and underivatized alkyl methylphosphonic acids using HILIC-MS/MS method. Very simple sample pretreatment with high recoveries for each analyte was developed. Methylphosphonic acid pre-column derivate and alkyl methylphosphonic acids were detected using tandem mass spectrometry with electrospray ionization after hydrophilic interaction liquid chromatography separation. The developed approach allows achieving ultra-low detection limits: 200 pg mL(-1) for methylphosphonic acid, 70 pg mL(-1) for ethyl methylphosphonic acid, 8 pg mL(-1) for i-propyl methylphosphonic acid, 8 pg mL(-1) for i-butyl methylphosphonic acid, 5 pg mL(-1) for pinacolyl methylphosphonic acid in the extracts of dust and ground mixed samples. This approach was successfully applied to the dust and ground mixed samples from decommissioned plant for the production of chemical weapons. PMID:26965649

  4. 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

  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. Evidence that the nonstructural protein of Tomato spotted wilt virus is the avirulence determinant in the interaction with resistant pepper carrying the TSW gene.

    PubMed

    Margaria, P; Ciuffo, M; Pacifico, D; Turina, M

    2007-05-01

    All known pepper cultivars resistant to Tomato spotted wilt virus (TSWV) possess a single dominant resistance gene, Tsw. Recently, naturally occurring resistance-breaking (RB) TSWV strains have been identified, causing major concerns. We used a collection of such strains to identify the specific genetic determinant that allows the virus to overcome the Tsw gene in Capsicum spp. A reverse genetic approach is still not feasible for TSWV; therefore, we analyzed reassortants between wild-type (WT) and RB strains. Our results confirmed that the S RNA, which encodes both the nucleocapsid protein (N) and a nonstructural protein (NSs), carries the genetic determinant responsible for Tsw resistance breakdown. We then used full-length S RNA segments or the proteins they encode to compare the sequences of WT and related RB strains, and obtained indirect evidence that the NSs protein is the avirulence factor in question. Transient expression of NSs protein from WT and RB strains showed that they both can equally suppress post-transcriptional gene silencing (PTGS). Moreover, biological characterization of two RB strains carrying deletions in the NSs protein showed that NSs is important in maintaining TSWV infection in newly emerging leaves over time, preventing recovery. Analysis of another RB strain phenotype allowed us to conclude that local necrotic response is not sufficient for resistance in Capsicum spp. carrying the Tsw gene.

  7. 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.

  8. 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.

  9. 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

  10. 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. PMID:24582391

  11. 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

  12. Development and validation of a sensitive solid phase extraction/hydrophilic interaction liquid chromatography/mass spectrometry method for the accurate determination of glucosamine in dog plasma.

    PubMed

    Hubert, C; Houari, S; Lecomte, F; Houbart, V; De Bleye, C; Fillet, M; Piel, G; Rozet, E; Hubert, Ph

    2010-05-01

    A sensitive and accurate LC/MS method was developed for the monitoring of glucosamine (GLcN) dog plasmatic concentration. In this scope, relatively low plasmatic concentrations of GLcN were expected, ranging from 50 to 1000 ng/mL. Liquid chromatography coupled to simple quadrupole mass spectrometry detection (LC/MS) was selected bringing the selectivity and the sensitivity needed for this application. Additionally, a solid phase extraction (SPE) step was performed to reduce matrix and ion suppression effects. Due to the ionisable character of the compound of interest, a mixed-mode strong cation exchange (Plexa PCX) disposable extraction cartridge (DEC) was selected. The separation was carried out on a Zorbax SB-CN column (5 microm, 4.6mm i.d. x 250 mm), considering hydrophilic interaction liquid chromatography (HILIC). Indeed, the mobile phase was made of methanol and 5mM ammonium hydrogen carbonate buffer at pH 7.5 (95/5, v/v). The detection was led at m/z ratios of 180.0 and 417.0, for GLcN and IS, respectively. Reliability of the results was demonstrated through the validation of the method using an approach based on the accuracy profile allowing managing the risk associated to the use of these methods in routine analysis: it is thus guaranteed that each future result will fall in the +/-30% acceptance limits with a probability of at least 90%. Successful application of the method to a preliminary pharmacokinetic study illustrated the usefulness of the method for pre-clinical studies.

  13. 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.

  14. 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.

  15. Hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) determination of cocaine and its metabolites benzoylecgonine, ecgonine methyl ester, and cocaethylene in hair samples.

    PubMed

    Quintela, Oscar; Lendoiro, Elena; Cruz, Angelines; de Castro, Ana; Quevedo, Alfredo; Jurado, Carmen; López-Rivadulla, Manuel

    2010-03-01

    This study reports the development and validation of a method using hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) for the analysis of cocaine and its metabolites benzoylecgonine (BE), ecgonine methyl ester (EME), and cocaethylene (CE) in hair samples. Decontamination was performed as follows: Firstly, the aliquot of hair was briefly rinsed with 2 mL dichloromethane, then was washed three times with 10 mL 0.01 M phosphate buffer, pH 6, for 15 min, followed by 2 mL 2-propanol for less than 2 min, and, finally, a last rinse with 2 mL dichloromethane was again done. Cocaine compounds were extracted from 10 mg of hair by incubation with 2 mL 0.1 M HCl at 50 °C for 12 h and purified by solid phase extraction with Oasis MCX cartridges. Analysis was performed by LC-MS/MS using an Atlantis HILIC silica chromatographic column. The method was fully validated. Linearity was established over the concentration range 0.020-10.0 ng/mg for cocaine (COC), 0.010-10.0 ng/mg for BE and CE, and 0.005-2.0 ng/mg for EME, and the correlation coefficients were all >0.99. Extraction efficiency was >70% for all analytes. Limits of detection were 0.0005 ng/mg for CE and 0.001 ng/mg for the other analytes (COC, BE, and EME). Lower limits of quantification were the lowest points of the calibration curves with acceptable accuracy and precision (coefficient of variation ≤20%). Intra- and inter-day imprecision ranged between 1.5% and 9.5% and 0.7% and 12.6%, respectively. Intra- and inter-day inaccuracy ranged from 0.5% to 12.3% and from 0.7% to 7.1%, respectively. With regard to matrix effects, suppression was <27.5% in all cases. The method was applied to the analysis of several samples derived from forensic cases. PMID:20052577

  16. Biased Gs versus Gq proteins and β-arrestin signaling in the NK1 receptor determined by interactions in the water hydrogen bond network.

    PubMed

    Valentin-Hansen, Louise; Frimurer, Thomas M; Mokrosinski, Jacek; Holliday, Nicholas D; Schwartz, Thue W

    2015-10-01

    X-ray structures, molecular dynamics simulations, and mutational analysis have previously indicated that an extended water hydrogen bond network between trans-membranes I-III, VI, and VII constitutes an allosteric interface essential for stabilizing different active and inactive helical constellations during the seven-trans-membrane receptor activation. The neurokinin-1 receptor signals efficiently through Gq, Gs, and β-arrestin when stimulated by substance P, but it lacks any sign of constitutive activity. In the water hydrogen bond network the neurokinin-1 has a unique Glu residue instead of the highly conserved AspII:10 (2.50). Here, we find that this GluII:10 occupies the space of a putative allosteric modulating Na(+) ion and makes direct inter-helical interactions in particular with SerIII:15 (3.39) and AsnVII:16 (7.49) of the NPXXY motif. Mutational changes in the interface between GluII:10 and AsnVII:16 created receptors that selectively signaled through the following: 1) Gq only; 2) β-arrestin only; and 3) Gq and β-arrestin but not through Gs. Interestingly, increased constitutive Gs but not Gq signaling was observed by Ala substitution of four out of the six core polar residues of the network, in particular SerIII:15. Three residues were essential for all three signaling pathways, i.e. the water-gating micro-switch residues TrpVI:13 (6.48) of the CWXP motif and TyrVII:20 (7.53) of the NPXXY motif plus the totally conserved AsnI:18 (1.50) stabilizing the kink in trans-membrane VII. It is concluded that the interface between position II:10 (2.50), III:15 (3.39), and VII:16 (7.49) in the center of the water hydrogen bond network constitutes a focal point for fine-tuning seven trans-membrane receptor conformations activating different signal transduction pathways.

  17. Open-label, single-dose, parallel-group study in healthy volunteers to determine the drug-drug interaction potential between KAE609 (cipargamin) and piperaquine.

    PubMed

    Stein, Daniel S; Jain, Jay Prakash; Kangas, Michael; Lefèvre, Gilbert; Machineni, Surendra; Griffin, Paul; Lickliter, Jason

    2015-01-01

    KAE609 represents a new class of potent, fast-acting, schizonticidal antimalarials. This study investigated the safety and pharmacokinetics of KAE609 in combination with the long-acting antimalarial piperaquine (PPQ) in healthy volunteers. A two-way pharmacokinetic interaction was hypothesized for KAE609 and PPQ, as both drugs are CYP3A4 substrates and inhibitors. The potential for both agents to affect the QT interval was also assessed. This was an open-label, parallel-group, single-dose study with healthy volunteers. Subjects were randomized to four parallel dosing arms with five cohorts (2:2:2:2:1), receiving 75 mg KAE609 plus 320 mg PPQ, 25 mg KAE609 plus 1,280 mg PPQ, 25 mg KAE609 alone, 320 mg PPQ alone, or 1,280 mg PPQ alone. Triplicate electrocardiograms were performed over the first 24 h after dosing, with single electrocardiograms at other time points. Routine safety (up to 89 days) and pharmacokinetic (up to 61 days) assessments were performed. Of the 110 subjects recruited, 99 completed the study. Coadministration of PPQ had no overall effect on exposure to KAE609, although 1,280 mg PPQ decreased the KAE609 maximum concentration (Cmax) by 17%. The group that received 25 mg KAE609 plus 1,280 mg PPQ showed a 32% increase in the PPQ area under the concentration-time curve from 0 to infinity (AUCinf), while the group that received 75 mg KAE609 plus 320 mg PPQ showed a 14% reduction. Mean changes from baseline in the QT interval corrected by Fridericia's method (QTcF) and the QT interval corrected by Bazett's method (QTcB) with PPQ were consistent with its known effects. PPQ but not KAE609 exposure correlated with corrected QT interval (QTc) increases, and KAE609 did not affect the PPQ exposure-QTc relationship. The QTcF effect for PPQ (least-squares estimate of the difference in mean maximal changes from baseline of 7.47 ms [90% confidence interval, 3.55 to 11.4 ms]) was consistent with the criteria for a positive thorough QT study. No subject had QTcF or

  18. Open-Label, Single-Dose, Parallel-Group Study in Healthy Volunteers To Determine the Drug-Drug Interaction Potential between KAE609 (Cipargamin) and Piperaquine

    PubMed Central

    Jain, Jay Prakash; Kangas, Michael; Lefèvre, Gilbert; Machineni, Surendra; Griffin, Paul; Lickliter, Jason

    2015-01-01

    KAE609 represents a new class of potent, fast-acting, schizonticidal antimalarials. This study investigated the safety and pharmacokinetics of KAE609 in combination with the long-acting antimalarial piperaquine (PPQ) in healthy volunteers. A two-way pharmacokinetic interaction was hypothesized for KAE609 and PPQ, as both drugs are CYP3A4 substrates and inhibitors. The potential for both agents to affect the QT interval was also assessed. This was an open-label, parallel-group, single-dose study with healthy volunteers. Subjects were randomized to four parallel dosing arms with five cohorts (2:2:2:2:1), receiving 75 mg KAE609 plus 320 mg PPQ, 25 mg KAE609 plus 1,280 mg PPQ, 25 mg KAE609 alone, 320 mg PPQ alone, or 1,280 mg PPQ alone. Triplicate electrocardiograms were performed over the first 24 h after dosing, with single electrocardiograms at other time points. Routine safety (up to 89 days) and pharmacokinetic (up to 61 days) assessments were performed. Of the 110 subjects recruited, 99 completed the study. Coadministration of PPQ had no overall effect on exposure to KAE609, although 1,280 mg PPQ decreased the KAE609 maximum concentration (Cmax) by 17%. The group that received 25 mg KAE609 plus 1,280 mg PPQ showed a 32% increase in the PPQ area under the concentration-time curve from 0 to infinity (AUCinf), while the group that received 75 mg KAE609 plus 320 mg PPQ showed a 14% reduction. Mean changes from baseline in the QT interval corrected by Fridericia's method (QTcF) and the QT interval corrected by Bazett's method (QTcB) with PPQ were consistent with its known effects. PPQ but not KAE609 exposure correlated with corrected QT interval (QTc) increases, and KAE609 did not affect the PPQ exposure-QTc relationship. The QTcF effect for PPQ (least-squares estimate of the difference in mean maximal changes from baseline of 7.47 ms [90% confidence interval, 3.55 to 11.4 ms]) was consistent with the criteria for a positive thorough QT study. No subject had QTcF or

  19. Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding.

    PubMed Central

    Allain, F H; Yen, Y M; Masse, J E; Schultze, P; Dieckmann, T; Johnson, R C; Feigon, J

    1999-01-01

    NHP6A is a chromatin-associated protein from Saccharomyces cerevisiae belonging to the HMG1/2 family of non-specific DNA binding proteins. NHP6A has only one HMG DNA binding domain and forms relatively stable complexes with DNA. We have determined the solution structure of NHP6A and constructed an NMR-based model structure of the DNA complex. The free NHP6A folds into an L-shaped three alpha-helix structure, and contains an unstructured 17 amino acid basic tail N-terminal to the HMG box. Intermolecular NOEs assigned between NHP6A and a 15 bp 13C,15N-labeled DNA duplex containing the SRY recognition sequence have positioned the NHP6A HMG domain onto the minor groove of the DNA at a site that is shifted by 1 bp and in reverse orientation from that found in the SRY-DNA complex. In the model structure of the NHP6A-DNA complex, the N-terminal basic tail is wrapped around the major groove in a manner mimicking the C-terminal tail of LEF1. The DNA in the complex is severely distorted and contains two adjacent kinks where side chains of methionine and phenylalanine that are important for bending are inserted. The NHP6A-DNA model structure provides insight into how this class of architectural DNA binding proteins may select preferential binding sites. PMID:10228169

  20. 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

  1. Cations modulate polysaccharide structure to determine FGF-FGFR signaling: a comparison of signaling and inhibitory polysaccharide interactions with FGF-1 in solution.

    PubMed

    Guimond, Scott E; Rudd, Timothy R; Skidmore, Mark A; Ori, Alessandro; Gaudesi, Davide; Cosentino, Cesare; Guerrini, Marco; Edge, Ruth; Collison, David; McInnes, Eric; Torri, Giangiacomo; Turnbull, Jeremy E; Fernig, David G; Yates, Edwin A

    2009-06-01

    For heparan sulfate (HS) to bind and regulate the activity of proteins, the polysaccharide must present an appropriate sequence and adopt a suitable conformation. The conformations of heparin derivatives, as models of HS, are altered via a change in the associated cations, and this can drastically modify their FGF signaling activities. Here, we report that changing the cations associated with an N-acetyl-enriched heparin polysaccharide, from sodium to copper(II), converted it from supporting signaling through the fibroblast growth factor receptor (FGF-1-FGFR1c) tyrosine kinase signaling system to being inhibitory in a cell-based BaF3 assay. Nuclear magnetic resonance and synchrotron radiation circular dichroism (SRCD) spectroscopy demonstrated that the polysaccharide conformation differed in the presence of sodium or copper(II) cations. Electron paramagnetic resonance confirmed the environment of the copper(II) ion on the N-acetyl-enriched polysaccharide was distinct from that previously observed with intact heparin, which supported signaling. Secondary structures in solution complexes of polysaccharides with FGF-1 (which either supported signaling through FGFR1c or were inhibitory) were determined by SRCD. This allowed direct comparison of the two FGF-1-polysaccharide complexes in solution, containing identical molecular components and differing only in their cation content. Subtle structural differences were revealed, including a reduction in the level of disordered structure in the inhibitory complex. PMID:19400583

  2. 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. PMID:25909504

  3. Thermodynamic investigation of the interaction between cyclodextrins and preservatives - Application and verification in a mathematical model to determine the needed preservative surplus in aqueous cyclodextrin formulations.

    PubMed

    Holm, René; Olesen, Niels Erik; Alexandersen, Signe Dalgaard; Dahlgaard, Birgitte N; Westh, Peter; Mu, Huiling

    2016-05-25

    Preservatives are inactivated when added to conserve aqueous cyclodextrin (CD) formulations due to complex formation between CDs and the preservative. To maintain the desired conservation effect the preservative needs to be added in apparent surplus to account for this inactivation. The purpose of the present work was to establish a mathematical model, which defines this surplus based upon knowledge of stability constants and the minimal concentration of preservation to inhibit bacterial growth. The stability constants of benzoic acid, methyl- and propyl-paraben with different frequently used βCDs were determined by isothermal titration calorimetry. Based upon this knowledge mathematical models were constructed to account for the equilibrium systems and to calculate the required concentration of the preservations, which was evaluated experimentally based upon the USP/Ph. Eur./JP monograph. The mathematical calculations were able to predict the needed concentration of preservation in the presence of CDs; it clearly demonstrated the usefulness of including all underlying chemical equilibria in a mathematical model, such that the formulation design can be based on quantitative arguments.

  4. Prodigiosin is not a determinant factor in lysis of Leishmania (Viannia) braziliensis after interaction with Serratia marcescens D-mannose sensitive fimbriae.

    PubMed

    Moraes, Caroline S; Seabra, Sergio H; Albuquerque-Cunha, José Maurício; Castro, Daniele P; Genta, Fernando A; de Souza, Wanderley; Brazil, Reginaldo P; Garcia, Eloi S; Azambuja, Patrícia

    2009-06-01

    In this paper, the lytic activity of two variants of Serratia marcescens against promastigotes of Leishmania braziliensis was studied. In vitro assays showed that S. marcescens variant SM365 lyses L. braziliensis promastigotes, while the variant DB11 did not. Scanning electron microscopy (SEM) revealed that S. marcescens SM365 adheres to all cellular body and flagellum of the parasite. Several filamentous structures were formed and identified as biofilms. After 120min incubation, they connect the protozoan to the developing bacterial clusters. SEM also demonstrated that bacteria, adhered onto L. braziliensis promastigote surface, formed small filamentous structures which apparently penetrates into the parasite membrane. d-mannose protects L. braziliensis against the S. marcescens SM365 lytic effect in a dose dependent manner. SM365 variant pre cultivated at 37 degrees C did not synthesize prodigiosin although the adherence and lysis of L. braziliensis were similar to the effect observed with bacteria cultivated at 28 degrees C, which produce high concentrations of prodigiosin. Thus, we suggest that prodigiosin is not involved in the lysis of promastigotes and that adherence promoted by bacterial mannose-sensitive (MS) fimbriae is a determinant factor in the lysis of L. braziliensis by S. marcescens SM365.

  5. 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.

  6. A new dual-signalling electrochemical sensing strategy based on competitive host-guest interaction of a β-cyclodextrin/poly(N-acetylaniline)/graphene-modified electrode: sensitive electrochemical determination of organic pollutants.

    PubMed

    Zhu, Gangbing; Wu, Liang; Zhang, Xia; Liu, Wei; Zhang, Xiaohua; Chen, Jinhua

    2013-05-10

    Based on the competitive host-guest interaction between a β-cyclodextrin/poly(N-acetylaniline)/electrogenerated-graphene (β-CD/PNAANI/EG) film and probe or target molecules, a new dual-signalling electrochemical sensing method has been developed for the sensitive and selective determination of organic pollutants. As a model system, rhodamine B (RhB) and 1-aminopyrene (1-AP) were adopted as the probe and target molecules, respectively. Due to the host-guest interaction, RhB molecules can enter into the hydrophobic inner cavity of β-CD, and the β-CD/PNAANI/EG-modified glassy carbon electrode displays a remarkable oxidation peak due to RhB. In the presence of 1-AP, competitive association to β-CD occurs and the RhB molecules are displaced by 1-AP. This results in a decreased oxidation peak current of RhB and the appearance of an oxidation peak current for 1-AP, and the changes of these signals correlate linearly with the concentration of 1-AP. When the value ΔI(1-AP)+∣ΔI(RhB)∣ (ΔI(1-AP) and ΔI(RhB) are the change values of the oxidation peak currents of 1-AP and RhB, respectively) is used as the response signal to quantitatively determine the concentration of 1-AP, the detection limit is much lower than that given by using ΔI(1-AP) or ΔI(RhB) as the response signal. This dual-signalling sensor can provide more sensitive target recognition and will have important applications in the sensitive and selective electrochemical determination of electroactive organic pollutants.

  7. Interaction intimacy organizes networks of antagonistic interactions in different ways

    PubMed Central

    Pires, Mathias M.; Guimarães, Paulo R.

    2013-01-01

    Interaction intimacy, the degree of biological integration between interacting individuals, shapes the ecology and evolution of species interactions. A major question in ecology is whether interaction intimacy also shapes the way interactions are organized within communities. We combined analyses of network structure and food web models to test the role of interaction intimacy in determining patterns of antagonistic interactions, such as host–parasite, predator–prey and plant–herbivore interactions. Networks describing interactions with low intimacy were more connected, more nested and less modular than high-intimacy networks. Moreover, the performance of the models differed across networks with different levels of intimacy. All models reproduced well low-intimacy networks, whereas the more elaborate models were also capable of reproducing networks depicting interactions with higher levels of intimacy. Our results indicate the key role of interaction intimacy in organizing antagonisms, suggesting that greater interaction intimacy might be associated with greater complexity in the assembly rules shaping ecological networks. PMID:23015523

  8. Interaction intimacy organizes networks of antagonistic interactions in different ways.

    PubMed

    Pires, Mathias M; Guimarães, Paulo R

    2013-01-01

    Interaction intimacy, the degree of biological integration between interacting individuals, shapes the ecology and evolution of species interactions. A major question in ecology is whether interaction intimacy also shapes the way interactions are organized within communities. We combined analyses of network structure and food web models to test the role of interaction intimacy in determining patterns of antagonistic interactions, such as host-parasite, predator-prey and plant-herbivore interactions. Networks describing interactions with low intimacy were more connected, more nested and less modular than high-intimacy networks. Moreover, the performance of the models differed across networks with different levels of intimacy. All models reproduced well low-intimacy networks, whereas the more elaborate models were also capable of reproducing networks depicting interactions with higher levels of intimacy. Our results indicate the key role of interaction intimacy in organizing antagonisms, suggesting that greater interaction intimacy might be associated with greater complexity in the assembly rules shaping ecological networks.

  9. [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3.

    PubMed

    Matias, P M; Soares, C M; Saraiva, L M; Coelho, R; Morais, J; Le Gall, J; Carrondo, M A

    2001-01-01

    The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfitricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and Rfree=0.223 using data to 1.8 A resolution. Two unique structural features are observed: the [4Fe-4S] cluster nearest the [NiFe] centre has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fold disorder was observed for Cys536 which binds to the nickel atom in the [NiFe] centre. Also, the bridging sulfur atom that caps the active site was found to have partial occupancy, thus corresponding to a partly activated enzyme. These structural features may have biological relevance. In particular, the two less-populated rotamers of Cys536 may be involved in the activation process of the enzyme, as well as in the catalytic cycle. Molecular modelling studies were carried out on the interaction between this [NiFe] hydrogenase and its physiological partner, the tetrahaem cytochrome c3 from the same organism. The lowest energy docking solutions were found to correspond to an interaction between the haem IV region in tetrahaem cytochrome c3 with the distal [4Fe-4S] cluster in [NiFe] hydrogenase. This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres and the fact that electron transfer decay coupling calculations show high coupling values and a short electron transfer pathway. On the other hand, other docking solutions have been found that, despite showing low electron transfer efficiency, may give clues on possible proton transfer mechanisms between the two molecules. PMID:11191224

  10. 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.

  11. 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

  12. Molecular Determinants in Phagocyte-Bacteria Interactions.

    PubMed

    Kaufmann, Stefan H E; Dorhoi, Anca

    2016-03-15

    Phagocytes are crucial for host defense against bacterial pathogens. As first demonstrated by Metchnikoff, neutrophils and mononuclear phagocytes share the capacity to engulf, kill, and digest microbial invaders. Generally, neutrophils focus on extracellular, and mononuclear phagocytes on intracellular, pathogens. Reciprocally, extracellular pathogens often capitalize on hindering phagocytosis and killing of phagocytes, whereas intracellular bacteria frequently allow their engulfment and then block intracellular killing. As foreseen by Metchnikoff, phagocytes become highly versatile by acquiring diverse phenotypes, but still retaining some plasticity. Further, phagocytes engage in active crosstalk with parenchymal and immune cells to promote adjunctive reactions, including inflammation, tissue healing, and remodeling. This dynamic network allows the host to cope with different types of microbial invaders. Here we present an update of molecular and cellular mechanisms underlying phagocyte functions in antibacterial defense. We focus on four exemplary bacteria ranging from an opportunistic extracellular to a persistent intracellular pathogen. PMID:26982355

  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. Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp- mRNAs

    PubMed Central

    Kumar, Parimal; Sweeney, Trevor R.; Skabkin, Maxim A.; Skabkina, Olga V.; Pestova, Tatyana V.

    2014-01-01

    Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA’s 5′-terminal ‘cap’. The minimal ‘cap0’ consists of N7-methylguanosine linked to the first nucleotide via a 5′-5′ triphosphate (ppp) bridge. Cap0 is further modified by 2′-O-methylation of the next two riboses, yielding ‘cap1’ (m7GpppNmN) and ‘cap2’ (m7GpppNmNm). However, some viral RNAs lack 2′-O-methylation, whereas others contain only ppp- at their 5′-end. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed effectors of innate immunity that inhibit viral replication by incompletely understood mechanisms. Here, we investigated the ability of IFIT family members to interact with cap1-, cap0- and 5′ppp- mRNAs and inhibit their translation. IFIT1 and IFIT1B showed very high affinity to cap-proximal regions of cap0-mRNAs (K1/2,app ∼9 to 23 nM). The 2′-O-methylation abrogated IFIT1/mRNA interaction, whereas IFIT1B retained the ability to bind cap1-mRNA, albeit with reduced affinity (K1/2,app ∼450 nM). The 5′-terminal regions of 5′ppp-mRNAs were recognized by IFIT5 (K1/2,app ∼400 nM). The activity of individual IFITs in inhibiting initiation on a specific mRNA was determined by their ability to interact with its 5′-terminal region: IFIT1 and IFIT1B efficiently outcompeted eIF4F and abrogated initiation on cap0-mRNAs, whereas inhibition on cap1- and 5′ppp- mRNAs by IFIT1B and IFIT5 was weaker and required higher protein concentrations. PMID:24371270

  15. First-in-man tau vaccine targeting structural determinants essential for pathological tau–tau interaction reduces tau oligomerisation and neurofibrillary degeneration in an Alzheimer’s disease model

    PubMed Central

    2014-01-01

    Introduction We have identified structural determinants on tau protein that are essential for pathological tau–tau interaction in Alzheimer’s disease (AD). These regulatory domains, revealed by monoclonal antibody DC8E8, represent a novel target for tau-directed therapy. In order to validate this target, we have developed an active vaccine, AADvac1. Methods A tau peptide encompassing the epitope revealed by DC8E8 was selected for the development of an active vaccine targeting structural determinants on mis-disordered tau protein that are essential for pathological tau–tau interaction. The efficacy of the vaccine was tested in a transgenic rat model of human tauopathies. Toxicology and safety pharmacology studies were conducted under good laboratory practice conditions in multiple rodent and nonrodent species. Results We have administered the tau peptide vaccine to a rat model of AD to investigate whether the vaccine can improve its clinical, histopathological and biochemical AD phenotype. Our results show that vaccination induced a robust protective humoral immune response, with antibodies discriminating between pathological and physiological tau. Active immunotherapy reduced the levels of tau oligomers and the extent of neurofibrillary pathology in the brains of transgenic rats. Strikingly, immunotherapy has reduced AD-type hyperphosphorylation of tau by approximately 95%. Also, the tau peptide vaccine improved the clinical phenotype of transgenic animals. Toxicology and safety pharmacology studies showed an excellent safety and tolerability profile of the AADvac1 vaccine. Conclusions Active immunisation targeting crucial domains of Alzheimer tau eliminated tau aggregation and neurofibrillary pathology. Most importantly, the AD type of tau hyperphosphorylation was abolished by vaccination across a wide range of AD phospho-epitopes. Our results demonstrate that active immunisation led to elimination of all major hallmarks of neurofibrillary pathology, which

  16. Synthesis, structure determination, and infrared spectroscopy of (NpO{sub 2}){sub 2}(SO{sub 4})(H{sub 2}O){sub 4}: Prevalence of cation-cation interactions and cationic nets in neptunyl sulfate compounds

    SciTech Connect

    Forbes, T.Z. Burns, P.C.

    2009-01-15

    The compound (NpO{sub 2}){sub 2}(SO{sub 4})(H{sub 2}O){sub 4} was synthesized by evaporation of a Np{sup 5+} sulfate solution. The crystal structure was determined using single crystal X-ray diffraction and refined to an R{sub 1}=0.0310. (NpO{sub 2}){sub 2}(SO{sub 4})(H{sub 2}O){sub 4} crystallizes in triclinic space group P-1, a=8.1102(7) A, b=8.7506(7) A, c=16.234(1) A, {alpha}=90.242(2){sup o}, {beta}=92.855(2){sup o}, {gamma}=113.067(2){sup o}, V=1058.3(2) A{sup 3}, and Z=2. The structure contains neptunyl pentagonal bipyramids that share vertices through cation-cation interactions to form a sheet or cationic net. The sheet is decorated on each side by vertex sharing with sulfate tetrahedra, and adjacent sheets are linked together through hydrogen bonding. A graphical representation of (NpO{sub 2}){sub 2}(SO{sub 4})(H{sub 2}O){sub 4} was constructed to facilitate the structural comparison to similar Np{sup 5+} compounds. The prevalence of the cationic nets in neptunyl sulfate compounds related to the overall stability of the structure is also discussed. - Graphical abstract: (NpO{sub 2}){sub 2}(SO{sub 4})(H{sub 2}O){sub 4} was synthesized by hydrothermal methods and its structure determined. A graphical representation of the compound was constructed to facilitate the structural comparison to similar Np{sup 5+} compounds and the prevalence of the cationic nets in neptunyl sulfate compounds related to the overall stability of the structure is discussed.

  17. A rapid and simple method for the simultaneous determination of four endogenous monoamine neurotransmitters in rat brain using hydrophilic interaction liquid chromatography coupled with atmospheric-pressure chemical ionization tandem mass spectrometry.

    PubMed

    Zhou, Wenbin; Zhu, Bangjie; Liu, Feng; Lyu, Chunming; Zhang, Shen; Yan, Chao; Cheng, Yu; Wei, Hai

    2015-10-01

    Endogenous monoamine neurotransmitters play an essential role in neural communication in mammalians. Many quantitative methods for endogenous monoamines have been developed during recent decades. Yet, matrix effect was usually a challenge in the quantification, in many cases asking for tedious sample preparation or sacrificing sensitivity. In this work, a simple, fast and sensitive method with no matrix effect was developed to simultaneously determine four endogenous monoamines including serotonin, dopamine, epinephrine and norepinephrine in rat brain tissues, using hydrophilic interaction liquid chromatography coupled with atmospheric-pressure chemical ionization tandem mass spectrometry. Various conditions, including columns, chromatographic conditions, ion source, MS/MS conditions, and brain tissue preparation methods, were optimized and validated. Pre-weighed 20mg brain sample could be effectively and reproducibly homogenized and protein-precipitated by 20 times value of 0.2% formic acid in cold organic solvents (methanol-acetonitrile, 10:90, v/v). This method exhibited excellent linearity for all analytes (regression coefficients>0.998 or 0.999). The precision, expressed as coefficients of variation, was less than 3.43% for intra-day analyses and ranged from 4.17% to 15.5% for inter-day analyses. Good performance was showed in limit of detection (between 0.3nM and 3.0nM for all analytes), recovery (90.8-120%), matrix effect (84.4-107%), accuracy (89.8-100%) and stability (88.3-104%). The validated method was well applied to simultaneously determine the endogenous serotonin, dopamine, epinephrine and norepinephrine in four brain sections of 18 Wistar rats. The quantification of four endogenous monoamines in rat brain performed excellently in the sensitivity, high throughput, simple sample preparation and matrix effect.

  18. Drug Interactions

    PubMed Central

    Tong Logan, Angela; Silverman, Andrew

    2012-01-01

    One of the most clinically significant complications related to the use of pharmacotherapy is the potential for drug-drug or drug-disease interactions. The gastrointestinal system plays a large role in the pharmacokinetic profile of most medications, and many medications utilized in gastroenterology have clinically significant drug interactions. This review will discuss the impact of alterations of intestinal pH, interactions mediated by phase I hepatic metabolism enzymes and P-glycoprotein, the impact of liver disease on drug metabolism, and interactions seen with commonly utilized gastrointestinal medications. PMID:22933873

  19. Separation and determination of metallocyanide complexes of Fe(II), Ni(II) and Co(III) by ion-interaction chromatography with membrane suppressed conductivity detection applied to analysis of oil refinery streams (sour water).

    PubMed

    Souza e Silva, Renata; de Carvalho, Maria de Fátima Batista; Santelli, Ricardo Erthal

    2006-09-15

    A separation and determination method for the analysis of cyanometallic complexes of Fe(II), Ni(II) and Co(III) was developed to be applied to the analysis of petroleum refinery streams (sour water). Ion-interaction chromatography was used employing an analytical column IonPac NS1 10 microm and a chromatographic system ICS 2500 equipped with a membrane conductivity suppression ASRS ultra 4mm, both supplied by Dionex Corporation. The mobile phase was composed of 2 mmol l(-1) TBAOH, 1 mmol l(-1) Na(2)CO(3), 0.1 mol l(-1) NaCN and ACN (77:23, v/v), flowing at 0.7 ml min(-1). At the optimized conditions, detection limits estimated by the calibration curve parameters and relative standard deviation were: 0.002 mg CNl(-1) and 3.1% for Fe(CN)(6)(4-); 0.003 mg CNl(-1) and 2.5% for Ni(CN)(4)(2-) and 0.003 mg CNl(-1) and 2.8% for Co(CN)(6)(3-). Sour water samples without any pretreatment (except membrane filtration) from a petroleum refinery in Brazil were analyzed successfully by external calibration method. PMID:16889783

  20. 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

    2012-01-01

    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

  1. Imagined Interactions

    ERIC Educational Resources Information Center

    Honeycutt, James M.

    2010-01-01

    Social scientists have been studying imagined interactions since the mid-1980s and have measured numerous physiological correlates (Honeycutt, 2010). In this commentary I assess the research reported in Crisp and Turner (May-June 2009) and highlight the underlying mechanisms of imagined interactions that have empirically been laid out across…

  2. Interacting parasites

    USGS Publications Warehouse

    Lafferty, Kevin D.

    2010-01-01

    Parasitism is the most popular life-style on Earth, and many vertebrates host more than one kind of parasite at a time. A common assumption is that parasite species rarely interact, because they often exploit different tissues in a host, and this use of discrete resources limits competition (1). On page 243 of this issue, however, Telfer et al. (2) provide a convincing case of a highly interactive parasite community in voles, and show how infection with one parasite can affect susceptibility to others. If some human parasites are equally interactive, our current, disease-by-disease approach to modeling and treating infectious diseases is inadequate (3).

  3. Magnetocrystalline interactions and oxidation state determination of Mn{sub (2−x)}V{sub (1+x)}O{sub 4} (x=0, 1/3 and 1) magnetorresistive spinel family

    SciTech Connect

    Pomiro, F.; Ceppi, S.; De Paoli, J.M.; Sánchez, R.D.; Mesquita, A.; Tirao, G.; and others

    2013-09-15

    Oxidation states of transition metal cations in spinels-type oxides are sometimes extremely difficult to determine by conventional spectroscopic methods. One of the most complex cases occurs when there are different cations, each one with several possible oxidation states, as in the case of the magnetoresistant Mn{sub (2−x)}V{sub (1+x)}O{sub 4} (x=0, 1/3 and 1) spinel-type family. In this contribution we describe the determination of the oxidation state of manganese and vanadium in Mn{sub (2−x)}V{sub (1+x)}O{sub 4} (x=0, 1/3,1) spinel-type compounds by analyzing XANES and high-resolution Kβ X-ray fluorescence spectra. The ionic models found are Mn{sup 2+}{sub 2}V{sup 4+}O{sub 4}, Mn{sup 2+}{sub 5/3}V{sup 3.5+}{sub 4/3}O{sub 4} and Mn{sup 2+}V{sup 3+}{sub 2}O{sub 4}. Combination of the present results with previous data provided a reliable cation distribution model. For these spinels, single magnetic electron paramagnetic resonance (EPR) lines are observed at 480 K showing the interaction among the different magnetic ions. The analysis of the EPR parameters show that g-values and relative intensities are highly influenced by the concentration and the high-spin state of Mn{sup 2+}. EPR broadening linewidth is explained in terms of the bottleneck effect, which is due to the presence of the fast relaxing V{sup 3+} ion instead of the weak Mn{sup 2+} (S state) coupled to the lattice. The EPR results, at high temperature, are well explained assuming the oxidation states of the magnetic ions obtained by the other spectroscopic techniques. - Graphical abstract: View of the crystallographic structure of a spinel. It shows as an example one of the models of ion distribution determined for the spinels Mn{sub (2−x)}V{sub (1+x)}O{sub 4} (x=0, 1/3,1). Display Omitted - Highlights: • Determination of oxidation state of the metallic ions in Mn{sub (2−x)}V{sub (1+x)}O{sub 4} (x=0,1/3,1) by XAS and XES techniques. • The ionic models found are Mn{sup 2+}{sub 2}V{sup 4+}O

  4. Analytical approach to determining human biogenic amines and their metabolites using eVol microextraction in packed syringe coupled to liquid chromatography mass spectrometry method with hydrophilic interaction chromatography column.

    PubMed

    Konieczna, Lucyna; Roszkowska, Anna; Synakiewicz, Anna; Stachowicz-Stencel, Teresa; Adamkiewicz-Drożyńska, Elżbieta; Bączek, Tomasz

    2016-04-01

    Analysis of biogenic amines (BAs) in different human samples provides insight into the mechanisms of various biological processes, including pathological conditions, and thus may be very important in diagnosing and monitoring several neurological disorders and cancerous tumors. In this work, we developed a simple and fast procedure using a digitally controlled microextraction in packed syringe (MEPS) coupled to liquid chromatography mass spectrometry (LC-MS) method for simultaneous determination of biogenic amines, their precursors and metabolites in human plasma and urine samples. The separation of 12 low molecular weight and hydrophilic molecules with a wide range of polarities was achieved with hydrophilic interaction chromatography (HILIC) column without derivatization step in 12 min. MEPS was implemented using the APS sorbent in semi-automated analytical syringe (eVol(®)) and small volume of urine and plasma samples, 5 0µL and 100 μL, respectively. We evaluated important parameters influencing MEPS efficiency, including stationary