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Sample records for affinity propagation reveals

  1. Classification of neocortical interneurons using affinity propagation.

    PubMed

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  2. Classification of neocortical interneurons using affinity propagation

    PubMed Central

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  3. Learning factorizations in estimation of distribution algorithms using affinity propagation.

    PubMed

    Santana, Roberto; Larrañaga, Pedro; Lozano, José A

    2010-01-01

    Estimation of distribution algorithms (EDAs) that use marginal product model factorizations have been widely applied to a broad range of mainly binary optimization problems. In this paper, we introduce the affinity propagation EDA (AffEDA) which learns a marginal product model by clustering a matrix of mutual information learned from the data using a very efficient message-passing algorithm known as affinity propagation. The introduced algorithm is tested on a set of binary and nonbinary decomposable functions and using a hard combinatorial class of problem known as the HP protein model. The results show that the algorithm is a very efficient alternative to other EDAs that use marginal product model factorizations such as the extended compact genetic algorithm (ECGA) and improves the quality of the results achieved by ECGA when the cardinality of the variables is increased.

  4. An Affinity Propagation-Based DNA Motif Discovery Algorithm.

    PubMed

    Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang

    2015-01-01

    The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  5. Conformational kinetics reveals affinities of protein conformational states.

    PubMed

    Daniels, Kyle G; Suo, Yang; Oas, Terrence G

    2015-07-28

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

  6. A multiobjective evolutionary algorithm to find community structures based on affinity propagation

    NASA Astrophysics Data System (ADS)

    Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng

    2016-07-01

    Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.

  7. A Poisson-based adaptive affinity propagation clustering for SAGE data.

    PubMed

    Tang, DongMing; Zhu, QingXin; Yang, Fan

    2010-02-01

    Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several real life SAGE datasets. The experimental results show that PoissonAPS can produce meaningful and interpretable clusters for SAGE data.

  8. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

    PubMed Central

    Heidelberg, John F.; Tully, Benjamin J.

    2017-01-01

    Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes. PMID:28289564

  9. Genomic affinities revealed by GISH suggests intergenomic restructuring between parental genomes of the paleopolyploid genus Zea.

    PubMed

    González, Graciela Esther; Poggio, Lidia

    2015-10-01

    The present work compares the molecular affinities, revealed by GISH, with the analysis of meiotic pairing in intra- and interspecific hybrids between species of Zea obtained in previous works. The joint analysis of these data provided evidence about the evolutionary relationships among the species from the paleopolyploid genus Zea (maize and teosintes). GISH and meiotic pairing of intraspecific hybrids revealed high genomic affinity between maize (Zea mays subsp. mays) and both Zea mays subsp. parviglumis and Zea mays subsp. mexicana. On the other hand, when Zea mays subsp. huehuetenanguensis DNA was probed on maize chromosomes, a lower affinity was detected, and the pattern of hybridization suggested intergenomical restructuring between the parental genomes of maize. When DNA from Zea luxurians was used as probe, homogeneous hybridization signals were observed through all maize chromosomes. Lower genomic affinity was observed when DNA from Zea diploperennis was probed on maize chromosomes, especially at knob regions. Maize chromosomes hybridized with Zea perennis DNA showed hybridization signals on four chromosome pairs: two chromosome pairs presented hybridization signal in only one chromosomal arm, whereas four chromosome pairs did not show any hybridization. These results are in agreement with previous GISH studies, which have identified the genomic source of the chromosomes involved in the meiotic configurations of Z. perennis × maize hybrids. These findings allow postulating that maize has a parental genome not shared with Z. perennis, and the existence of intergenomic restructuring between the parental genomes of maize. Moreover, the absence of hybridization signals in all maize knobs indicate that these heterochromatic regions were lost during the Z. perennis genome evolution.

  10. Fatigue damage prognosis of internal delamination in composite plates under cyclic compression loadings using affine arithmetic as uncertainty propagation tool

    NASA Astrophysics Data System (ADS)

    Gbaguidi, Audrey J.-M.

    compressive-buckling loadings is experimentally studied, and the delamination lengths obtained are compared with the predicted values to check the performance of Affine Arithmetic as an uncertainty propagation tool.

  11. A Mixed Approach to Similarity Metric Selection in Affinity Propagation-Based WiFi Fingerprinting Indoor Positioning.

    PubMed

    Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella

    2015-10-30

    The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different

  12. A Novel User Classification Method for Femtocell Network by Using Affinity Propagation Algorithm and Artificial Neural Network

    PubMed Central

    Ahmed, Afaz Uddin; Tariqul Islam, Mohammad; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina

    2014-01-01

    An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation. PMID:25133214

  13. A novel user classification method for femtocell network by using affinity propagation algorithm and artificial neural network.

    PubMed

    Ahmed, Afaz Uddin; Islam, Mohammad Tariqul; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina

    2014-01-01

    An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation.

  14. Thermochronometry reveals headward propagation of erosion in an alpine landscape.

    PubMed

    Shuster, David L; Cuffey, Kurt M; Sanders, Johnny W; Balco, Greg

    2011-04-01

    Glacial erosion of mountain ranges produces spectacular alpine landscapes and, by linking climate with tectonics, influences a broad array of geophysical phenomena. Although the resultant landforms are easily identified, the timing and spatial pattern of topographic adjustment to Pleistocene glaciations remain poorly known. We investigated topographic evolution in the archetypal glacial landscape of Fiordland, New Zealand, using (U-Th)/He thermochronometry. We find that erosion during the past 2 million years removed the entire pre-Pleistocene landscape and fundamentally reshaped the topography. Erosion focused on steep valley segments and propagated from trunk valleys toward the heads of drainage basins, a behavior expected if subglacial erosion rate depends on ice sliding velocity. The Fiordland landscape illustrates complex effects of climate on Earth's surface morphology.

  15. pH-dependent binding engineering reveals an FcRn affinity threshold that governs IgG recycling.

    PubMed

    Borrok, M Jack; Wu, Yanli; Beyaz, Nurten; Yu, Xiang-Qing; Oganesyan, Vaheh; Dall'Acqua, William F; Tsui, Ping

    2015-02-13

    The Fc domain of IgG has been the target of multiple mutational studies aimed at altering the pH-dependent IgG/FcRn interaction to modulate IgG pharmacokinetics. These studies have yielded antibody variants with disparate pharmacokinetic characteristics, ranging from extended in vivo half-life to those exhibiting extremely rapid clearance. To better understand pH-dependent binding parameters that govern these outcomes and limit FcRn-mediated half-life extension, we generated a panel of novel Fc variants with high affinity binding at acidic pH that vary in pH 7.4 affinities and assessed pharmacokinetic outcomes. Pharmacokinetic studies in human FcRn transgenic mice and cynomolgus monkeys showed that multiple variants with increased FcRn affinities at acidic pH exhibited extended serum half-lives relative to the parental IgG. Importantly, the results reveal an underappreciated affinity threshold of neutral pH binding that determines IgG recycling efficiency. Variants with pH 7.4 FcRn affinities below this threshold recycle efficiently and can exhibit increased serum persistence. Increasing neutral pH FcRn affinity beyond this threshold reduced serum persistence by offsetting the benefits of increased pH 6.0 binding. Ultra-high affinity binding to FcRn at both acidic and neutral pH leads to rapid serum clearance.

  16. Evolved Streptavidin Mutants Reveal Key Role of Loop Residue in High-affinity Binding

    SciTech Connect

    M Magalhaes; C Melo Czekster; R Guan; V Malashkevich; S Almo; M Levy

    2011-12-31

    We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a {approx}10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

  17. Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing

    PubMed Central

    Reshetova, Polina; van Schaik, Barbera D. C.; Klarenbeek, Paul L.; Doorenspleet, Marieke E.; Esveldt, Rebecca E. E.; Tak, Paul-Peter; Guikema, Jeroen E. J.; de Vries, Niek; van Kampen, Antoine H. C.

    2017-01-01

    Immunoglobulin repertoire sequencing has successfully been applied to identify expanded antigen-activated B-cell clones that play a role in the pathogenesis of immune disorders. One challenge is the selection of the Ag-specific B cells from the measured repertoire for downstream analyses. A general feature of an immune response is the expansion of specific clones resulting in a set of subclones with common ancestry varying in abundance and in the number of acquired somatic mutations. The expanded subclones are expected to have BCR affinities for the Ag higher than the affinities of the naive B cells in the background population. For these reasons, several groups successfully proceeded or suggested selecting highly abundant subclones from the repertoire to obtain the Ag-specific B cells. Given the nature of affinity maturation one would expect that abundant subclones are of high affinity but since repertoire sequencing only provides information about abundancies, this can only be verified with additional experiments, which are very labor intensive. Moreover, this would also require knowledge of the Ag, which is often not available for clinical samples. Consequently, in general we do not know if the selected highly abundant subclone(s) are also the high(est) affinity subclones. Such knowledge would likely improve the selection of relevant subclones for further characterization and Ag screening. Therefore, to gain insight in the relation between subclone abundancy and affinity, we developed a computational model that simulates affinity maturation in a single GC while tracking individual subclones in terms of abundancy and affinity. We show that the model correctly captures the overall GC dynamics, and that the amount of expansion is qualitatively comparable to expansion observed from B cells isolated from human lymph nodes. Analysis of the fraction of high- and low-affinity subclones among the unexpanded and expanded subclones reveals a limited correlation between

  18. Combining self-organizing mapping and supervised affinity propagation clustering approach to investigate functional brain networks involved in motor imagery and execution with fMRI measurements.

    PubMed

    Zhang, Jiang; Liu, Qi; Chen, Huafu; Yuan, Zhen; Huang, Jin; Deng, Lihua; Lu, Fengmei; Zhang, Junpeng; Wang, Yuqing; Wang, Mingwen; Chen, Liangyin

    2015-01-01

    Clustering analysis methods have been widely applied to identifying the functional brain networks of a multitask paradigm. However, the previously used clustering analysis techniques are computationally expensive and thus impractical for clinical applications. In this study a novel method, called SOM-SAPC that combines self-organizing mapping (SOM) and supervised affinity propagation clustering (SAPC), is proposed and implemented to identify the motor execution (ME) and motor imagery (MI) networks. In SOM-SAPC, SOM was first performed to process fMRI data and SAPC is further utilized for clustering the patterns of functional networks. As a result, SOM-SAPC is able to significantly reduce the computational cost for brain network analysis. Simulation and clinical tests involving ME and MI were conducted based on SOM-SAPC, and the analysis results indicated that functional brain networks were clearly identified with different response patterns and reduced computational cost. In particular, three activation clusters were clearly revealed, which include parts of the visual, ME and MI functional networks. These findings validated that SOM-SAPC is an effective and robust method to analyze the fMRI data with multitasks.

  19. Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution.

    PubMed

    Jain, Niyati; Lin, Hsuan-Chun; Morgan, Christopher E; Harris, Michael E; Tolbert, Blanton S

    2017-02-28

    Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo.

  20. Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution

    PubMed Central

    Jain, Niyati; Lin, Hsuan-Chun; Morgan, Christopher E.; Harris, Michael E.; Tolbert, Blanton S.

    2017-01-01

    Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5′-YAG-3′ and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo. PMID:28193894

  1. Affinity chromatography reveals RuBisCO as an ecdysteroid-binding protein.

    PubMed

    Uhlik, Ondrej; Kamlar, Marek; Kohout, Ladislav; Jezek, Rudolf; Harmatha, Juraj; Macek, Tomas

    2008-12-22

    The aim of this work was to isolate plant ecdysteroid-binding proteins using affinity chromatography. Ecdysteroids as insect hormones have been investigated thoroughly but their function and the mechanism of action in plants and other organisms is still unknown although ecdysteroids occur in some plants in a relatively large amount. Therefore, 20-hydroxyecdysone was immobilized on a polymeric carrier as a ligand for affinity chromatography in order to isolate plant ecdysteroid-binding proteins from the cytosolic extract of New Zealand spinach (Tetragonia tetragonoides). Non-specifically bound proteins were eluted with a rising gradient of concentration of sodium chloride, and 3% (v/v) acetic acid was used for the elution of the specifically bound proteins. Using this method, ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was isolated. The influence of ecdysteroids on RuBisCO was further studied. Our results show that ecdysteroids are able to increase the yield of RuBisCO-mediated reaction in which CO(2) is fixed into organic matter by more than 10%.

  2. Propagating Neural Source Revealed by Doppler Shift of Population Spiking Frequency

    PubMed Central

    Zhang, Mingming; Shivacharan, Rajat S.; Chiang, Chia-Chu; Gonzalez-Reyes, Luis E.

    2016-01-01

    Electrical activity in the brain during normal and abnormal function is associated with propagating waves of various speeds and directions. It is unclear how both fast and slow traveling waves with sometime opposite directions can coexist in the same neural tissue. By recording population spikes simultaneously throughout the unfolded rodent hippocampus with a penetrating microelectrode array, we have shown that fast and slow waves are causally related, so a slowly moving neural source generates fast-propagating waves at ∼0.12 m/s. The source of the fast population spikes is limited in space and moving at ∼0.016 m/s based on both direct and Doppler measurements among 36 different spiking trains among eight different hippocampi. The fact that the source is itself moving can account for the surprising direction reversal of the wave. Therefore, these results indicate that a small neural focus can move and that this phenomenon could explain the apparent wave reflection at tissue edges or multiple foci observed at different locations in neural tissue. SIGNIFICANCE STATEMENT The use of novel techniques with an unfolded hippocampus and penetrating microelectrode array to record and analyze neural activity has revealed the existence of a source of neural signals that propagates throughout the hippocampus. The source itself is electrically silent, but its location can be inferred by building isochrone maps of population spikes that the source generates. The movement of the source can also be tracked by observing the Doppler frequency shift of these spikes. These results have general implications for how neural signals are generated and propagated in the hippocampus; moreover, they have important implications for the understanding of seizure generation and foci localization. PMID:27013678

  3. Single-molecule peptide-lipid affinity assay reveals interplay between solution structure and partitioning.

    PubMed

    Matin, Tina R; Sigdel, Krishna P; Utjesanovic, Milica; Marsh, Brendan P; Gallazzi, Fabio; Smith, Virginia F; Kosztin, Ioan; King, Gavin M

    2017-03-27

    Interactions between short protein segments and phospholipid bilayers dictate fundamental aspects of cellular activity and have important applications in biotechnology. Yet, a lack of suitable methodology for directly probing these interactions has hindered mechanistic understanding. We developed a precision atomic force microscope (AFM)-based single-molecule force spectroscopy assay and probed partitioning into lipid bilayers by measuring the mechanical force experienced by a peptide. Protein segments were constructed from the peripheral membrane protein SecA, a key ATPase in bacterial secretion. We focused on the first 10 amino-terminal residues of SecA (SecA2-11) which are known to be lipophilic. In addition to the core SecA2-11 sequence, constructs with nearly identical chemical composition but with differing geometry were used: two copies of SecA2-11 linked in series, and two copies in parallel. Lipid bilayer partitioning interactions of peptides with differing structures were distinguished. To model the energetic landscape, a theory of diffusive barrier crossing was extended to incorporate a superposition of potential barriers with variable weights. Analysis revealed two dissociation pathways for the core SecA2-11 sequence with well-separated intrinsic dissociation rates. Molecular dynamics simulations showed that the three peptides had significant conformational differences in solution that correlated well with measured variations in the propensity to partition into the bilayer. The methodology is generalizable and can be applied to other peptide and lipid species.

  4. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.

    PubMed

    U'ren, Jana M; Lutzoni, François; Miadlikowska, Jolanta; Arnold, A Elizabeth

    2010-08-01

    Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as

  5. CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity.

    PubMed

    Novikov, Fedor N; Zeifman, Alexey A; Stroganov, Oleg V; Stroylov, Viktor S; Kulkov, Val; Chilov, Ghermes G

    2011-09-26

    The dG prediction accuracy by the Lead Finder docking software on the CSAR test set was characterized by R(2)=0.62 and rmsd=1.93 kcal/mol, and the method of preparation of the full-atom structures of the test set did not significantly affect the resulting accuracy of predictions. The primary factors determining the correlation between the predicted and experimental values were the van der Waals interactions and solvation effects. Those two factors alone accounted for R(2)=0.50. The other factors that affected the accuracy of predictions, listed in the order of decreasing importance, were the change of ligand's internal energy upon binding with protein, the electrostatic interactions, and the hydrogen bonds. It appears that those latter factors contributed to the independence of the prediction results from the method of full-atom structure preparation. Then, we turned our attention to the other factors that could potentially improve the scoring function in order to raise the accuracy of the dG prediction. It turned out that the ligand-centric factors, including Mw, cLogP, PSA, etc. or protein-centric factors, such as the functional class of protein, did not improve the prediction accuracy. Following that, we explored if the weak molecular interactions such as X-H...Ar, X-H...Hal, CO...Hal, C-H...X, stacking and π-cationic interactions (where X is N or O), that are generally of interest to the medicinal chemists despite their lack of proper molecular mechanical parametrization, could improve dG prediction. Our analysis revealed that out of these new interactions only CO...Hal is statistically significant for dG predictions using Lead FInder scoring function. Accounting for the CO...Hal interaction resulted in the reduction of the rmsd from 2.19 to 0.69 kcal/mol for the corresponding structures. The other weak interaction factors were not statistically significant and therefore irrelevant to the accuracy of dG prediction. On the basis of our findings from our

  6. Application of a New Dual Localization-Affinity Purification Tag Reveals Novel Aspects of Protein Kinase Biology in Aspergillus nidulans

    PubMed Central

    De Souza, Colin P.; Hashmi, Shahr B.; Osmani, Aysha H.; Osmani, Stephen A.

    2014-01-01

    Filamentous fungi occupy critical environmental niches and have numerous beneficial industrial applications but devastating effects as pathogens and agents of food spoilage. As regulators of essentially all biological processes protein kinases have been intensively studied but how they regulate the often unique biology of filamentous fungi is not completely understood. Significant understanding of filamentous fungal biology has come from the study of the model organism Aspergillus nidulans using a combination of molecular genetics, biochemistry, cell biology and genomic approaches. Here we describe dual localization-affinity purification (DLAP) tags enabling endogenous N or C-terminal protein tagging for localization and biochemical studies in A. nidulans. To establish DLAP tag utility we endogenously tagged 17 protein kinases for analysis by live cell imaging and affinity purification. Proteomic analysis of purifications by mass spectrometry confirmed association of the CotA and NimXCdk1 kinases with known binding partners and verified a predicted interaction of the SldABub1/R1 spindle assembly checkpoint kinase with SldBBub3. We demonstrate that the single TOR kinase of A. nidulans locates to vacuoles and vesicles, suggesting that the function of endomembranes as major TOR cellular hubs is conserved in filamentous fungi. Comparative analysis revealed 7 kinases with mitotic specific locations including An-Cdc7 which unexpectedly located to mitotic spindle pole bodies (SPBs), the first such localization described for this family of DNA replication kinases. We show that the SepH septation kinase locates to SPBs specifically in the basal region of apical cells in a biphasic manner during mitosis and again during septation. This results in gradients of SepH between G1 SPBs which shift along hyphae as each septum forms. We propose that SepH regulates the septation initiation network (SIN) specifically at SPBs in the basal region of G1 cells and that localized gradients

  7. Epitope structure and binding affinity of single chain llama anti-β-amyloid antibodies revealed by proteolytic excision affinity-mass spectrometry.

    PubMed

    Paraschiv, Gabriela; Vincke, Cécile; Czaplewska, Paulina; Manea, Marilena; Muyldermans, Serge; Przybylski, Michael

    2013-01-01

    ß-Amyloid (Aß) immunotherapy has become a promising strategy for reducing the level of Aß in brain. New immunological approaches have been recently proposed for rapid, early diagnosis, and molecular treatment of neurodegenerative diseases related to Alzheimer's Disease (AD). The combination of proteolytic epitope excision and extraction and mass spectrometry using digestion with various proteases has been shown to be an efficient tool for the identification and molecular characterization of antigenic determinants. Here, we report the identification of the Aβ epitope recognized by the variable domain of single chain llama anti-Aβ-antibodies, termed Aβ-nanobodies, that have been discovered in the blood of camelids and found to be promising candidates for immunotherapy of AD. The epitope recognized by two Aβ-specific nanobodies was identified by proteolytic epitope extraction- and excision-mass spectrometry using a series of proteases (trypsin, chymotrypsin, GluC-protease, and LysC-protease). Matrix-assisted laser desorption ionization--mass spectrometric analysis of the affinity--elution fraction provided the epitope, Aβ(17-28), in the mid- to carboxy-terminal domain of Aβ, which has been shown to exert an Aß-fibril inhibiting effect. Affinity studies of the synthetic epitope confirmed that the Aβ(17-28) peptide is the minimal fragment that binds to the nanobodies. The interactions between the nanobodies and full length Aβ(1-40) or Aβ-peptides containing or lacking the epitope sequence were further characterized by enzyme linked immunosorbent assay and bioaffinity analysis. Determinations of binding affinities between the Aβ-nanobodies and Aβ(1-40) and the Aβ(17-28) epitope provided K(D) values of approximately 150 and 700 nmol, respectively. Thus, the knowledge of the epitope may be highly useful for future studies of Aβ-aggregation (oligomerization and fibril formation) and for designing new aggregation inhibitors.

  8. Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft.

    PubMed

    Kandra, Lili; Hachem, Maher Abou; Gyémánt, Gyöngyi; Kramhøft, Birte; Svensson, Birte

    2006-09-18

    Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites as binding barriers. Barley alpha-amylase 1 mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in alpha-amylases.

  9. Structure of a TCR with High Affinity for Self-antigen Reveals Basis for Escape from Negative Selection

    SciTech Connect

    Y Yin; Y Li; M Kerzic; R Martin; R Mariuzza

    2011-12-31

    The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding topologies compared with anti-microbial TCRs. Alternatively, escape can occur by weak binding between self-peptides and MHC. We determined the structure of a human autoimmune TCR (MS2-3C8) bound to a self-peptide from myelin basic protein (MBP) and the multiple sclerosis-associated MHC molecule HLA-DR4. MBP is loosely accommodated in the HLA-DR4-binding groove, accounting for its low affinity. Conversely, MS2-3C8 binds MBP-DR4 as tightly as the most avid anti-microbial TCRs. MS2-3C8 engages self-antigen via a docking mode that resembles the optimal topology of anti-foreign TCRs, but is distinct from that of other autoreactive TCRs. Combined with a unique CDR3 conformation, this docking mode compensates for the weak binding of MBP to HLA-DR4 by maximizing interactions between MS2-3C8 and MBP. Thus, the MS2-3C8-MBP-DR4 complex reveals the basis for an alternative strategy whereby autoreactive T cells escape negative selection, yet retain the ability to initiate autoimmunity.

  10. Paleogenetic Analyses Reveal Unsuspected Phylogenetic Affinities between Mice and the Extinct Malpaisomys insularis, an Endemic Rodent of the Canaries

    PubMed Central

    Gros-Balthazard, Muriel; Hughes, Sandrine; Alcover, Josep Antoni; Hutterer, Rainer; Rando, Juan Carlos; Michaux, Jacques; Hänni, Catherine

    2012-01-01

    Background The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. Methodology/Principal Findings In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse. PMID:22363563

  11. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Malaisree, Maturos; Long, Ben; McIntosh-Smith, Simon; Mulholland, Adrian J.

    2013-12-01

    The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational `assay.'

  12. Equations of interdoublet separation during flagella motion reveal mechanisms of wave propagation and instability.

    PubMed

    Bayly, Philip V; Wilson, Kate S

    2014-10-07

    The motion of flagella and cilia arises from the coordinated activity of dynein motor protein molecules arrayed along microtubule doublets that span the length of axoneme (the flagellar cytoskeleton). Dynein activity causes relative sliding between the doublets, which generates propulsive bending of the flagellum. The mechanism of dynein coordination remains incompletely understood, although it has been the focus of many studies, both theoretical and experimental. In one leading hypothesis, known as the geometric clutch (GC) model, local dynein activity is thought to be controlled by interdoublet separation. The GC model has been implemented as a numerical simulation in which the behavior of a discrete set of rigid links in viscous fluid, driven by active elements, was approximated using a simplified time-marching scheme. A continuum mechanical model and associated partial differential equations of the GC model have remained lacking. Such equations would provide insight into the underlying biophysics, enable mathematical analysis of the behavior, and facilitate rigorous comparison to other models. In this article, the equations of motion for the flagellum and its doublets are derived from mechanical equilibrium principles and simple constitutive models. These equations are analyzed to reveal mechanisms of wave propagation and instability in the GC model. With parameter values in the range expected for Chlamydomonas flagella, solutions to the fully nonlinear equations closely resemble observed waveforms. These results support the ability of the GC hypothesis to explain dynein coordination in flagella and provide a mathematical foundation for comparison to other leading models.

  13. Disease-associated mutant alpha-actinin-4 reveals a mechanism for regulating its F-actin-binding affinity.

    PubMed

    Weins, Astrid; Schlondorff, Johannes S; Nakamura, Fumihiko; Denker, Bradley M; Hartwig, John H; Stossel, Thomas P; Pollak, Martin R

    2007-10-09

    Alpha-actinin-4 is a widely expressed protein that employs an actin-binding site with two calponin homology domains to crosslink actin filaments (F-actin) in a Ca(2+)-sensitive manner in vitro. An inherited, late-onset form of kidney failure is caused by point mutations in the alpha-actinin-4 actin-binding domain. Here we show that alpha-actinin-4/F-actin aggregates, observed in vivo in podocytes of humans and mice with disease, likely form as a direct result of the increased actin-binding affinity of the protein. We document that exposure of a buried actin-binding site 1 in mutant alpha-actinin-4 causes an increase in its actin-binding affinity, abolishes its Ca(2+) regulation in vitro, and diverts its normal localization from actin stress fibers and focal adhesions in vivo. Inactivation of this buried actin-binding site returns the affinity of the mutant to that of the WT protein and abolishes aggregate formation in cells. In vitro, actin filaments crosslinked by the mutant alpha-actinin-4 exhibit profound changes of structural and biomechanical properties compared with WT alpha-actinin-4. On a molecular level, our findings elucidate the physiological importance of a dynamic interaction of alpha-actinin with F-actin in podocytes in vivo. We propose that a conformational change with full exposure of actin-binding site 1 could function as a switch mechanism to regulate the actin-binding affinity of alpha-actinin and possibly other calponin homology domain proteins under physiological conditions.

  14. Inter-allelic prion propagation reveals conformational relationships among a multitude of [PSI] strains.

    PubMed

    Lin, Jia-Yu; Liao, Tzu-Ya; Lee, Han-Chung; King, Chih-Yen

    2011-09-01

    Immense diversity of prion strains is observed, but its underlying mechanism is less clear. Three [PSI] prion strains--named VH, VK, and VL--were previously isolated in the wild-type yeast genetic background. Here we report the generation and characterization of eight new [PSI] isolates, obtained by propagating the wild-type strains with Sup35 proteins containing single amino-acid alterations. The VH strain splits into two distinct strains when propagated in each of the three genetic backgrounds, harboring respectively single mutations of N21L, R28P, and Gi47 (i.e. insertion of a glycine residue at position 47) on the Sup35 N-terminal prion-forming segment. The six new strains exhibit complex inter-conversion patterns, and one of them continuously mutates into another. However, when they are introduced back into the wild-type background, all 6 strains revert to the VH strain. We obtain two more [PSI] isolates by propagating VK and VL with the Gi47 and N21L backgrounds, respectively. The two isolates do not transmit to other mutant backgrounds but revert to their parental strains in the wild-type background. Our data indicate that a large number of [PSI] strains can be built on three basic Sup35 amyloid structures. It is proposed that the three basic structures differ by chain folding topologies, and sub-strains with the same topology differ in distinct ways by local structural adjustments. This "large number of variations on a small number of basic themes" may also be operative in generating strain diversities in other prion elements. It thus suggests a possible general scheme to classify a multitude of prion strains.

  15. Mycobacterium tuberculosis dihydrofolate reductase reveals two conformational states and a possible low affinity mechanism to antifolate drugs.

    PubMed

    Dias, Marcio Vinicius Bertacine; Tyrakis, Petros; Domingues, Romenia Ramos; Paes Leme, Adriana Franco; Blundell, Tom L

    2014-01-07

    Inhibition of the biosynthesis of tetrahydrofolate (THF) has long been a focus in the treatment of both cancer and infectious diseases. Dihydrofolate reductase (DHFR), which catalyzes the last step, is one of the most thoroughly explored targets of this pathway, but there are no DHFR inhibitors used for tuberculosis treatment. Here, we report a structural, site-directed mutagenesis and calorimetric analysis of Mycobacterium tuberculosis DHFR (MtDHFR) in complex with classical DHFR inhibitors. Our study provides insights into the weak inhibition of MtDHFR by trimethoprim and other antifolate drugs, such as pyrimethamine and cycloguanil. The construction of the mutant Y100F, together with calorimetric studies, gives insights into low affinity of MtDHFR for classical DHFR inhibitors. Finally, the structures of MtDHFR in complex with pyrimethamine and cycloguanil define important interactions in the active site and provide clues to the more effective design of antibiotics targeted against MtDHFR.

  16. High Affinity Small Protein Inhibitors of Human Chymotrypsin C (CTRC) Selected by Phage Display Reveal Unusual Preference for P4′ Acidic Residues*

    PubMed Central

    Szabó, András; Héja, Dávid; Szakács, Dávid; Zboray, Katalin; Kékesi, Katalin A.; Radisky, Evette S.; Sahin-Tóth, Miklós; Pál, Gábor

    2011-01-01

    Human chymotrypsin C (CTRC) is a pancreatic protease that participates in the regulation of intestinal digestive enzyme activity. Other chymotrypsins and elastases are inactive on the regulatory sites cleaved by CTRC, suggesting that CTRC recognizes unique sequence patterns. To characterize the molecular determinants underlying CTRC specificity, we selected high affinity substrate-like small protein inhibitors against CTRC from a phage library displaying variants of SGPI-2, a natural chymotrypsin inhibitor from Schistocerca gregaria. On the basis of the sequence pattern selected, we designed eight inhibitor variants in which amino acid residues in the reactive loop at P1 (Met or Leu), P2′ (Leu or Asp), and P4′ (Glu, Asp, or Ala) were varied. Binding experiments with CTRC revealed that (i) inhibitors with Leu at P1 bind 10-fold stronger than those with P1 Met; (ii) Asp at P2′ (versus Leu) decreases affinity but increases selectivity, and (iii) Glu or Asp at P4′ (versus Ala) increase affinity 10-fold. The highest affinity SGPI-2 variant (KD 20 pm) bound to CTRC 575-fold tighter than the parent molecule. The most selective inhibitor variant exhibited a KD of 110 pm and a selectivity ranging from 225- to 112,664-fold against other human chymotrypsins and elastases. Homology modeling and mutagenesis identified a cluster of basic amino acid residues (Lys51, Arg56, and Arg80) on the surface of human CTRC that interact with the P4′ acidic residue of the inhibitor. The acidic preference of CTRC at P4′ is unique among pancreatic proteases and might contribute to the high specificity of CTRC-mediated digestive enzyme regulation. PMID:21515688

  17. In vivo imaging reveals that pregabalin inhibits cortical spreading depression and propagation to subcortical brain structures

    PubMed Central

    Cain, Stuart M.; Bohnet, Barry; LeDue, Jeffrey; Yung, Andrew C.; Garcia, Esperanza; Tyson, John R.; Alles, Sascha R. A.; Han, Huili; van den Maagdenberg, Arn M. J. M.; Kozlowski, Piotr; MacVicar, Brian A.; Snutch, Terrance P.

    2017-01-01

    Migraine is characterized by severe headaches that can be preceded by an aura likely caused by cortical spreading depression (SD). The antiepileptic pregabalin (Lyrica) shows clinical promise for migraine therapy, although its efficacy and mechanism of action are unclear. As detected by diffusion-weighted MRI (DW-MRI) in wild-type (WT) mice, the acute systemic administration of pregabalin increased the threshold for SD initiation in vivo. In familial hemiplegic migraine type 1 mutant mice expressing human mutations (R192Q and S218L) in the CaV2.1 (P/Q-type) calcium channel subunit, pregabalin slowed the speed of SD propagation in vivo. Acute systemic administration of pregabalin in vivo also selectively prevented the migration of SD into subcortical striatal and hippocampal regions in the R192Q strain that exhibits a milder phenotype and gain of CaV2.1 channel function. At the cellular level, pregabalin inhibited glutamatergic synaptic transmission differentially in WT, R192Q, and S218L mice. The study describes a DW-MRI analysis method for tracking the progression of SD and provides support and a mechanism of action for pregabalin as a possible effective therapy in the treatment of migraine. PMID:28223480

  18. Monte Carlo Modeling of Photon Propagation Reveals Highly Scattering Coral Tissue

    PubMed Central

    Wangpraseurt, Daniel; Jacques, Steven L.; Petrie, Tracy; Kühl, Michael

    2016-01-01

    Corals are very efficient at using solar radiation, with photosynthetic quantum efficiencies approaching theoretical limits. Here, we investigated potential mechanisms underlying such outstanding photosynthetic performance through extracting inherent optical properties of the living coral tissue and skeleton in a massive faviid coral. Using Monte Carlo simulations developed for medical tissue optics it is shown that for the investigated faviid coral, the coral tissue was a strongly light scattering matrix with a reduced scattering coefficient of μs’ = 10 cm-1 (at 636 nm). In contrast, the scattering coefficient of the coral skeleton was μs’ = 3.4 cm-1, which facilitated the efficient propagation of light to otherwise shaded coral tissue layers, thus supporting photosynthesis in lower tissues. Our study provides a quantification of coral tissue optical properties in a massive faviid coral and suggests a novel light harvesting strategy, where tissue and skeletal optics act in concert to optimize the illumination of the photosynthesizing algal symbionts embedded within the living coral tissue. PMID:27708657

  19. A dualistic conformational response to substrate binding in the human serotonin transporter reveals a high affinity state for serotonin.

    PubMed

    Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida; Wiborg, Ove; Sinning, Steffen

    2015-03-20

    Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across the membrane. Our understanding of these conformational changes is mainly based on crystal structures of a bacterial homolog in various conformations, derived homology models of eukaryotic neurotransmitter transporters, and substituted cysteine accessibility method of SERT. However, the dynamic changes that occur in the human SERT upon binding of ions, the translocation of substrate, and the role of cholesterol in this interplay are not fully elucidated. Here we show that serotonin induces a dualistic conformational response in SERT. We exploited the substituted cysteine scanning method under conditions that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation. Furthermore, we found that membrane cholesterol plays a role in the dualistic conformational response in SERT induced by serotonin. Our results indicate the existence of a subpopulation of SERT responding differently to serotonin binding than hitherto believed and that membrane cholesterol plays a role in this subpopulation of SERT.

  20. Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography.

    PubMed

    Shetty, Kartika N; Latha, Vakada Lavanya; Rao, Rameshwaram Nagender; Nadimpalli, Siva Kumar; Suguna, Kaza

    2013-07-01

    Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.

  1. Substrate and Substrate-Mimetic Chaperone Binding Sites in Human α-Galactosidase A Revealed by Affinity-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Moise, Adrian; Maeser, Stefan; Rawer, Stephan; Eggers, Frederike; Murphy, Mary; Bornheim, Jeff; Przybylski, Michael

    2016-06-01

    Fabry disease (FD) is a rare metabolic disorder of a group of lysosomal storage diseases, caused by deficiency or reduced activity of the enzyme α-galactosidase. Human α-galactosidase A (hαGAL) hydrolyses the terminal α-galactosyl moiety from glycosphingolipids, predominantly globotriaosylceramide (Gb3). Enzyme deficiency leads to incomplete or blocked breakdown and progressive accumulation of Gb3, with detrimental effects on normal organ functions. FD is successfully treated by enzyme replacement therapy (ERT) with purified recombinant hαGAL. An emerging treatment strategy, pharmacologic chaperone therapy (PCT), employs small molecules that can increase and/or reconstitute the activity of lysosomal enzyme trafficking by stabilizing misfolded isoforms. One such chaperone, 1-deoxygalactonojirimycin (DGJ), is a structural galactose analogue currently validated in clinical trials. DGJ is an active-site-chaperone that binds at the same or similar location as galactose; however, the molecular determination of chaperone binding sites in lysosomal enzymes represents a considerable challenge. Here we report the identification of the galactose and DGJ binding sites in recombinant α-galactosidase through a new affinity-mass spectrometry-based approach that employs selective proteolytic digestion of the enzyme-galactose or -inhibitor complex. Binding site peptides identified by mass spectrometry, [39-49], [83-100], and [141-168], contain the essential ligand-contacting amino acids, in agreement with the known X-ray crystal structures. The inhibitory effect of DGJ on galactose recognition was directly characterized through competitive binding experiments and mass spectrometry. The methods successfully employed in this study should have high potential for the characterization of (mutated) enzyme-substrate and -chaperone interactions, and for identifying chaperones without inhibitory effects.

  2. Phase Boundary Propagation in Li-Alloying Battery Electrodes Revealed by Liquid-Cell Transmission Electron Microscopy.

    PubMed

    Leenheer, Andrew J; Jungjohann, Katherine L; Zavadil, Kevin R; Harris, Charles T

    2016-06-28

    Battery cycle life is directly influenced by the microstructural changes occurring in the electrodes during charge and discharge cycles. Here, we image in situ the nanoscale phase evolution in negative electrode materials for Li-ion batteries using a fully enclosed liquid cell in a transmission electron microscope (TEM) to reveal early degradation that is not evident in the charge-discharge curves. To compare the electrochemical phase transformation behavior between three model materials, thin films of amorphous Si, crystalline Al, and crystalline Au were lithiated and delithiated at controlled rates while immersed in a commercial liquid electrolyte. This method allowed for the direct observation of lithiation mechanisms in nanoscale negative electrodes, revealing that a simplistic model of a surface-to-interior lithiation front is insufficient. For the crystalline films, a lithiation front spread laterally from a few initial nucleation points, with continued grain nucleation along the growing interface. The intermediate lithiated phases were identified using electron diffraction, and high-resolution postmortem imaging revealed the details of the final microstructure. Our results show that electrochemically induced solid-solid phase transformations can lead to highly concentrated stresses at the laterally propagating phase boundary which should be considered for future designs of nanostructured electrodes for Li-ion batteries.

  3. Phase Boundary Propagation in Li-Alloying Battery Electrodes Revealed by Liquid-Cell Transmission Electron Microscopy

    DOE PAGES

    Leenheer, Andrew J.; Jungjohann, Katherine L.; Zavadil, Kevin R.; ...

    2016-05-31

    Battery cycle life is directly influenced by the microstructural changes occurring in the electrodes during charge and discharge cycles. In this study, we image in situ the nanoscale phase evolution in negative electrode materials for Li-ion batteries using a fully enclosed liquid cell in a transmission electron microscope (TEM) to reveal early degradation that is not evident in the charge–discharge curves. To compare the electrochemical phase transformation behavior between three model materials, thin films of amorphous Si, crystalline Al, and crystalline Au were lithiated and delithiated at controlled rates while immersed in a commercial liquid electrolyte. This method allowed formore » the direct observation of lithiation mechanisms in nanoscale negative electrodes, revealing that a simplistic model of a surface-to-interior lithiation front is insufficient. For the crystalline films, a lithiation front spread laterally from a few initial nucleation points, with continued grain nucleation along the growing interface. The intermediate lithiated phases were identified using electron diffraction, and high-resolution postmortem imaging revealed the details of the final microstructure. Lastly, our results show that electrochemically induced solid–solid phase transformations can lead to highly concentrated stresses at the laterally propagating phase boundary which should be considered for future designs of nanostructured electrodes for Li-ion batteries.« less

  4. Phase Boundary Propagation in Li-Alloying Battery Electrodes Revealed by Liquid-Cell Transmission Electron Microscopy

    SciTech Connect

    Leenheer, Andrew J.; Jungjohann, Katherine L.; Zavadil, Kevin R.; Harris, Charles T.

    2016-05-31

    Battery cycle life is directly influenced by the microstructural changes occurring in the electrodes during charge and discharge cycles. In this study, we image in situ the nanoscale phase evolution in negative electrode materials for Li-ion batteries using a fully enclosed liquid cell in a transmission electron microscope (TEM) to reveal early degradation that is not evident in the charge–discharge curves. To compare the electrochemical phase transformation behavior between three model materials, thin films of amorphous Si, crystalline Al, and crystalline Au were lithiated and delithiated at controlled rates while immersed in a commercial liquid electrolyte. This method allowed for the direct observation of lithiation mechanisms in nanoscale negative electrodes, revealing that a simplistic model of a surface-to-interior lithiation front is insufficient. For the crystalline films, a lithiation front spread laterally from a few initial nucleation points, with continued grain nucleation along the growing interface. The intermediate lithiated phases were identified using electron diffraction, and high-resolution postmortem imaging revealed the details of the final microstructure. Lastly, our results show that electrochemically induced solid–solid phase transformations can lead to highly concentrated stresses at the laterally propagating phase boundary which should be considered for future designs of nanostructured electrodes for Li-ion batteries.

  5. Amide hydrogens reveal a temperature-dependent structural transition that enhances site-II Ca(2+)-binding affinity in a C-domain mutant of cardiac troponin C.

    PubMed

    Veltri, Tiago; de Oliveira, Guilherme A P; Bienkiewicz, Ewa A; Palhano, Fernando L; Marques, Mayra de A; Moraes, Adolfo H; Silva, Jerson L; Sorenson, Martha M; Pinto, Jose R

    2017-04-06

    The hypertrophic cardiomyopathy-associated mutant D145E, in cardiac troponin C (cTnC) C-domain, causes generalised instability at multiple sites in the isolated protein. As a result, structure and function of the mutant are more susceptible to higher temperatures. Above 25 °C there are large, progressive increases in N-domain Ca(2+)-binding affinity for D145E but only small changes for the wild-type protein. NMR-derived backbone amide temperature coefficients for many residues show a sharp transition above 30-40 °C, indicating a temperature-dependent conformational change that is most prominent around the mutated EF-hand IV, as well as throughout the C-domain. Smaller, isolated changes occur in the N-domain. Cardiac skinned fibres reconstituted with D145E are more sensitive to Ca(2+) than fibres reconstituted with wild-type, and this defect is amplified near body-temperature. We speculate that the D145E mutation destabilises the native conformation of EF-hand IV, leading to a transient unfolding and dissociation of helix H that becomes more prominent at higher temperatures. This creates exposed hydrophobic surfaces that may be capable of binding unnaturally to a variety of targets, possibly including the N-domain of cTnC when it is in its open Ca(2+)-saturated state. This would constitute a potential route for propagating signals from one end of TnC to the other.

  6. In Vivo Analysis of HPr Reveals a Fructose-Specific Phosphotransferase System That Confers High-Affinity Uptake in Streptomyces coelicolor

    PubMed Central

    Nothaft, Harald; Parche, Stephan; Kamionka, Annette; Titgemeyer, Fritz

    2003-01-01

    HPr, the histidine-containing phosphocarrier protein of the bacterial phosphotransferase system (PTS), serves multiple functions in carbohydrate uptake and carbon source regulation in low-G+C-content gram-positive bacteria and in gram-negative bacteria. To assess the role of HPr in the high-G+C-content gram-positive organism Streptomyces coelicolor, the encoding gene, ptsH, was deleted. The ptsH mutant BAP1 was impaired in fructose utilization, while growth on other carbon sources was not affected. Uptake assays revealed that BAP1 could not transport appreciable amounts of fructose, while the wild type showed inducible high-affinity fructose transport with an apparent Km of 2 μM. Complementation and reconstitution experiments demonstrated that HPr is indispensable for a fructose-specific PTS activity. Investigation of the putative fruKA gene locus led to identification of the fructose-specific enzyme II permease encoded by the fruA gene. Synthesis of HPr was not specifically enhanced in fructose-grown cells and occurred also in the presence of non-PTS carbon sources. Transcriptional analysis of ptsH revealed two promoters that are carbon source regulated. In contrast to what happens in other bacteria, glucose repression of glycerol kinase was still operative in a ptsH background, which suggests that HPr is not involved in general carbon regulation. However, fructose repression of glycerol kinase was lost in BAP1, indicating that the fructose-PTS is required for transduction of the signal. This study provides the first molecular genetic evidence of a physiological role of the PTS in S. coelicolor. PMID:12533468

  7. Cytoarchitecture-Dependent Decrease in Propagation Velocity of Cortical Spreading Depression in the Rat Insular Cortex Revealed by Optical Imaging.

    PubMed

    Fujita, Satoshi; Mizoguchi, Naoko; Aoki, Ryuhei; Cui, Yilong; Koshikawa, Noriaki; Kobayashi, Masayuki

    2016-04-01

    Cortical spreading depression (SD) is a self-propagating wave of depolarization accompanied by a substantial disturbance of the ionic distribution between the intra- and extracellular compartments. Glial cells, including astrocytes, play critical roles in maintenance of the extracellular environment, including ionic distribution. Therefore, SD propagation in the cerebral cortex may depend on the density of astrocytes. The present study aimed to examine the profile of SD propagation in the insular cortex (IC), which is located between the neocortex and paleocortex and is where the density of astrocytes gradually changes. The velocity of SD propagation in the neocortex, including the somatosensory, motor, and granular insular cortices (5.7 mm/min), was higher than that (2.8 mm/min) in the paleocortex (agranular insular and piriform cortices). Around thick vessels, including the middle cerebral artery, SD propagation was frequently delayed and sometimes disappeared. Immunohistological analysis of glial fibrillary acidic protein (GFAP) demonstrated the sparse distribution of astrocytes in the somatosensory cortex and the IC dorsal to the rhinal fissure, whereas the ventral IC showed a higher density of astrocytes. These results suggest that cortical cytoarchitectonic features, which possibly involve the distribution of astrocytes, are crucial for regulating the velocity of SD propagation in the cerebral cortex.

  8. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics.

    PubMed

    Beresova, Lucie; Vesela, Eva; Chamrad, Ivo; Voller, Jiri; Yamada, Masayuki; Furst, Tomas; Lenobel, Rene; Chroma, Katarina; Gursky, Jan; Krizova, Katerina; Mistrik, Martin; Bartek, Jiri

    2016-12-02

    Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.

  9. Structures of Streptococcus pneumoniae PiaA and Its Complex with Ferrichrome Reveal Insights into the Substrate Binding and Release of High Affinity Iron Transporters

    PubMed Central

    Cheng, Wang; Li, Qiong; Jiang, Yong-Liang; Zhou, Cong-Zhao; Chen, Yuxing

    2013-01-01

    Iron scarcity is one of the nutrition limitations that the Gram-positive infectious pathogens Streptococcus pneumoniae encounter in the human host. To guarantee sufficient iron supply, the ATP binding cassette (ABC) transporter Pia is employed to uptake iron chelated by hydroxamate siderophore, via the membrane-anchored substrate-binding protein PiaA. The high affinity towards ferrichrome enables PiaA to capture iron at a very low concentration in the host. We presented here the crystal structures of PiaA in both apo and ferrichrome-complexed forms at 2.7 and 2.1 Å resolution, respectively. Similar to other class III substrate binding proteins, PiaA is composed of an N-terminal and a C-terminal domain bridged by an α-helix. At the inter-domain cleft, a molecule of ferrichrome is stabilized by a number of highly conserved residues. Upon ferrichrome binding, two highly flexible segments at the entrance of the cleft undergo significant conformational changes, indicating their contribution to the binding and/or release of ferrichrome. Superposition to the structure of Escherichia coli ABC transporter BtuF enabled us to define two conserved residues: Glu119 and Glu262, which were proposed to form salt bridges with two arginines of the permease subunits. Further structure-based sequence alignment revealed that the ferrichrome binding pattern is highly conserved in a series of PiaA homologs encoded by both Gram-positive and negative bacteria, which were predicted to be sensitive to albomycin, a sideromycin antibiotic derived from ferrichrome. PMID:23951167

  10. Combined Crystal Structure of a Type I Cohesin: MUTATION AND AFFINITY BINDING STUDIES REVEAL STRUCTURAL DETERMINANTS OF COHESIN-DOCKERIN SPECIFICITIES.

    PubMed

    Cameron, Kate; Weinstein, Jonathan Y; Zhivin, Olga; Bule, Pedro; Fleishman, Sarel J; Alves, Victor D; Gilbert, Harry J; Ferreira, Luís M A; Fontes, Carlos M G A; Bayer, Edward A; Najmudin, Shabir

    2015-06-26

    Cohesin-dockerin interactions orchestrate the assembly of one of nature's most elaborate multienzyme complexes, the cellulosome. Cellulosomes are produced exclusively by anaerobic microbes and mediate highly efficient hydrolysis of plant structural polysaccharides, such as cellulose and hemicellulose. In the canonical model of cellulosome assembly, type I dockerin modules of the enzymes bind to reiterated type I cohesin modules of a primary scaffoldin. Each type I dockerin contains two highly conserved cohesin-binding sites, which confer quaternary flexibility to the multienzyme complex. The scaffoldin also bears a type II dockerin that anchors the entire complex to the cell surface by binding type II cohesins of anchoring scaffoldins. In Bacteroides cellulosolvens, however, the organization of the cohesin-dockerin types is reversed, whereby type II cohesin-dockerin pairs integrate the enzymes into the primary scaffoldin, and type I modules mediate cellulosome attachment to an anchoring scaffoldin. Here, we report the crystal structure of a type I cohesin from B. cellulosolvens anchoring scaffoldin ScaB to 1.84-Å resolution. The structure resembles other type I cohesins, and the putative dockerin-binding site, centered at β-strands 3, 5, and 6, is likely to be conserved in other B. cellulosolvens type I cohesins. Combined computational modeling, mutagenesis, and affinity-based binding studies revealed similar hydrogen-bonding networks between putative Ser/Asp recognition residues in the dockerin at positions 11/12 and 45/46, suggesting that a dual-binding mode is not exclusive to the integration of enzymes into primary cellulosomes but can also characterize polycellulosome assembly and cell-surface attachment. This general approach may provide valuable structural information of the cohesin-dockerin interface, in lieu of a definitive crystal structure.

  11. Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding

    PubMed Central

    Lu, Jinghua; Chu, Jonathan; Zou, Zhongcheng; Hamacher, Nels B.; Rixon, Mark W.; Sun, Peter D.

    2015-01-01

    Fc gamma receptor I (FcγRI) contributes to protective immunity against bacterial infections, but exacerbates certain autoimmune diseases. The sole high-affinity IgG receptor, FcγRI plays a significant role in immunotherapy. To elucidate the molecular mechanism of its high-affinity IgG binding, we determined the crystal structure of the extracellular domains of human FcγRI in complex with the Fc domain of human IgG1. FcγRI binds to the Fc in a similar mode as the low-affinity FcγRII and FcγRIII receptors. In addition to many conserved contacts, FcγRI forms additional hydrogen bonds and salt bridges with the lower hinge region of Fc. Unique to the high-affinity receptor-Fc complex, however, is the conformation of the receptor D2 domain FG loop, which enables a charged KHR motif to interact with proximal carbohydrate units of the Fc glycans. Both the length and the charge of the FcγRI FG loop are well conserved among mammalian species. Ala and Glu mutations of the FG loop KHR residues showed significant contributions of His-174 and Arg-175 to antibody binding, and the loss of the FG loop–glycan interaction resulted in an ∼20- to 30-fold decrease in FcγRI affinity to all three subclasses of IgGs. Furthermore, deglycosylation of IgG1 resulted in a 40-fold loss in FcγRI binding, demonstrating involvement of the receptor FG loop in glycan recognition. These results highlight a unique glycan recognition in FcγRI function and open potential therapeutic avenues based on antibody glycan engineering or small molecular glycan mimics to target FcγRI for certain autoimmune diseases. PMID:25561553

  12. A systematic analysis reveals an essential role for high-affinity iron uptake system, haemolysin and CFEM domain-containing protein in iron homoeostasis and virulence in Candida glabrata.

    PubMed

    Srivastava, Vivek Kumar; Suneetha, Korivi Jyothiraj; Kaur, Rupinder

    2014-10-01

    Iron is an essential nutrient for all living organisms and human pathogens employ a battery of factors to scavenge iron from the high-affinity iron-binding host proteins. In the present study, we have elucidated, via a candidate gene approach, major iron acquisition and homoeostatic mechanisms operational in an opportunistic human fungal pathogen Candida glabrata. Phenotypic, biochemical and molecular analysis of a set of 13 C. glabrata strains, deleted for proteins potentially implicated in iron metabolism, revealed that the high-affinity reductive iron uptake system is required for utilization of alternate carbon sources and for growth under both in vitro iron-limiting and in vivo conditions. Furthermore, we show for the first time that the cysteine-rich CFEM (common in fungal extracellular membranes) domain-containing cell wall structural protein, CgCcw14, and a putative haemolysin, CgMam3, are essential for maintenance of intracellular iron content, adherence to epithelial cells and virulence. Consistent with their roles in iron homoeostasis, mitochondrial aconitase activity was lower and higher in mutants disrupted for high-affinity iron transport, and haemolysin respectively. Additionally, we present evidence that the mitochondrial frataxin, CgYfh1, is pivotal to iron metabolism. Besides yielding insights into major in vitro and in vivo iron acquisition strategies, our findings establish high-affinity iron uptake mechanisms as critical virulence determinants in C. glabrata.

  13. High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation.

    PubMed

    Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J; Fox, Catherine A

    2016-04-07

    The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid

  14. Electron Affinity Calculations for Thioethers

    NASA Technical Reports Server (NTRS)

    Sulton, Deley L.; Boothe, Michael; Ball, David W.; Morales, Wilfredo

    1997-01-01

    Previous work indicated that polyphenyl thioethers possessed chemical properties, related to their electron affinities, which could allow them to function as vapor phase lubricants (VPL). Indeed, preliminary tribological tests revealed that the thioethers could function as vapor phase lubricants but not over a wide temperature and hertzian pressure range. Increasing the electron affinity of the thioethers may improve their VPL properties over this range. Adding a substituent group to the thioether will alter its electron affinity in many cases. Molecular orbital calculations were undertaken to determine the effect of five different substituent groups on the electron affinity of polyphenyl thioethers. It was found that the NO2, F, and I groups increased the thioethers electron affinity by the greatest amount. Future work will involve the addition of these groups to the thioethers followed by tribological testing to assess their VPL properties.

  15. Antibody VH and VL recombination using phage and ribosome display technologies reveals distinct structural routes to affinity improvements with VH-VL interface residues providing important structural diversity.

    PubMed

    Groves, Maria A T; Amanuel, Lily; Campbell, Jamie I; Rees, D Gareth; Sridharan, Sudharsan; Finch, Donna K; Lowe, David C; Vaughan, Tristan J

    2014-01-01

    In vitro selection technologies are an important means of affinity maturing antibodies to generate the optimal therapeutic profile for a particular disease target. Here, we describe the isolation of a parent antibody, KENB061 using phage display and solution phase selections with soluble biotinylated human IL-1R1. KENB061 was affinity matured using phage display and targeted mutagenesis of VH and VL CDR3 using NNS randomization. Affinity matured VHCDR3 and VLCDR3 library blocks were recombined and selected using phage and ribosome display protocol. A direct comparison of the phage and ribosome display antibodies generated was made to determine their functional characteristics.In our analyses, we observed distinct differences in the pattern of beneficial mutations in antibodies derived from phage and ribosome display selections, and discovered the lead antibody Jedi067 had a ~3700-fold improvement in KD over the parent KENB061. We constructed a homology model of the Fv region of Jedi067 to map the specific positions where mutations occurred in the CDR3 loops. For VL CDR3, positions 94 to 97 carry greater diversity in the ribosome display variants compared with the phage display. The positions 95a, 95b and 96 of VLCDR3 form part of the interface with VH in this model. The model shows that positions 96, 98, 100e, 100f, 100 g, 100h, 100i and 101 of the VHCDR3 include residues at the VH and VL interface. Importantly, Leu96 and Tyr98 are conserved at the interface positions in both phage and ribosome display indicating their importance in maintaining the VH-VL interface. For antibodies derived from ribosome display, there is significant diversity at residues 100a to 100f of the VH CDR3 compared with phage display. A unique deletion of isoleucine at position 102 of the lead candidate, Jedi067, also occurs in the VHCDR3.As anticipated, recombining the mutations via ribosome display led to a greater structural diversity, particularly in the heavy chain CDR3, which in turn

  16. Video monitoring reveals pulsating vents and propagation path of fissure eruption during the March 2011 Pu'u 'Ō'ō eruption, Kilauea volcano

    NASA Astrophysics Data System (ADS)

    Witt, Tanja; Walter, Thomas R.

    2017-01-01

    Lava fountains are a common eruptive feature of basaltic volcanoes. Many lava fountains result from fissure eruptions and are associated with the alignment of active vents and rising gas bubbles in the conduit. Visual reports suggest that lava fountain pulses may occur in chorus at adjacent vents. The mechanisms behind such a chorus of lava fountains and the underlying processes are, however, not fully understood. The March 2011 eruption at Pu'u 'Ō'ō (Kilauea volcano) was an exceptional fissure eruption that was well monitored and could be closely approached by field geologists. The fissure eruption occurred along groups of individual vents aligned above the feeding dyke. We investigate video data acquired during the early stages of the eruption to measure the height, width and velocity of the ejecta leaving eight vents. Using a Sobel edge-detection algorithm, the activity level of the lava fountains at the vents was determined, revealing a similarity in the eruption height and frequency. Based on this lava fountain time series, we estimate the direction and degree of correlation between the different vents. We find that the height and velocity of the eruptions display a small but systematic shift in time along the vents, indicating a lateral migration of lava fountaining at a rate of 11 m/s from W to E. This finding is in agreement with a propagation model of a pressure wave originating at the Kilauea volcano and propagating through the dyke at 10 m/s from W to E. Based on this approach from videos only 30 s long, we are able to obtain indirect constraints on the physical dyke parameters, with important implications for lateral magma flow processes at depth. This work shows that the recording and analysis of video data provide important constraints on the mechanisms of lava fountain pulses. Even though the video sequence is short, it allows for the confirmation of the magma propagation direction and a first-order estimation of the dyke dimensions.

  17. Simulating disease propagation across white matter connectome reveals anatomical substrate for neuropathology staging in amyotrophic lateral sclerosis.

    PubMed

    Schmidt, Ruben; de Reus, Marcel A; Scholtens, Lianne H; van den Berg, Leonard H; van den Heuvel, Martijn P

    2016-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, characterized by progressive loss of motor function. While the pathogenesis of ALS remains largely unknown, recent histological examinations of Brettschneider and colleagues have proposed four time-sequential stages of neuropathology in ALS based on levels of phosphorylated 43kDa TAR DNA-binding protein (pTDP-43) aggregation. What governs dissemination of these aggregates between segregated regions of the brain is unknown. Here, we cross-reference stages of pTDP-43 pathology with in vivo diffusion weighted imaging data of 215 adult healthy control subjects, and reveal that regions involved in pTDP-43 pathology form a strongly interconnected component of the brain network (p=0.04) likely serving as an anatomical infrastructure facilitating pTDP-43 spread. Furthermore, brain regions of subsequent stages of neuropathology are shown to be more closely interconnected than regions of more distant stages (p=0.002). Computational simulation of disease spread from first-stage motor regions across the connections of the brain network reveals a pattern of pTDP-43 aggregation that reflects the stages of sequential involvement in neuropathology (p=0.02), a pattern in favor of the hypothesis of pTDP-43 pathology to spread across the brain along axonal pathways. Our findings thus provide computational evidence of disease spread in ALS to be directed and constrained by the topology of the anatomical brain network.

  18. Mutant cycle analysis with modified saxitoxins reveals specific interactions critical to attaining high-affinity inhibition of hNaV1.7

    PubMed Central

    Thomas-Tran, Rhiannon; Du Bois, J.

    2016-01-01

    Improper function of voltage-gated sodium channels (NaVs), obligatory membrane proteins for bioelectrical signaling, has been linked to a number of human pathologies. Small-molecule agents that target NaVs hold considerable promise for treatment of chronic disease. Absent a comprehensive understanding of channel structure, the challenge of designing selective agents to modulate the activity of NaV subtypes is formidable. We have endeavored to gain insight into the 3D architecture of the outer vestibule of NaV through a systematic structure–activity relationship (SAR) study involving the bis-guanidinium toxin saxitoxin (STX), modified saxitoxins, and protein mutagenesis. Mutant cycle analysis has led to the identification of an acetylated variant of STX with unprecedented, low-nanomolar affinity for human NaV1.7 (hNaV1.7), a channel subtype that has been implicated in pain perception. A revised toxin-receptor binding model is presented, which is consistent with the large body of SAR data that we have obtained. This new model is expected to facilitate subsequent efforts to design isoform-selective NaV inhibitors. PMID:27162340

  19. Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling.

    PubMed

    Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie

    2017-04-01

    Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors.

  20. Virtual Screening of Plant Volatile Compounds Reveals a High Affinity of Hylamorpha elegans (Coleoptera: Scarabaeidae) Odorant-Binding Proteins for Sesquiterpenes From Its Native Host

    PubMed Central

    Palma-Millanao, Rubén; Yáñez, Osvaldo; Rojas, Maximiliano; Mutis, Ana; Venthur, Herbert; Quiroz, Andrés; Ramírez, Claudio C.

    2016-01-01

    Hylamorpha elegans (Burmeister) is a native Chilean scarab beetle considered to be a relevant agricultural pest to pasture and cereal and small fruit crops. Because of their cryptic habits, control with conventional methods is difficult; therefore, alternative and environmentally friendly control strategies are highly desirable. The study of proteins that participate in the recognition of odorants, such as odorant-binding proteins (OBPs), offers interesting opportunities to identify new compounds with the potential to modify pest behavior and computational screening of compounds, which is commonly used in drug discovery, may help to accelerate the discovery of new semiochemicals. Here, we report the discovery of four OBPs in H. elegans as well as six new volatiles released by its native host Nothofagus obliqua (Mirbel). Molecular docking performed between OBPs and new and previously reported volatiles from N. obliqua revealed the best binding energy values for sesquiterpenic compounds. Despite remarkable divergence at the amino acid level, three of the four OBPs evaluated exhibited the best interaction energy for the same ligands. Molecular dynamics investigation reinforced the importance of sesquiterpenes, showing that hydrophobic residues of the OBPs interacted most frequently with the tested ligands, and binding free energy calculations demonstrated van der Waals and hydrophobic interactions to be the most important. Altogether, the results suggest that sesquiterpenes are interesting candidates for in vitro and in vivo assays to assess their potential application in pest management strategies. PMID:27012867

  1. COII/tRNA[sup Lys] intergenic 9-bp deletion and other mtDNA markers clearly reveal that the Tharus (Southern Nepal) have oriental affinities

    SciTech Connect

    Passarino, G.; Semino, O.; Santachiara-Benerecetti, A.S.; Modiano, G. )

    1993-09-01

    The authors searched for the East Asian mtDNA 9-bp deletion in the intergenic COII/tRNA[sup Lys] region in a sample of 107 Tharus (50 from central Terai and 57 from eastern Terai), a population whose anthropological origin has yet to be completely clarified. The deletion, detected by electrophoresis of the PCR-amplified nt 7392-8628 mtDNA fragment after digestion with HaeIII, was found in about 8% of both Tharu groups but was found in none of the 76 Hindus who were examined as a non-Oriental neighboring control population. A complete triplication of the 9-bp unit, the second case so far reported, was also observed in one eastern Tharu. All the mtDNAs with the deletion, and that with the triplication, were further characterized (by PCR amplification of the relevant mTDNA fragments and their digestion with the appropriate enzymes) to locate them in the Ballinger et al. phylogeny of East Asian mtDNA haplotypes. The deletion was found to be associated with four different haplotypes, two of which are reported for the first time. One of the deletions and especially the triplication could be best explained by the assumption of novel length-change events. Ballinger's classification of East Asian mtDNA haplotypes is mainly based on the phenotypes for the DdeI site at nt 10394 and the AluI site at nt 10397. Analysis of the entire Tharu sample revealed that more than 70% of the Tharus have both sites, the association of which has been suggested as an ancient East Asian peculiarity. These results conclusively indicate that the Tharus have a predominantly maternal Oriental ancestry. Moreover, they show at least one and perhaps two further distinct length mutations, and this suggests that the examined region is a hot spot of rearrangements. 21 refs., 5 figs., 6 tabs.

  2. Affinity based information diffusion model in social networks

    NASA Astrophysics Data System (ADS)

    Liu, Hongli; Xie, Yun; Hu, Haibo; Chen, Zhigao

    2014-12-01

    There is a widespread intuitive sense that people prefer participating in spreading the information in which they are interested. The affinity of people with information disseminated can affect the information propagation in social networks. In this paper, we propose an information diffusion model incorporating the mechanism of affinity of people with information which considers the fitness of affinity values of people with affinity threshold of the information. We find that the final size of information diffusion is affected by affinity threshold of the information, average degree of the network and the probability of people's losing their interest in the information. We also explore the effects of other factors on information spreading by numerical simulations and find that the probabilities of people's questioning and confirming the information can affect the propagation speed, but not the final scope.

  3. A dielectric affinity microbiosensor

    NASA Astrophysics Data System (ADS)

    Huang, Xian; Li, Siqi; Schultz, Jerome S.; Wang, Qian; Lin, Qiao

    2010-01-01

    We present an affinity biosensing approach that exploits changes in dielectric properties of a polymer due to its specific, reversible binding with an analyte. The approach is demonstrated using a microsensor comprising a pair of thin-film capacitive electrodes sandwiching a solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid), a synthetic polymer with specific affinity to glucose. Binding with glucose induces changes in the permittivity of the polymer, which can be measured capacitively for specific glucose detection, as confirmed by experimental results at physiologically relevant concentrations. The dielectric affinity biosensing approach holds the potential for practical applications such as long-term continuous glucose monitoring.

  4. Affinity in electrophoresis.

    PubMed

    Heegaard, Niels H H

    2009-06-01

    The journal Electrophoresis has greatly influenced my approaches to biomolecular affinity studies. The methods that I have chosen as my main tools to study interacting biomolecules--native gel and later capillary zone electrophoresis--have been the topic of numerous articles in Electrophoresis. Below, the role of the journal in the development and dissemination of these techniques and applications reviewed. Many exhaustive reviews on affinity electrophoresis and affinity CE have been published in the last few years and are not in any way replaced by the present deliberations that are focused on papers published by the journal.

  5. High-Speed imaging reveals opposing effects of chronic stress and antidepressants on neuronal activity propagation through the hippocampal trisynaptic circuit

    PubMed Central

    Stepan, Jens; Hladky, Florian; Uribe, Andrés; Holsboer, Florian; Schmidt, Mathias V.; Eder, Matthias

    2015-01-01

    Antidepressants (ADs) are used as first-line treatment for most stress-related psychiatric disorders. The alterations in brain circuit dynamics that can arise from stress exposure and underlie therapeutic actions of ADs remain, however, poorly understood. Here, enabled by a recently developed voltage-sensitive dye imaging (VSDI) assay in mouse brain slices, we examined the impact of chronic stress and concentration-dependent effects of eight clinically used ADs (belonging to different chemical/functional classes) on evoked neuronal activity propagations through the hippocampal trisynaptic circuitry (HTC: perforant path → dentate gyrus (DG) → area CA3 → area CA1). Exposure of mice to chronic social defeat stress led to markedly weakened activity propagations (“HTC-Waves”). In contrast, at concentrations in the low micromolar range, all ADs, which were bath applied to slices, caused an amplification of HTC-Waves in CA regions (invariably in area CA1). The fast-acting “antidepressant” ketamine, the mood stabilizer lithium, and brain-derived neurotrophic factor (BDNF) exerted comparable enhancing effects, whereas the antipsychotic haloperidol and the anxiolytic diazepam attenuated HTC-Waves. Collectively, we provide direct experimental evidence that chronic stress can depress neuronal signal flow through the HTC and demonstrate shared opposing effects of ADs. Thus, our study points to a circuit-level mechanism of ADs to counteract stress-induced impairment of hippocampal network function. However, the observed effects of ADs are impossible to depend on enhanced neurogenesis. PMID:26594153

  6. High-Speed imaging reveals opposing effects of chronic stress and antidepressants on neuronal activity propagation through the hippocampal trisynaptic circuit.

    PubMed

    Stepan, Jens; Hladky, Florian; Uribe, Andrés; Holsboer, Florian; Schmidt, Mathias V; Eder, Matthias

    2015-01-01

    Antidepressants (ADs) are used as first-line treatment for most stress-related psychiatric disorders. The alterations in brain circuit dynamics that can arise from stress exposure and underlie therapeutic actions of ADs remain, however, poorly understood. Here, enabled by a recently developed voltage-sensitive dye imaging (VSDI) assay in mouse brain slices, we examined the impact of chronic stress and concentration-dependent effects of eight clinically used ADs (belonging to different chemical/functional classes) on evoked neuronal activity propagations through the hippocampal trisynaptic circuitry (HTC: perforant path → dentate gyrus (DG) → area CA3 → area CA1). Exposure of mice to chronic social defeat stress led to markedly weakened activity propagations ("HTC-Waves"). In contrast, at concentrations in the low micromolar range, all ADs, which were bath applied to slices, caused an amplification of HTC-Waves in CA regions (invariably in area CA1). The fast-acting "antidepressant" ketamine, the mood stabilizer lithium, and brain-derived neurotrophic factor (BDNF) exerted comparable enhancing effects, whereas the antipsychotic haloperidol and the anxiolytic diazepam attenuated HTC-Waves. Collectively, we provide direct experimental evidence that chronic stress can depress neuronal signal flow through the HTC and demonstrate shared opposing effects of ADs. Thus, our study points to a circuit-level mechanism of ADs to counteract stress-induced impairment of hippocampal network function. However, the observed effects of ADs are impossible to depend on enhanced neurogenesis.

  7. Affine dynamics with torsion

    NASA Astrophysics Data System (ADS)

    Gültekin, Kemal

    2016-03-01

    In this study, we give a thorough analysis of a general affine gravity with torsion. After a brief exposition of the affine gravities considered by Eddington and Schrödinger, we construct and analyze different affine gravities based on the determinants of the Ricci tensor, the torsion tensor, the Riemann tensor, and their combinations. In each case we reduce equations of motion to their simplest forms and give a detailed analysis of their solutions. Our analyses lead to the construction of the affine connection in terms of the curvature and torsion tensors. Our solutions of the dynamical equations show that the curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor.

  8. Lectin affinity electrophoresis.

    PubMed

    Kobayashi, Yuka

    2014-01-01

    An interaction or a binding event typically changes the electrophoretic properties of a molecule. Affinity electrophoresis methods detect changes in the electrophoretic pattern of molecules (mainly macromolecules) that occur as a result of biospecific interactions or complex formation. Lectin affinity electrophoresis is a very effective method for the detection and analysis of trace amounts of glycobiological substances. It is particularly useful for isolating and separating the glycoisomers of target molecules. Here, we describe a sensitive technique for the detection of glycoproteins separated by agarose gel-lectin affinity electrophoresis that uses antibody-affinity blotting. The technique is tested using α-fetoprotein with lectin (Lens culinaris agglutinin and Phaseolus vulgaris agglutinin)-agarose gels.

  9. Atmospheric Propagation

    NASA Technical Reports Server (NTRS)

    Embleton, Tony F. W.; Daigle, Gilles A.

    1991-01-01

    Reviewed here is the current state of knowledge with respect to each basic mechanism of sound propagation in the atmosphere and how each mechanism changes the spectral or temporal characteristics of the sound received at a distance from the source. Some of the basic processes affecting sound wave propagation which are present in any situation are discussed. They are geometrical spreading, molecular absorption, and turbulent scattering. In geometrical spreading, sound levels decrease with increasing distance from the source; there is no frequency dependence. In molecular absorption, sound energy is converted into heat as the sound wave propagates through the air; there is a strong dependence on frequency. In turbulent scattering, local variations in wind velocity and temperature induce fluctuations in phase and amplitude of the sound waves as they propagate through an inhomogeneous medium; there is a moderate dependence on frequency.

  10. Dynamic Neurovascular Coupling and Uncoupling during Ictal Onset, Propagation, and Termination Revealed by Simultaneous In Vivo Optical Imaging of Neural Activity and Local Blood Volume

    PubMed Central

    Zhao, Mingrui; Schwartz, Theodore H.

    2013-01-01

    Traditional models of ictal propagation involve the concept of an initiation site and a progressive outward march of activation. The process of neurovascular coupling, whereby the brain supplies oxygenated blood to metabolically active neurons presumably results in a similar outward cascade of hyperemia. However, ictal neurovascular coupling has never been assessed in vivo using simultaneous measurements of membrane potential change and hyperemia with wide spatial sampling. In an acute rat ictal model, using simultaneous intrinsic optical signal (IOS) and voltage-sensitive dye (VSD) imaging of cerebral blood volume and membrane potential changes, we demonstrate that seizures consist of multiple dynamic multidirectional waves of membrane potential change with variable onset sites that spread through a widespread network. Local blood volume evolves on a much slower spatiotemporal scale. At seizure onset, the VSD waves extend beyond the IOS signal. During evolution, spatial correlation with hemodynamic signal only exists briefly at the maximal spread of the VSD signal. At termination, the IOS signal extends spatially and temporally beyond the VSD waves. Hence, vascular reactivity evolves in a separate but parallel fashion to membrane potential changes resulting in a mechanism of neurovascular coupling and uncoupling, which is as dynamic as the seizure itself. PMID:22499798

  11. Effects of GABAergic agonists and antagonists on oscillatory signal propagation in the guinea-pig accessory olfactory bulb slice revealed by optical recording.

    PubMed

    Sugai, T; Sugitani, M; Onoda, N

    1999-08-01

    To investigate the action of GABAergic agents on oscillatory signal propagation induced by electrical stimulation of the vomeronasal nerve layer, optical and electrophysiological recordings were carried out in slice preparations of the guinea-pig accessory olfactory bulb. In response to electrical stimuli, characteristic optical signals appeared in each layer: in the vomeronasal nerve layer, a transient presynaptic response; in the glomerular layer, pre- and postsynaptic responses; in the external plexiform, mitral cell and granule cell layers, a damped oscillatory response. Application of the GABAergic agonists, that is, GABA, muscimol (a GABAA receptor agonist) and baclofen (a GABAB receptor agonist), suggested that the GABAB action existed mainly in the glomeruli, whereas the GABAA action was present in both the glomeruli and the external plexiform layer. Bicuculline (a GABAA receptor antagonist) produced long-lasting but nonoscillating excitation in the external plexiform and mitral cell layers, indicating that the GABAA action contributes to the formation of oscillatory responses. When double-pulse stimulation was applied to the vomeronasal nerve layer, the test responses in the glomerular layer and external plexiform and mitral cell layers were depressed, but those in the vomeronasal nerve layer were not. Application of 2-hydroxysaclofen (a GABAB receptor antagonist) mostly blocked paired-pulse depression occurring in the glomerular layer and restored the reduced transmission to mitral cells, but had only a small effect on the depressed oscillatory response in the external plexiform and mitral cell layers. These observations suggest that GABAB action in the glomerular layer might, at least, regulate information flow from vomeronasal afferents to apical dendrites of mitral cells, like a gate inhibition. However, actions other than GABAB could also be involved in the depression of the oscillation in the external plexiform and mitral cell layers.

  12. Genomic Diversity of Burkholderia pseudomallei Clinical Isolates: Subtractive Hybridization Reveals a Burkholderia mallei-Specific Propage in B. pseudomallei 1026b

    DTIC Science & Technology

    2004-06-01

    in this study included Burkholderia cepacia LMG 1222 (44), Burkholderia multivorans C5568, B. multivorans LMG 18823 (44), Burkholderia cenocepacia... Burkholderia cepacia complex. J. Clin. Microbiol. 38:910–913. 45. Manzeniuk, O. I., N. V. Volozhantsev, and E. A. Svetoch. 1994. Identification of Pseudomonas...diversity of Burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a Burkholderia mallei-specific prophage in B. pseudomallei 1026b

  13. Affine Sphere Relativity

    NASA Astrophysics Data System (ADS)

    Minguzzi, E.

    2017-03-01

    We investigate spacetimes whose light cones could be anisotropic. We prove the equivalence of the structures: (a) Lorentz-Finsler manifold for which the mean Cartan torsion vanishes, (b) Lorentz-Finsler manifold for which the indicatrix (observer space) at each point is a convex hyperbolic affine sphere centered on the zero section, and (c) pair given by a spacetime volume and a sharp convex cone distribution. The equivalence suggests to describe (affine sphere) spacetimes with this structure, so that no algebraic-metrical concept enters the definition. As a result, this work shows how the metric features of spacetime emerge from elementary concepts such as measure and order. Non-relativistic spacetimes are obtained replacing proper spheres with improper spheres, so the distinction does not call for group theoretical elements. In physical terms, in affine sphere spacetimes the light cone distribution and the spacetime measure determine the motion of massive and massless particles (hence the dispersion relation). Furthermore, it is shown that, more generally, for Lorentz-Finsler theories non-differentiable at the cone, the lightlike geodesics and the transport of the particle momentum over them are well defined, though the curve parametrization could be undefined. Causality theory is also well behaved. Several results for affine sphere spacetimes are presented. Some results in Finsler geometry, for instance in the characterization of Randers spaces, are also included.

  14. Striving for Empathy: Affinities, Alliances and Peer Sexuality Educators

    ERIC Educational Resources Information Center

    Fields, Jessica; Copp, Martha

    2015-01-01

    Peer sexuality educators' accounts of their work reveal two approaches to empathy with their students: affinity and alliance. "Affinity-based empathy" rests on the idea that the more commonalities sexuality educators and students share (or perceive they share), the more they will be able to empathise with one another, while…

  15. On constructing purely affine theories with matter

    NASA Astrophysics Data System (ADS)

    Cervantes-Cota, Jorge L.; Liebscher, D.-E.

    2016-08-01

    We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schrödinger's purely affine theory (Schrödinger in Space-time structure. Cambridge UP, Cambridge, 1950), where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.

  16. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop

    PubMed Central

    Sardos, Julie; Rouard, Mathieu; Hueber, Yann; Cenci, Alberto; Hyma, Katie E.; van den Houwe, Ines; Hribova, Eva; Courtois, Brigitte; Roux, Nicolas

    2016-01-01

    Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement. PMID:27144345

  17. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop.

    PubMed

    Sardos, Julie; Rouard, Mathieu; Hueber, Yann; Cenci, Alberto; Hyma, Katie E; van den Houwe, Ines; Hribova, Eva; Courtois, Brigitte; Roux, Nicolas

    2016-01-01

    Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.

  18. Studies on human eRF3-PABP interaction reveal the influence of eRF3a N-terminal glycin repeat on eRF3-PABP binding affinity and the lower affinity of eRF3a 12-GGC allele involved in cancer susceptibility

    PubMed Central

    Jerbi, Soumaya; Jolles, Béatrice; Bouceba, Tahar; Jean-Jean, Olivier

    2016-01-01

    ABSTRACT The eukaryotic release factor 3 (eRF3) has been involved in the control of mRNA degradation through its association with the cytoplasmic Poly(A) Binding Protein, PABP. In mammals, eRF3 N-terminal domain contains two overlapping PAM2 motifs which specifically recognize the MLLE domain of PABP. In humans, eRF3a/GSPT1 gene contains a stable GGC repeat encoding a repeat of glycine residues in eRF3a N-terminus. There are five known eRF3a/GSPT1 alleles in the human population, encoding 7, 9, 10, 11 and 12 glycines. Several studies have reported that the presence of eRF3a 12-GGC allele is correlated with an increased risk of cancer development. Using surface plasmon resonance, we have studied the interaction of the various allelic forms of eRF3a with PABP alone or poly(A)-bound PABP. We found that the N-terminal glycine repeat of eRF3a influences eRF3a-PABP interaction and that eRF3a 12-GGC allele has a decreased binding affinity for PABP. Our comparative analysis on eRF3a alleles suggests that the presence of eRF3a 12-GGC allele could modify the coupling between translation termination and mRNA deadenylation. PMID:26818177

  19. The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes

    PubMed Central

    Wegrecki, Marcin; Rodríguez-Galán, Olga; de la Cruz, Jesús; Bravo, Jeronimo

    2015-01-01

    Ribosome biogenesis is one of the most essential pathways in eukaryotes although it is still not fully characterized. Given the importance of this process in proliferating cells, it is obvious that understanding the macromolecular details of the interactions that take place between the assembly factors, ribosomal proteins and nascent pre-rRNAs is essentially required for the development of new non-genotoxic treatments for cancer. Herein, we have studied the association between the WD40-repeat domains of Erb1 and Ytm1 proteins. These are essential factors for the biogenesis of 60S ribosomal subunits in eukaryotes that form a heterotrimeric complex together with the also essential Nop7 protein. We provide the crystal structure of a dimer formed by the C-terminal part of Erb1 and Ytm1 from Chaetomium thermophilum at 2.1 Å resolution. Using a multidisciplinary approach we show that the β-propeller domains of these proteins interact in a novel manner that leads to a high-affinity binding. We prove that a point mutation within the interface of the complex impairs the interaction between the two proteins and negatively affects growth and ribosome production in yeast. Our study suggests insights into the association of the Erb1-Ytm1 dimer with pre-ribosomal particles. PMID:26476442

  20. The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes.

    PubMed

    Wegrecki, Marcin; Rodríguez-Galán, Olga; de la Cruz, Jesús; Bravo, Jeronimo

    2015-12-15

    Ribosome biogenesis is one of the most essential pathways in eukaryotes although it is still not fully characterized. Given the importance of this process in proliferating cells, it is obvious that understanding the macromolecular details of the interactions that take place between the assembly factors, ribosomal proteins and nascent pre-rRNAs is essentially required for the development of new non-genotoxic treatments for cancer. Herein, we have studied the association between the WD40-repeat domains of Erb1 and Ytm1 proteins. These are essential factors for the biogenesis of 60S ribosomal subunits in eukaryotes that form a heterotrimeric complex together with the also essential Nop7 protein. We provide the crystal structure of a dimer formed by the C-terminal part of Erb1 and Ytm1 from Chaetomium thermophilum at 2.1 Å resolution. Using a multidisciplinary approach we show that the β-propeller domains of these proteins interact in a novel manner that leads to a high-affinity binding. We prove that a point mutation within the interface of the complex impairs the interaction between the two proteins and negatively affects growth and ribosome production in yeast. Our study suggests insights into the association of the Erb1-Ytm1 dimer with pre-ribosomal particles.

  1. Kernel Affine Projection Algorithms

    NASA Astrophysics Data System (ADS)

    Liu, Weifeng; Príncipe, José C.

    2008-12-01

    The combination of the famed kernel trick and affine projection algorithms (APAs) yields powerful nonlinear extensions, named collectively here, KAPA. This paper is a follow-up study of the recently introduced kernel least-mean-square algorithm (KLMS). KAPA inherits the simplicity and online nature of KLMS while reducing its gradient noise, boosting performance. More interestingly, it provides a unifying model for several neural network techniques, including kernel least-mean-square algorithms, kernel adaline, sliding-window kernel recursive-least squares (KRLS), and regularization networks. Therefore, many insights can be gained into the basic relations among them and the tradeoff between computation complexity and performance. Several simulations illustrate its wide applicability.

  2. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein

    PubMed Central

    Pawlik, Timothy M; Hawke, David H; Liu, Yanna; Krishnamurthy, Savitri; Fritsche, Herbert; Hunt, Kelly K; Kuerer, Henry M

    2006-01-01

    Background Isotope-coded affinity tag (ICAT) tandem mass spectrometry (MS) allows for qualitative and quantitative analysis of paired protein samples. We sought to determine whether ICAT technology could quantify and identify differential expression of tumor-specific proteins in nipple aspirate fluid (NAF) from the tumor-bearing and contralateral disease-free breasts of patients with unilateral early-stage breast cancer. Methods Paired NAF samples from 18 women with stage I or II unilateral invasive breast carcinoma and 4 healthy volunteers were analyzed using ICAT labeling, sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE), liquid chromatography, and MS. Proteins were identified by sequence database analysis. Western blot analysis of NAF from an independent sample set from 12 women (8 with early-stage breast cancer and 4 healthy volunteers) was also performed. Results 353 peptides were identified from tandem mass spectra and matched to peptide sequences in the National Center for Biotechnology Information database. Equal numbers of peptides were up- versus down-regulated. Alpha2HS-glycoprotein [Heavy:Light (H:L) ratio 0.63] was underexpressed in NAF from tumor-bearing breasts, while lipophilin B (H:L ratio 1.42), beta-globin (H:L ratio 1.98), hemopexin (H:L ratio 1.73), and vitamin D-binding protein precursor (H:L ratio 1.82) were overexpressed. Western blot analysis of pooled samples of NAF from healthy volunteers versus NAF from women with breast cancer confirmed the overexpression of vitamin D-binding protein in tumor-bearing breasts. Conclusion ICAT tandem MS was able to identify and quantify differences in specific protein expression between NAF samples from tumor-bearing and disease-free breasts. Proteomic screening techniques using ICAT and NAF may be used to find markers for diagnosis of breast cancer. PMID:16542425

  3. Adjoint affine fusion and tadpoles

    NASA Astrophysics Data System (ADS)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  4. O(2)-dependent K(+) fluxes in trout red blood cells: the nature of O(2) sensing revealed by the O(2) affinity, cooperativity and pH dependence of transport.

    PubMed

    Berenbrink, M; Völkel, S; Heisler, N; Nikinmaa, M

    2000-07-01

    The effects of pH and O(2) tension on the isotonic ouabain-resistant K(+) (Rb+) flux pathway and on haemoglobin O2 binding were studied in trout red blood cells (RBCs) in order to test for a direct effect of haemoglobin O(2) saturation on K(+) transport across the RBC membrane. At pH values corresponding to in vivo control arterial plasma pH and higher, elevation of the O(2) partial pressure (PO(2)) from 7.8 to 157 mmHg increased unidirectional K(+) influx across the RBC membrane several-fold. At lower extracellular pH values, stimulation of K(+) influx by O(2) was depressed, exhibiting an apparent pK(a) (pK'(a)) for the process of 8.0. Under similar conditions the pK'(a) for acid-induced deoxygenation of haemoglobin (Hb) was 7.3. When trout RBCs were exposed to PO(2) values between 0 and 747 mmHg, O(2) equilibrium curves typical of Hb O(2) saturation were also obtained for K(+) influx and efflux. However, at pH 7.9, the PO(2) for half-maximal K(+) efflux and K(+) influx (P50) was about 8- to 12-fold higher than the P(50) for Hb-O(2) binding. While K(+) influx and efflux stimulation by O(2) was essentially non-cooperative, Hb-O(2) equilibrium curves were distinctly sigmoidal (Hill parameters close to 1 and 3, respectively). O(2)-stimulated K(+) influx and efflux were strongly pH dependent. When the definition of the Bohr factor for respiratory pigments (Phi = delta logP50 x delta pH(-1)) was extended to the effect of pH on O(2)-dependent K(+) influx and efflux, extracellular Bohr factors (Phi(o) of -2.00 and -2.06 were obtained, values much higher than that for Hb (Phi(o) = -0.49). The results of this study are consistent with an O(2) sensing mechanism differing markedly in affinity and cooperativity of O(2) binding, as well as in pH sensitivity, from bulk Hb.

  5. Validation of affinity reagents using antigen microarrays.

    PubMed

    Sjöberg, Ronald; Sundberg, Mårten; Gundberg, Anna; Sivertsson, Asa; Schwenk, Jochen M; Uhlén, Mathias; Nilsson, Peter

    2012-06-15

    There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.

  6. Fatigue damage prognosis using affine arithmetic

    NASA Astrophysics Data System (ADS)

    Gbaguidi, Audrey; Kim, Daewon

    2014-02-01

    Among the essential steps to be taken in structural health monitoring systems, damage prognosis would be the field that is least investigated due to the complexity of the uncertainties. This paper presents the possibility of using Affine Arithmetic for uncertainty propagation of crack damage in damage prognosis. The structures examined are thin rectangular plates made of titanium alloys with central mode I cracks and a composite plate with an internal delamination caused by mixed mode I and II fracture modes, under a harmonic uniaxial loading condition. The model-based method for crack growth rates are considered using the Paris Erdogan law model for the isotropic plates and the delamination growth law model proposed by Kardomateas for the composite plate. The parameters for both models are randomly taken and their uncertainties are considered as defined by an interval instead of a probability distribution. A Monte Carlo method is also applied to check whether Affine Arithmetic (AA) leads to tight bounds on the lifetime of the structure.

  7. Contractions of affine spherical varieties

    SciTech Connect

    Arzhantsev, I V

    1999-08-31

    The language of filtrations and contractions is used to describe the class of G-varieties obtainable as the total spaces of the construction of contraction applied to affine spherical varieties, which is well-known in invariant theory. These varieties are local models for arbitrary affine G-varieties of complexity 1 with a one-dimensional categorical quotient. As examples, reductive algebraic semigroups and three-dimensional SL{sub 2}-varieties are considered.

  8. GALPROP: New Developments in CR Propagation Code

    NASA Technical Reports Server (NTRS)

    Moskalenko, I. V.; Jones, F. C.; Mashnik, S. G.; Strong, A. W.; Ptuskin, V. S.

    2003-01-01

    The numerical Galactic CR propagation code GALPROP has been shown to reproduce simultaneously observational data of many kinds related to CR origin and propagation. It has been validated on direct measurements of nuclei, antiprotons, electrons, positrons as well as on astronomical measurements of gamma rays and synchrotron radiation. Such data provide many independent constraints on model parameters while revealing some contradictions in the conventional view of Galactic CR propagation. Using a new version of GALPROP we study new effects such as processes of wave-particle interactions in the interstellar medium. We also report about other developments in the CR propagation code.

  9. Electro-Optic Propagation

    DTIC Science & Technology

    2003-09-30

    Electro - Optic Propagation Stephen Doss-Hammel SPAWARSYSCEN San Diego code 2858 49170 Propagation Path San Diego, CA 92152-7385 phone: (619...scenarios to extend the capabilities of TAWS to surface and low altitude situations. OBJECTIVES The electro - optical propagation objectives are: 1...development of a new propagation assessment tool called EOSTAR ( Electro - Optical Signal Transmission and Ranging). The goal of the EOSTAR project is to

  10. Chemical binding affinity estimation using MSB

    NASA Astrophysics Data System (ADS)

    Weaver, John B.; Rauwerdink, Adam M.

    2011-03-01

    Binding affinity can be estimated in several ways in the laboratory but there is no viable way to estimate binding affinity in vivo without assumptions on the number of binding sites. Magnetic spectroscopy of nanoparticle Brownian motion, MSB, measures the rotational Brownian motion. The MSB signal is affected by nanoparticle binding affinity so it provides a mechanism to measure the chemical binding affinity. We present a possible mechanism to quantify the binding affinity and test that mechanism using viscous solutions.

  11. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

    Celik, D.; Ozdemir, Y.; Ureyen, M.

    2007-01-01

    Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

  12. Affinity-aware checkpoint restart

    SciTech Connect

    Saini, Ajay; Rezaei, Arash; Mueller, Frank; Hargrove, Paul; Roman, Eric

    2014-12-08

    Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core maps and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.

  13. Affinity-aware checkpoint restart

    DOE PAGES

    Saini, Ajay; Rezaei, Arash; Mueller, Frank; ...

    2014-12-08

    Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core mapsmore » and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.« less

  14. ELECTRON AFFINITIES OF INORGANIC RADICALS.

    DTIC Science & Technology

    energy in the latter compound is 110 kcals/mole, distinctly higher than in ammonia. Cyanogen (CN)2 and hydrocyanic acid (HCN) yield values for the...ions very readily, and the electron affinity is 49 kcals/mole. A comparison with the results from thiocyanic acid (HNCS) indicates that the H-N bond

  15. Structural origins of high-affinity biotin binding to streptavidin.

    PubMed

    Weber, P C; Ohlendorf, D H; Wendoloski, J J; Salemme, F R

    1989-01-06

    The high affinity of the noncovalent interaction between biotin and streptavidin forms the basis for many diagnostic assays that require the formation of an irreversible and specific linkage between biological macromolecules. Comparison of the refined crystal structures of apo and a streptavidin:biotin complex shows that the high affinity results from several factors. These factors include the formation of multiple hydrogen bonds and van der Waals interactions between biotin and the protein, together with the ordering of surface polypeptide loops that bury the biotin in the protein interior. Structural alterations at the biotin binding site produce quaternary changes in the streptavidin tetramer. These changes apparently propagate through cooperative deformations in the twisted beta sheets that link tetramer subunits.

  16. Theoretical proton affinity and fluoride affinity of nerve agent VX.

    PubMed

    Bera, Narayan C; Maeda, Satoshi; Morokuma, Keiji; Viggiano, Al A

    2010-12-23

    Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -ΔE ∼ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(═O)(Me)-S-(CH(2))(2)-N(+)(iPr)═CHMe] product and the destruction product forming Et-O-P(═O)(Me)-SMe + CH(2)═N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(═O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -ΔE ∼ 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems.

  17. Affinity learning with diffusion on tensor product graph.

    PubMed

    Yang, Xingwei; Prasad, Lakshman; Latecki, Longin Jan

    2013-01-01

    In many applications, we are given a finite set of data points sampled from a data manifold and represented as a graph with edge weights determined by pairwise similarities of the samples. Often the pairwise similarities (which are also called affinities) are unreliable due to noise or due to intrinsic difficulties in estimating similarity values of the samples. As observed in several recent approaches, more reliable similarities can be obtained if the original similarities are diffused in the context of other data points, where the context of each point is a set of points most similar to it. Compared to the existing methods, our approach differs in two main aspects. First, instead of diffusing the similarity information on the original graph, we propose to utilize the tensor product graph (TPG) obtained by the tensor product of the original graph with itself. Since TPG takes into account higher order information, it is not a surprise that we obtain more reliable similarities. However, it comes at the price of higher order computational complexity and storage requirement. The key contribution of the proposed approach is that the information propagation on TPG can be computed with the same computational complexity and the same amount of storage as the propagation on the original graph. We prove that a graph diffusion process on TPG is equivalent to a novel iterative algorithm on the original graph, which is guaranteed to converge. After its convergence we obtain new edge weights that can be interpreted as new, learned affinities. We stress that the affinities are learned in an unsupervised setting. We illustrate the benefits of the proposed approach for data manifolds composed of shapes, images, and image patches on two very different tasks of image retrieval and image segmentation. With learned affinities, we achieve the bull's eye retrieval score of 99.99 percent on the MPEG-7 shape dataset, which is much higher than the state-of-the-art algorithms. When the data

  18. Marker-Based Estimates Reveal Significant Non-additive Effects in Clonally Propagated Cassava (Manihot esculenta): Implications for the Prediction of Total Genetic Value and the Selection of Varieties.

    PubMed

    Wolfe, Marnin D; Kulakow, Peter; Rabbi, Ismail Y; Jannink, Jean-Luc

    2016-08-31

    In clonally propagated crops, non-additive genetic effects can be effectively exploited by the identification of superior genetic individuals as varieties. Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop that feeds hundreds of millions. We quantified the amount and nature of non-additive genetic variation for three key traits in a breeding population of cassava from sub-Saharan Africa using additive and non-additive genome-wide marker-based relationship matrices. We then assessed the accuracy of genomic prediction for total (additive plus non-additive) genetic value. We confirmed previous findings based on diallel populations, that non-additive genetic variation is significant for key cassava traits. Specifically, we found that dominance is particularly important for root yield and epistasis contributes strongly to variation in CMD resistance. Further, we showed that total genetic value predicted observed phenotypes more accurately than additive only models for root yield but not for dry matter content, which is mostly additive or for CMD resistance, which has high narrow-sense heritability. We address the implication of these results for cassava breeding and put our work in the context of previous results in cassava, and other plant and animal species.

  19. Modeling turbulent flame propagation

    SciTech Connect

    Ashurst, W.T.

    1994-08-01

    Laser diagnostics and flow simulation techniques axe now providing information that if available fifty years ago, would have allowed Damkoehler to show how turbulence generates flame area. In the absence of this information, many turbulent flame speed models have been created, most based on Kolmogorov concepts which ignore the turbulence vortical structure, Over the last twenty years, the vorticity structure in mixing layers and jets has been shown to determine the entrainment and mixing behavior and these effects need to be duplicated by combustion models. Turbulence simulations reveal the intense vorticity structure as filaments and simulations of passive flamelet propagation show how this vorticity Creates flame area and defines the shape of the expected chemical reaction surface. Understanding how volume expansion interacts with flow structure should improve experimental methods for determining turbulent flame speed. Since the last decade has given us such powerful new tools to create and see turbulent combustion microscopic behavior, it seems that a solution of turbulent combustion within the next decade would not be surprising in the hindsight of 2004.

  20. Coenzyme-like ligands for affinity isolation of cholesterol oxidase.

    PubMed

    Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu

    2016-05-15

    Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%.

  1. Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling.

    PubMed

    Hackel, Benjamin J; Kapila, Atul; Wittrup, K Dane

    2008-09-19

    The 10th type III domain of human fibronectin (Fn3) has been validated as an effective scaffold for molecular recognition. In the current work, it was desired to improve the robustness of selection of stable, high-affinity Fn3 domains. A yeast surface display library of Fn3 was created in which three solvent-exposed loops were diversified in terms of amino acid composition and loop length. The library was screened by fluorescence-activated cell sorting to isolate binders to lysozyme. An affinity maturation scheme was developed to rapidly and broadly diversify populations of clones by random mutagenesis as well as homologous recombination-driven shuffling of mutagenized loops. The novel library and affinity maturation scheme combined to yield stable, monomeric Fn3 domains with 3 pM affinity for lysozyme. A secondary affinity maturation identified a stable 1.1 pM binder, the highest affinity yet reported for an Fn3 domain. In addition to extension of the affinity limit for this scaffold, the results demonstrate the ability to achieve high-affinity binding while preserving stability and the monomeric state. This library design and affinity maturation scheme is highly efficient, utilizing an initial diversity of 2x10(7) clones and screening only 1x10(8) mutants (totaled over all affinity maturation libraries). Analysis of intermediate populations revealed that loop length diversity, loop shuffling, and recursive mutagenesis of diverse populations are all critical components.

  2. Propagation research in Japan

    NASA Technical Reports Server (NTRS)

    Wakana, Hiromitsu

    1991-01-01

    L-band propagation measurements for land-mobile, maritime, and aeronautical satellite communications have been carried out by using the Japanese Engineering Test Satellite-Five (ETS-5) which was launched in Aug. 1987. This paper presents propagation characteristics for each of the mobile satellite communication channels.

  3. NASA Propagation Information Center

    NASA Technical Reports Server (NTRS)

    Smith, Ernest K.; Flock, Warren L.

    1989-01-01

    The NASA Propagation Information Center became formally operational in July 1988. It is located in the Department of Electrical and Computer Engineering of the University of Colorado at Boulder. The Center is several things: a communications medium for the propagation with the outside world, a mechanism for internal communication within the program, and an aid to management.

  4. Shallow-Water Propagation

    DTIC Science & Technology

    2016-06-07

    Shallow- Water Propagation William L. Siegmann Rensselaer Polytechnic Institute 110 Eighth Street Troy, New York 12180-3590 phone: (518) 276...ocean_acoustics LONG-TERM GOALS Develop methods for propagation and coherence calculations in complex shallow- water environments, determine...intensity and coherence. APPROACH (A) Develop high accuracy PE techniques for applications to shallow- water sediments, accounting for

  5. Millimeter wavelength propagation studies

    NASA Technical Reports Server (NTRS)

    Hodge, D. B.

    1974-01-01

    The investigations conducted for the Millimeter Wavelength Propagation Studies during the period December, 1966, to June 1974 are reported. These efforts included the preparation for the ATS-5 Millimeter Wavelength Propagation Experiment and the subsequent data acquisition and data analysis. The emphasis of the OSU participation in this experiment was placed on the determination of reliability improvement resulting from the use of space diversity on a millimeter wavelength earth-space communication link. Related measurements included the determination of the correlation between radiometric temperature and attenuation along the earth-space propagation path. Along with this experimental effort a theoretical model was developed for the prediction of attenuation statistics on single and spatially separated earth space propagation paths. A High Resolution Radar/Radiometer System and Low Resolution Radar System were developed and implemented for the study of intense rain cells in preparation for the ATS-6 Millimeter Wavelength Propagation Experiment.

  6. Gear crack propagation investigations

    NASA Technical Reports Server (NTRS)

    Lewicki, David G.; Ballarini, Roberto

    1996-01-01

    Analytical and experimental studies were performed to investigate the effect of gear rim thickness on crack propagation life. The FRANC (FRacture ANalysis Code) computer program was used to simulate crack propagation. The FRANC program used principles of linear elastic fracture mechanics, finite element modeling, and a unique re-meshing scheme to determine crack tip stress distributions, estimate stress intensity factors, and model crack propagation. Various fatigue crack growth models were used to estimate crack propagation life based on the calculated stress intensity factors. Experimental tests were performed in a gear fatigue rig to validate predicted crack propagation results. Test gears were installed with special crack propagation gages in the tooth fillet region to measure bending fatigue crack growth. Good correlation between predicted and measured crack growth was achieved when the fatigue crack closure concept was introduced into the analysis. As the gear rim thickness decreased, the compressive cyclic stress in the gear tooth fillet region increased. This retarded crack growth and increased the number of crack propagation cycles to failure.

  7. Structure of a High-Affinity

    SciTech Connect

    Saphire, E.O.; Montero, M.; Menendez, A.; Houten, N.E.van; Irving, M.B.; Pantophlet, R.; Swick, M.B.; Parren, P.W.H.I.; Burton, D.R.; Scott, J.K.; Wilson, I.A.; /Scripps Res. Inst. /Simon Fraser U. /British Columbia U.

    2007-07-13

    The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 Angstrom resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining

  8. Gear Crack Propagation Investigation

    NASA Technical Reports Server (NTRS)

    1995-01-01

    Reduced weight is a major design goal in aircraft power transmissions. Some gear designs incorporate thin rims to help meet this goal. Thin rims, however, may lead to bending fatigue cracks. These cracks may propagate through a gear tooth or into the gear rim. A crack that propagates through a tooth would probably not be catastrophic, and ample warning of a failure could be possible. On the other hand, a crack that propagates through the rim would be catastrophic. Such cracks could lead to disengagement of a rotor or propeller from an engine, loss of an aircraft, and fatalities. To help create and validate tools for the gear designer, the NASA Lewis Research Center performed in-house analytical and experimental studies to investigate the effect of rim thickness on gear-tooth crack propagation. Our goal was to determine whether cracks grew through gear teeth (benign failure mode) or through gear rims (catastrophic failure mode) for various rim thicknesses. In addition, we investigated the effect of rim thickness on crack propagation life. A finite-element-based computer program simulated gear-tooth crack propagation. The analysis used principles of linear elastic fracture mechanics, and quarter-point, triangular elements were used at the crack tip to represent the stress singularity. The program had an automated crack propagation option in which cracks were grown numerically via an automated remeshing scheme. Crack-tip stress-intensity factors were estimated to determine crack-propagation direction. Also, various fatigue crack growth models were used to estimate crack-propagation life. Experiments were performed in Lewis' Spur Gear Fatigue Rig to validate predicted crack propagation results. Gears with various backup ratios were tested to validate crack-path predictions. Also, test gears were installed with special crack-propagation gages in the tooth fillet region to measure bending-fatigue crack growth. From both predictions and tests, gears with backup ratios

  9. Fick's Law Assisted Propagation for Semisupervised Learning.

    PubMed

    Gong, Chen; Tao, Dacheng; Fu, Keren; Yang, Jie

    2015-09-01

    How to propagate the label information from labeled examples to unlabeled examples is a critical problem for graph-based semisupervised learning. Many label propagation algorithms have been developed in recent years and have obtained promising performance on various applications. However, the eigenvalues of iteration matrices in these algorithms are usually distributed irregularly, which slow down the convergence rate and impair the learning performance. This paper proposes a novel label propagation method called Fick's law assisted propagation (FLAP). Unlike the existing algorithms that are directly derived from statistical learning, FLAP is deduced on the basis of the theory of Fick's First Law of Diffusion, which is widely known as the fundamental theory in fluid-spreading. We prove that FLAP will converge with linear rate and show that FLAP makes eigenvalues of the iteration matrix distributed regularly. Comprehensive experimental evaluations on synthetic and practical datasets reveal that FLAP obtains encouraging results in terms of both accuracy and efficiency.

  10. Affinity membrane introduction mass spectrometry

    SciTech Connect

    Xu, C.; Patrick, J.S.; Cooks, R.G. )

    1995-02-15

    A new technique, affinity membrane introduction mass spectrometry, is described. In this method, a chemically modified membrane is used to selectively adsorb analytes bearing a particular functional group and concentrate them from solution. Release of the bound analyte results in its transfer across the membrane and allows it to be monitored mass spectrometrically, using, in the present case, a benchtop ion trap instrument. Alkylamine-modified cellulose membranes are used to bind substituted benzaldehydes through imine formation at high pH. Release of the bound aldehyde is achieved by acid hydrolysis of the surface-bound imine. Benzaldehyde is detected with excellent specificity at 10 ppm in a complex mixture using this method. Using the enrichment capability of the membrane, a full mass spectrum of benzaldehyde can be measured at a concentration of 10 ppb. The behavior of a variety of other aldehydes is also discussed to illustrate the capabilities of the method. 21 refs., 5 figs., 2 tabs.

  11. Propagation of Environmental Noise

    ERIC Educational Resources Information Center

    Lyon, R. H.

    1973-01-01

    Solutions for environmental noise pollution lie in systematic study of many basic processes such as reflection, scattering, and spreading. Noise propagation processes should be identified in different situations and assessed for their relative importance. (PS)

  12. Wave Propagation Program

    SciTech Connect

    McCandless, Kathleen; Petersson, Anders; Nilsson, Stefan; Sjogreen, Bjorn

    2007-01-08

    WPP is a massively parallel, 3D, C++, finite-difference elastodynamic wave propagation code. Typical applications for wave propagation with WPP include: evaluation of seismic event scenarios and damage from earthquakes, non-destructive evaluation of materials, underground facility detection, oil and gas exploration, predicting the electro-magnetic fields in accelerators, and acoustic noise generation. For more information, see User’s Manual [1].

  13. Antisymmetric tensor generalizations of affine vector fields

    PubMed Central

    Morisawa, Yoshiyuki; Tomoda, Kentaro

    2016-01-01

    Tensor generalizations of affine vector fields called symmetric and antisymmetric affine tensor fields are discussed as symmetry of spacetimes. We review the properties of the symmetric ones, which have been studied in earlier works, and investigate the properties of the antisymmetric ones, which are the main theme in this paper. It is shown that antisymmetric affine tensor fields are closely related to one-lower-rank antisymmetric tensor fields which are parallelly transported along geodesics. It is also shown that the number of linear independent rank-p antisymmetric affine tensor fields in n-dimensions is bounded by (n + 1)!/p!(n − p)!. We also derive the integrability conditions for antisymmetric affine tensor fields. Using the integrability conditions, we discuss the existence of antisymmetric affine tensor fields on various spacetimes. PMID:26858463

  14. Conformal field theory on affine Lie groups

    SciTech Connect

    Clubok, Kenneth Sherman

    1996-04-01

    Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs.

  15. A Novel Vertex Affinity for Community Detection

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

  16. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  17. Dynamic friction of self-affine surfaces

    NASA Astrophysics Data System (ADS)

    Schmittbuhl, Jean; Vilotte, Jean-Pierre; Roux, Stéphane

    1994-02-01

    We investigate the velocity dependence of the friction between two rigid blocks limited by a self-affine surface such as the one generated by a crack. The upper solid is subjected either to gravity or to an external elastic stiffness, and is driven horizontally at constant velocity, V, while the lower solid is fixed. For low velocities, the apparent friction coefficient is constant. For high velocities, the apparent friction is shown to display a velocity weakening. The weakening can be related to the variation of the mean contact time due to the occurrence of jumps during the motions. The cross-over between these two regimes corresponds to a characteristic velocity which depends on the geometry of the surfaces and on the mean normal force. In the case of simple gravity loading, the velocity dependence of the apparent friction at high velocities is proportional to 1/V^2 where V is the imposed tangential velocity. In the case of external elastic stiffness, two velocity weakening regimes can be identified, the first is identical to the gravity case with a 1/V^2 dependence, the second appears at higher velocities and is characterized by a 1/V variation. The characteristic velocity of this second cross-over depends on the roughness and the elastic stiffness. The statistical distribution of ballistic flight distances is analysed, and is shown to reveal in all cases the self-affinity of the contacting surfaces. Nous analysons la dépendence en vitesse du frottement entre deux solides limités par une surface rugueuse auto-affine comme celle d'une surface de fracture. Le solide supérieur est soumis soit à la gravité, soit à une raideur élastique externe, et est entraîné à vitesse horizontale constante V sur le solide inférieur fixe. A faible vitesse, le coefficient de friction apparent, est constant. A forte vitesse, le coefficient de friction apparent devient inversement proportionnel à la vitesse. Cette dépendance peut être reliée à la variation du temps

  18. Structure of classical affine and classical affine fractional W-algebras

    SciTech Connect

    Suh, Uhi Rinn

    2015-01-15

    We introduce a classical BRST complex (See Definition 3.2.) and show that one can construct a classical affine W-algebra via the complex. This definition clarifies that classical affine W-algebras can be considered as quasi-classical limits of quantum affine W-algebras. We also give a definition of a classical affine fractional W-algebra as a Poisson vertex algebra. As in the classical affine case, a classical affine fractional W-algebra has two compatible λ-brackets and is isomorphic to an algebra of differential polynomials as a differential algebra. When a classical affine fractional W-algebra is associated to a minimal nilpotent, we describe explicit forms of free generators and compute λ-brackets between them. Provided some assumptions on a classical affine fractional W-algebra, we find an infinite sequence of integrable systems related to the algebra, using the generalized Drinfel’d and Sokolov reduction.

  19. DROMO Propagator Revisited

    NASA Astrophysics Data System (ADS)

    Urrutxua, H.; Sanjurjo-Rivo, M.; Peláez, J.

    2013-12-01

    In year 2000 a house-made orbital propagator was developed by the SDGUPM (former Grupo de Dinámica de Tethers) based in a set of redundant variables including Euler parameters. This propagator was called DROMO. and it was mainly used in numerical simulations of electrodynamic tethers. It was presented for the first time in the international meeting V Jornadas de Trabajo en Mecánica Celeste, held in Albarracín, Spain, in 2002 (see reference 1). The special perturbation method associated with DROMO can be consulted in the paper.2 In year 1975, Andre Deprit in reference 3 proposes a propagation scheme very similar to the one in which DROMO is based, by using the ideal frame concept of Hansen. The different approaches used in references 3 and 2 gave rise to a small controversy. In this paper we carried out a different deduction of the DROMO propagator, underlining its close relation with the Hansen ideal frame concept, and also the similarities and the differences with the theory carried out by Deprit in 3. Simultaneously we introduce some improvements in the formulation that leads to a more synthetic propagator.

  20. Antigen affinity and antigen dose exert distinct influences on CD4 T-cell differentiation.

    PubMed

    Keck, Simone; Schmaler, Mathias; Ganter, Stefan; Wyss, Lena; Oberle, Susanne; Huseby, Eric S; Zehn, Dietmar; King, Carolyn G

    2014-10-14

    Cumulative T-cell receptor signal strength and ensuing T-cell responses are affected by both antigen affinity and antigen dose. Here we examined the distinct contributions of these parameters to CD4 T-cell differentiation during infection. We found that high antigen affinity positively correlates with T helper (Th)1 differentiation at both high and low doses of antigen. In contrast, follicular helper T cell (TFH) effectors are generated after priming with high, intermediate, and low affinity ligand. Unexpectedly, memory T cells generated after priming with very low affinity antigen remain impaired in their ability to generate secondary Th1 effectors, despite being recalled with high affinity antigen. These data challenge the view that only strongly stimulated CD4 T cells are capable of differentiating into the TFH and memory T-cell compartments and reveal that differential strength of stimulation during primary T-cell activation imprints unique and long lasting T-cell differentiation programs.

  1. Experimental allergic encephalomyelitis (EAE) in mice selectively bred to produce high affinity (HA) or low affinity (LA) antibody responses.

    PubMed Central

    Devey, M E; Major, P J; Bleasdale-Barr, K M; Holland, G P; Dal Canto, M C; Paterson, P Y

    1990-01-01

    Induction of experimental allergic encephalomyelitis (EAE) in mice genetically selected to produce either high affinity (HA) or low affinity (LA) antibody responses has revealed significant differences in disease susceptibility between the two lines. HA mice were highly susceptible to EAE following subcutaneous sensitization to mouse central nervous system (CNS) tissue emulsified in Freund's complete adjuvant (FCA). Furthermore, of HA mice surviving acute EAE, up to 93% subsequently developed chronic relapsing disease (CREAE) characterized by variable demyelinating inflammatory changes within the spinal cord. In contrast, LA mice, despite having a major histocompatability complex (MHC) haplotype associated with susceptibility to EAE, were highly resistant to the disease and showed no signs of CREAE when observed for up to 100 days post-sensitization. Antibodies to myelin basic protein (MBP) were detected in both lines but rising titres of high functional affinity antibodies were only seen in HA mice. These HA and LA lines of mice provide a new approach to the study of EAE and, in particular, the role of antibody and antibody affinity in the chronic relapsing form of the disease. Images Figure 2 PMID:2335373

  2. Elevated Temperature Crack Propagation

    NASA Technical Reports Server (NTRS)

    Orange, Thomas W.

    1994-01-01

    This paper is a summary of two NASA contracts on high temperature fatigue crack propagation in metals. The first evaluated the ability of fairly simple nonlinear fracture parameters to correlate crack propagation. Hastelloy-X specimens were tested under isothermal and thermomechanical cycling at temperatures up to 980 degrees C (1800 degrees F). The most successful correlating parameter was the crack tip opening displacement derived from the J-integral. The second evaluated the ability of several path-independent integrals to correlate crack propagation behavior. Inconel 718 specimens were tested under isothermal, thermomechanical, temperature gradient, and creep conditions at temperatures up to 650 degrees C (1200 degrees F). The integrals formulated by Blackburn and by Kishimoto correlated the data reasonably well under all test conditions.

  3. Elevated temperature crack propagation

    SciTech Connect

    Orange, T.W.

    1994-02-01

    This paper is a summary of two NASA contracts on high temperature fatigue crack propagation in metals. The first evaluated the ability of fairly simple nonlinear fracture parameters to correlate crack propagation. Hastelloy-X specimens were tested under isothermal and thermomechanical cycling at temperatures up to 980 degrees C (1800 degrees F). The most successful correlating parameter was the crack tip opening displacement derived from the J-integral. The second evaluated the ability of several path-independent integrals to correlate crack propagation behavior. Inconel 718 specimens were tested under isothermal, thermomechanical, temperature gradient, and creep conditions at temperatures up to 650 degrees C (1200 degrees F). The integrals formulated by Blackburn and by Kishimoto correlated the data reasonably well under all test conditions.

  4. Improving image segmentation by learning region affinities

    SciTech Connect

    Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  5. Turbofan Duct Propagation Model

    NASA Technical Reports Server (NTRS)

    Lan, Justin H.; Posey, Joe W. (Technical Monitor)

    2001-01-01

    The CDUCT code utilizes a parabolic approximation to the convected Helmholtz equation in order to efficiently model acoustic propagation in acoustically treated, complex shaped ducts. The parabolic approximation solves one-way wave propagation with a marching method which neglects backwards reflected waves. The derivation of the parabolic approximation is presented. Several code validation cases are given. An acoustic lining design process for an example aft fan duct is discussed. It is noted that the method can efficiently model realistic three-dimension effects, acoustic lining, and flow within the computational capabilities of a typical computer workstation.

  6. Comments on 'Rapid pulsed microwave propagation'

    NASA Technical Reports Server (NTRS)

    Steffes, Paul G.; Rodrigue, George P.

    1992-01-01

    Giakos and Ishii (1991) claim conclusive experimental evidence that microwave pulse propagation in waveguides and in air occurs at velocities exceeding the free-space speed of light, and assert that it is possible to transmit both energy and information in a non-TEM waveguiding medium at the lightspeed-exceeding phase velocity. The present analysis of their results reveals several significant potential sources of error in both their laboratory findings and those findings' interpretation. Giakos and Ishii reply that the accuracy of the propagation measurements presented in their study exceeds 0.2 percent.

  7. Mapping mechanical force propagation through biomolecular complexes

    SciTech Connect

    Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; Durner, Ellis; Ott, Wolfgang; Bayer, Edward A.; Schulten, Klaus; Nash, Michael A.; Gaub, Hermann E.

    2015-08-11

    In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

  8. Structure of Greyhound hemoglobin: origin of high oxygen affinity.

    PubMed

    Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

    2011-05-01

    This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

  9. Seismotectonics of mid-ocean ridge propagation in Hess Deep.

    PubMed

    Floyd, Jacqueline S; Tolstoy, Maya; Mutter, John C; Scholz, Christopher H

    2002-11-29

    Hydroacoustic data from the eastern equatorial Pacific reveal low-magnitude seismicity concentrated at the propagating tip of the Galapagos Rise in Hess Deep. The patterns of seismicity and faulting are similar to those observed in the process zone of laboratory-scale propagating tensile cracks. Because the fracture energy required for propagation scales with crack length and process zone size, it follows that ridges can propagate stably in the brittle crust without exceptional resisting forces as proposed by previous models based on linear elastic fracture mechanics.

  10. DROMO propagator revisited

    NASA Astrophysics Data System (ADS)

    Urrutxua, Hodei; Sanjurjo-Rivo, Manuel; Peláez, Jesús

    2016-01-01

    In the year 2000 an in-house orbital propagator called DROMO (Peláez et al. in Celest Mech Dyn Astron 97:131-150, 2007. doi: 10.1007/s10569-006-9056-3) was developed by the Space Dynamics Group of the Technical University of Madrid, based in a set of redundant variables including Euler-Rodrigues parameters. An original deduction of the DROMO propagator is carried out, underlining its close relation with the ideal frame concept introduced by Hansen (Abh der Math-Phys Cl der Kon Sachs Ges der Wissensch 5:41-218, 1857). Based on the very same concept, Deprit (J Res Natl Bur Stand Sect B Math Sci 79B(1-2):1-15, 1975) proposed a formulation for orbit propagation. In this paper, similarities and differences with the theory carried out by Deprit are analyzed. Simultaneously, some improvements are introduced in the formulation, that lead to a more synthetic and better performing propagator. Also, the long-term effect of the oblateness of the primary is studied in terms of DROMO variables, and new numerical results are presented to evaluate the performance of the method.

  11. PROPER: Optical propagation routines

    NASA Astrophysics Data System (ADS)

    Krist, John E.

    2014-05-01

    PROPER simulates the propagation of light through an optical system using Fourier transform algorithms (Fresnel, angular spectrum methods). Distributed as IDL source code, it includes routines to create complex apertures, aberrated wavefronts, and deformable mirrors. It is especially useful for the simulation of high contrast imaging telescopes (extrasolar planet imagers like TPF).

  12. GRC RF Propagation Studies

    NASA Technical Reports Server (NTRS)

    Nessel, James

    2013-01-01

    NASA Glenn Research Center has been involved in the characterization of atmospheric effects on space communications links operating at Ka-band and above for the past 20 years. This presentation reports out on the most recent activities of propagation characterization that NASA is currently involved in.

  13. The Cutting Edge of Affinity Electrophoresis Technology

    PubMed Central

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

    2015-01-01

    Affinity electrophoresis is an important technique that is widely used to separate and analyze biomolecules in the fields of biology and medicine. Both quantitative and qualitative information can be gained through affinity electrophoresis. Affinity electrophoresis can be applied through a variety of strategies, such as mobility shift electrophoresis, charge shift electrophoresis or capillary affinity electrophoresis. These strategies are based on changes in the electrophoretic patterns of biological macromolecules that result from interactions or complex-formation processes that induce changes in the size or total charge of the molecules. Nucleic acid fragments can be characterized through their affinity to other molecules, for example transcriptional factor proteins. Hydrophobic membrane proteins can be identified by means of a shift in the mobility induced by a charged detergent. The various strategies have also been used in the estimation of association/disassociation constants. Some of these strategies have similarities to affinity chromatography, in that they use a probe or ligand immobilized on a supported matrix for electrophoresis. Such methods have recently contributed to profiling of major posttranslational modifications of proteins, such as glycosylation or phosphorylation. Here, we describe advances in analytical techniques involving affinity electrophoresis that have appeared during the last five years. PMID:28248262

  14. Coronal Structures Observed by Radio Propagation Measurements

    NASA Technical Reports Server (NTRS)

    Woo, R.

    1995-01-01

    This paper summarizes (1) advances in our knowledge of coronal structures inferred from radio propagation measurements, and (2) gains in our understanding of the relationship between radio propagation and white-light coronagraph measurements. Radio propagation measurements confirm that streamers are ray-like structures as depicted in coronagraph pictures, but also reveal a hierarchy of filamentary structures throughout the corona, extending from the size of streamers down to scale sizes as small as about 1 km at the Sun (10(ghe) arcsec). Doppler scintillation measurements, therefore, open a new window on small-scale structure that has long eluded coronagraph measurements. In addition, high precision ranging measurements make it possible to investigate large-scale structures not yet observed in corona graphs, such as plumes in equatorial coronal regions.

  15. A Database for Propagation Models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Rucker, James

    1997-01-01

    The Propagation Models Database is designed to allow the scientists and experimenters in the propagation field to process their data through many known and accepted propagation models. The database is an Excel 5.0 based software that houses user-callable propagation models of propagation phenomena. It does not contain a database of propagation data generated out of the experiments. The database not only provides a powerful software tool to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables and producing impressive and crisp hard copy for presentation and filing.

  16. Propagating Instabilities in Solids

    NASA Astrophysics Data System (ADS)

    Kyriakides, Stelios

    1998-03-01

    Instability is one of the factors which limit the extent to which solids can be loaded or deformed and plays a pivotal role in the design of many structures. Such instabilities often result in localized deformation which precipitates catastrophic failure. Some materials have the capacity to recover their stiffness following a certain amount of localized deformation. This local recovery in stiffness arrests further local deformation and spreading of the instability to neighboring material becomes preferred. Under displacement controlled loading the propagation of the transition fronts can be achieved in a steady-state manner at a constant stress level known as the propagation stress. The stresses in the transition fronts joining the highly deformed zone to the intact material overcome the instability nucleation stresses and, as a result, the propagation stress is usually much lower than the stress required to nucleate the instability. The classical example of this class of material instabilities is L/"uders bands which tend to affect mild steels and other metals. Recent work has demonstrated that propagating instabilities occur in several other materials. Experimental and analytical results from four examples will be used to illustrate this point: First the evolution of L=FCders bands in mild steel strips will be revisited. The second example involves the evolution of stress induced phase transformations (austenite to martensite phases and the reverse) in a shape memory alloy under displacement controlled stretching. The third example is the crushing behavior of cellular materials such as honeycombs and foams made from metals and polymers. The fourth example involves the axial broadening/propagation of kink bands in aligned fiber/matrix composites under compression. The microstructure and, as a result, the micromechanisms governing the onset, localization, local arrest and propagation of instabilities in each of the four materials are vastly different. Despite this

  17. Slow wave propagation in soft adhesive interfaces.

    PubMed

    Viswanathan, Koushik; Sundaram, Narayan K; Chandrasekar, Srinivasan

    2016-11-16

    Stick-slip in sliding of soft adhesive surfaces has long been associated with the propagation of Schallamach waves, a type of slow surface wave. Recently it was demonstrated using in situ experiments that two other kinds of slow waves-separation pulses and slip pulses-also mediate stick-slip (Viswanathan et al., Soft Matter, 2016, 12, 5265-5275). While separation pulses, like Schallamach waves, involve local interface detachment, slip pulses are moving stress fronts with no detachment. Here, we present a theoretical analysis of the propagation of these three waves in a linear elastodynamics framework. Different boundary conditions apply depending on whether or not local interface detachment occurs. It is shown that the interface dynamics accompanying slow waves is governed by a system of integral equations. Closed-form analytical expressions are obtained for the interfacial pressure, shear stress, displacements and velocities. Separation pulses and Schallamach waves emerge naturally as wave solutions of the integral equations, with oppositely oriented directions of propagation. Wave propagation is found to be stable in the stress regime where linearized elasticity is a physically valid approximation. Interestingly, the analysis reveals that slow traveling wave solutions are not possible in a Coulomb friction framework for slip pulses. The theory provides a unified picture of stick-slip dynamics and slow wave propagation in adhesive contacts, consistent with experimental observations.

  18. Visualizing Antibody Affinity Maturation in Germinal Centers

    PubMed Central

    Tas, Jeroen M.J.; Mesin, Luka; Pasqual, Giulia; Targ, Sasha; Jacobsen, Johanne T.; Mano, Yasuko M.; Chen, Casie S.; Weill, Jean-Claude; Reynaud, Claude-Agnès; Browne, Edward P.; Meyer-Hermann, Michael; Victora, Gabriel D.

    2016-01-01

    Antibodies somatically mutate to attain high affinity in germinal centers (GCs). There, competition between B cell clones and among somatic mutants of each clone drives an increase in average affinity across the population. The extent to which higher-affinity cells eliminating competitors restricts clonal diversity is unknown. By combining multiphoton microscopy and sequencing, we show that tens to hundreds of distinct B cell clones seed each GC, and that GCs lose clonal diversity at widely disparate rates. Furthermore, efficient affinity maturation can occur in the absence of homogenizing selection, ensuring that many clones can mature in parallel within the same GC. Our findings have implications for development of vaccines in which antibodies with non-immunodominant specificities must be elicited, as is the case for HIV-1 and influenza. PMID:26912368

  19. PRINCIPLES OF AFFINITY-BASED BIOSENSORS

    EPA Science Inventory

    Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...

  20. Protein purification using PDZ affinity chromatography.

    PubMed

    Walkup, Ward G; Kennedy, Mary B

    2015-04-01

    PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands.

  1. Affinity Electrophoresis Using Ligands Attached To Polymers

    NASA Technical Reports Server (NTRS)

    Van Alstine, James M.; Snyder, Robert S.; Harris, J. M.; Brooks, D. E.

    1990-01-01

    In new technique, reduction of electrophoretic mobilities by addition of polyethylene glycol to ligands increases electrophoretic separabilities. In immuno-affinity electrophoresis, modification of ligands extends specificity of electrophoretic separation to particles having surface electric-charge structures otherwise making them electrophoretically inseparable. Modification of antibodies by polyethylene glycol greatly reduces ability to aggregate while enhancing ability to affect electrophoretic mobilities of cells. In hydrophobic-affinity electrophoresis, addition of polyethylene glycol reduces tendency toward aggregation of cells or macromolecules.

  2. Atmospheric sound propagation

    NASA Technical Reports Server (NTRS)

    Cook, R. K.

    1969-01-01

    The propagation of sound waves at infrasonic frequencies (oscillation periods 1.0 - 1000 seconds) in the atmosphere is being studied by a network of seven stations separated geographically by distances of the order of thousands of kilometers. The stations measure the following characteristics of infrasonic waves: (1) the amplitude and waveform of the incident sound pressure, (2) the direction of propagation of the wave, (3) the horizontal phase velocity, and (4) the distribution of sound wave energy at various frequencies of oscillation. Some infrasonic sources which were identified and studied include the aurora borealis, tornadoes, volcanos, gravity waves on the oceans, earthquakes, and atmospheric instability waves caused by winds at the tropopause. Waves of unknown origin seem to radiate from several geographical locations, including one in the Argentine.

  3. Florida's propagation report

    NASA Technical Reports Server (NTRS)

    Helmken, Henry; Henning, Rudolf

    1994-01-01

    One of the key goals of the Florida Center is to obtain a maximum of useful information on propagation behavior unique to its subtropical weather and subtropical climate. Such weather data is of particular interest when it is (or has the potential to become) useful for developing and implementing techniques to compensate for adverse weather effects. Also discussed are data observations, current challenges, CDF's, sun movement, and diversity experiments.

  4. Transionospheric Propagation Code (TIPC)

    SciTech Connect

    Roussel-Dupre, R.; Kelley, T.A.

    1990-10-01

    The Transionospheric Propagation Code is a computer program developed at Los Alamos National Lab to perform certain tasks related to the detection of vhf signals following propagation through the ionosphere. The code is written in Fortran 77, runs interactively and was designed to be as machine independent as possible. A menu format in which the user is prompted to supply appropriate parameters for a given task has been adopted for the input while the output is primarily in the form of graphics. The user has the option of selecting from five basic tasks, namely transionospheric propagation, signal filtering, signal processing, DTOA study, and DTOA uncertainty study. For the first task a specified signal is convolved against the impulse response function of the ionosphere to obtain the transionospheric signal. The user is given a choice of four analytic forms for the input pulse or of supplying a tabular form. The option of adding Gaussian-distributed white noise of spectral noise to the input signal is also provided. The deterministic ionosphere is characterized to first order in terms of a total electron content (TEC) along the propagation path. In addition, a scattering model parameterized in terms of a frequency coherence bandwidth is also available. In the second task, detection is simulated by convolving a given filter response against the transionospheric signal. The user is given a choice of a wideband filter or a narrowband Gaussian filter. It is also possible to input a filter response. The third task provides for quadrature detection, envelope detection, and three different techniques for time-tagging the arrival of the transionospheric signal at specified receivers. The latter algorithms can be used to determine a TEC and thus take out the effects of the ionosphere to first order. Task four allows the user to construct a table of delta-times-of-arrival (DTOAs) vs TECs for a specified pair of receivers.

  5. Nonlinear Wave Propagation

    DTIC Science & Technology

    2009-02-09

    of parameters. Hence one expects that the solutions of the two equations , PES and NLS, are comparable. In Fig. 3 we plot the two solutions for...power saturated term, in the PES equation ) have stable soliton solutions or mode-locking evolution. In general the solitons are found to be unstable...literature. Generally speaking, the above lattice equations omitting nonlinear terms have solutions propagating along z direction, i.e., ψ(r, z) = e−iµzϕ(r

  6. Olympus propagation experiments

    NASA Technical Reports Server (NTRS)

    Arbesser-Rastburg, Bertram

    1994-01-01

    A summary of the activities of the OPEX (Olympus Propagation EXperimenters) group is given and some of the recent findings are presented. OLYMPUS, a telecommunication satellite owned by the European Space Agency, was launched on 12 June 1989. After the in-orbit tests were completed (in September 1989) the first propagation experiments started. Throughout 1990 the spacecraft functioned very well and a large number of experimenters received the beacon signals. On 29 May 1991 the spacecraft became inoperational after a major technical problem. With a series of complicated procedures OLYMPUS was recovered on 15 August 1991 - the first time in history that a civilian telecommunications satellite was brought back to service after losing power and telemetry. The propagation experiments were back on track. However, the recovery had used up so much fuel that the North-South station keeping had to be abandoned, which led to a natural increase of inclination at a rate of about 0.8 deg per year. On 10 October 1992 the second 30 GHz beacon tube failed, causing a loss of this beacon signal. The other two beacon frequencies continued to deliver a stable signal for more than two years. On 12 August 1993 the spacecraft experienced another problem with the altitude control, but this time there was not enough fuel left for a recovery maneuver and thus the mission came to an end.

  7. Low-affinity CD4+ T cells are major responders in the primary immune response

    PubMed Central

    Martinez, Ryan J.; Andargachew, Rakieb; Martinez, Hunter A.; Evavold, Brian D.

    2016-01-01

    A robust primary immune response has been correlated with the precursor number of antigen-specific T cells, as identified using peptide MHCII tetramers. However, these tetramers identify only the highest-affinity T cells. Here we show the entire CD4+ T-cell repertoire, inclusive of low-affinity T cells missed by tetramers, using a T-cell receptor (TCR) signalling reporter and micropipette assay to quantify naive precursors and expanded populations. In vivo limiting dilution assays reveal hundreds more precursor T cells than previously thought, with higher-affinity tetramer-positive T cells, comprising only 5–30% of the total antigen-specific naive repertoire. Lower-affinity T cells maintain their predominance as the primary immune response progresses, with no enhancement of survival of T cells with high-affinity TCRs. These findings demonstrate that affinity for antigen does not control CD4+ T-cell entry into the primary immune response, as a diverse range in affinity is maintained from precursor through peak of T-cell expansion. PMID:27976744

  8. Low-affinity CD4+ T cells are major responders in the primary immune response.

    PubMed

    Martinez, Ryan J; Andargachew, Rakieb; Martinez, Hunter A; Evavold, Brian D

    2016-12-15

    A robust primary immune response has been correlated with the precursor number of antigen-specific T cells, as identified using peptide MHCII tetramers. However, these tetramers identify only the highest-affinity T cells. Here we show the entire CD4+ T-cell repertoire, inclusive of low-affinity T cells missed by tetramers, using a T-cell receptor (TCR) signalling reporter and micropipette assay to quantify naive precursors and expanded populations. In vivo limiting dilution assays reveal hundreds more precursor T cells than previously thought, with higher-affinity tetramer-positive T cells, comprising only 5-30% of the total antigen-specific naive repertoire. Lower-affinity T cells maintain their predominance as the primary immune response progresses, with no enhancement of survival of T cells with high-affinity TCRs. These findings demonstrate that affinity for antigen does not control CD4+ T-cell entry into the primary immune response, as a diverse range in affinity is maintained from precursor through peak of T-cell expansion.

  9. Telonemia, a new protist phylum with affinity to chromist lineages

    PubMed Central

    Shalchian-Tabrizi, K; Eikrem, W; Klaveness, D; Vaulot, D; Minge, M.A; Le Gall, F; Romari, K; Throndsen, J; Botnen, A; Massana, R; Thomsen, H.A; Jakobsen, K.S

    2006-01-01

    Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup. PMID:16790418

  10. Gas-phase nitronium ion affinities.

    PubMed Central

    Cacace, F; de Petris, G; Pepi, F; Angelelli, F

    1995-01-01

    Evaluation of nitronium ion-transfer equilibria, L1NO2+ + L2 = L2NO2+ + L1 (where L1 and L2 are ligands 1 and 2, respectively) by Fourier-transform ion cyclotron resonance mass spectrometry and application of the kinetic method, based on the metastable fragmentation of L1(NO2+)L2 nitronium ion-bound dimers led to a scale of relative gas-phase nitronium ion affinities. This scale, calibrated to a recent literature value for the NO2+ affinity of water, led for 18 ligands, including methanol, ammonia, representative ketones, nitriles, and nitroalkanes, to absolute NO2+ affinities, that fit a reasonably linear general correlation when plotted vs. the corresponding proton affinities (PAs). The slope of the plot depends to a certain extent on the specific nature of the ligands and, hence, the correlations between the NO2+ affinities, and the PAs of a given class of compounds display a better linearity than the general correlation and may afford a useful tool for predicting the NO2+ affinity of a molecule based on its PA. The NO2+ binding energies are considerably lower than the corresponding PAs and well below the binding energies of related polyatomic cations, such as NO+, a trend consistent with the available theoretical results on the structure and the stability of simple NO2+ complexes. The present study reports an example of extension of the kinetic method to dimers, such as L1(NO2+)L2, bound by polyatomic ions, which may considerably widen its scope. Finally, measurement of the NO2+ affinity of ammonia allowed evaluation of the otherwise inaccessible PA of the amino group of nitramide and, hence, direct experimental verification of previous theoretical estimates. PMID:11607578

  11. Twist Propagation in Dinucleosome Arrays

    PubMed Central

    Dobrovolskaia, Irina V.; Kenward, Martin; Arya, Gaurav

    2010-01-01

    We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry along with the bending and twisting mechanics of the linkers is employed and external twist is applied in stepwise increments to mimic quasistatic twisting of chromatin fibers. Simulation results reveal that the magnitude and sign of the imposed and induced twist on contiguous linkers depend strongly on their relative orientation. Remarkably, the relative direction of the induced and applied twist can become inverted for a subset of linker orientations—a phenomenon we refer to as “twist inversion”. We characterize the twist inversion, as a function of relative linker orientation, in a phase diagram and explain its key features using a simple model based on the geometry of the nucleosome/linker complex. In addition to twist inversion, our simulations reveal “nucleosome flipping”, whereby nucleosomes may undergo sudden flipping in response to applied twist, causing a rapid bending of the linker and a significant change in the overall twist and writhe of the array. Our findings shed light on the underlying mechanisms by which torsional stresses impact chromatin organization. PMID:21081084

  12. Temporal scaling in information propagation

    NASA Astrophysics Data System (ADS)

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-01

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  13. Temporal scaling in information propagation.

    PubMed

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-18

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  14. [Reliability and validity of the Japanese revised version of the television affinity scale].

    PubMed

    Erikawa, Shigeru; Yamada, Kazunari

    2012-02-01

    The purpose of this study was to improve the Japanese version of the Television Affinity Scale (TAS), and to examine the relationship between affinity for television and viewing behavior. Data was based on a random sample of 552 people in Hachioji City (Tokyo, Japan); the response rate was 55.2%. The results revealed the following: (a) the TAS 6-item version had sufficient reliability and validity, (b) the TAS provided information which could not be explained directly by demographic factors, and (c) affinity for television was positively correlated with unplanned and non-concentrated television viewing. These results are consistent with the findings of Erikawa, Yamada, Kawabata, and Numazaki (2007). In addition, the TAS scores correlated positively with entertainment program viewing. This is consistent with the findings of Rubin (1984) that television affinity correlated with ritualized television viewing. The implications of these results for contemporary television viewing are discussed.

  15. Crack propagation modeling using Peridynamic theory

    NASA Astrophysics Data System (ADS)

    Hafezi, M. H.; Alebrahim, R.; Kundu, T.

    2016-04-01

    Crack propagation and branching are modeled using nonlocal peridynamic theory. One major advantage of this nonlocal theory based analysis tool is the unifying approach towards material behavior modeling - irrespective of whether the crack is formed in the material or not. No separate damage law is needed for crack initiation and propagation. This theory overcomes the weaknesses of existing continuum mechanics based numerical tools (e.g. FEM, XFEM etc.) for identifying fracture modes and does not require any simplifying assumptions. Cracks grow autonomously and not necessarily along a prescribed path. However, in some special situations such as in case of ductile fracture, the damage evolution and failure depend on parameters characterizing the local stress state instead of peridynamic damage modeling technique developed for brittle fracture. For brittle fracture modeling the bond is simply broken when the failure criterion is satisfied. This simulation helps us to design more reliable modeling tool for crack propagation and branching in both brittle and ductile materials. Peridynamic analysis has been found to be very demanding computationally, particularly for real-world structures (e.g. vehicles, aircrafts, etc.). It also requires a very expensive visualization process. The goal of this paper is to bring awareness to researchers the impact of this cutting-edge simulation tool for a better understanding of the cracked material response. A computer code has been developed to implement the peridynamic theory based modeling tool for two-dimensional analysis. A good agreement between our predictions and previously published results is observed. Some interesting new results that have not been reported earlier by others are also obtained and presented in this paper. The final objective of this investigation is to increase the mechanics knowledge of self-similar and self-affine cracks.

  16. Stability of flavin semiquinones in the gas phase: the electron affinity, proton affinity, and hydrogen atom affinity of lumiflavin.

    PubMed

    Zhang, Tianlan; Papson, Kaitlin; Ochran, Richard; Ridge, Douglas P

    2013-11-07

    Examination of electron transfer and proton transfer reactions of lumiflavin and proton transfer reactions of the lumiflavin radical anion by Fourier transform ion cyclotron resonance mass spectrometry is described. From the equilibrium constant determined for electron transfer between 1,4-naphthoquinone and lumiflavin the electron affinity of lumiflavin is deduced to be 1.86 ± 0.1 eV. Measurements of the rate constants and efficiencies for proton transfer reactions indicate that the proton affinity of the lumiflavin radical anion is between that of difluoroacetate (331.0 kcal/mol) and p-formyl-phenoxide (333.0 kcal/mol). Combining the electron affinity of lumiflavin with the proton affinity of the lumiflavin radical anion gives a lumiflavin hydrogen atom affinity of 59.7 ± 2.2 kcal/mol. The ΔG298 deduced from these results for adding an H atom to gas phase lumiflavin, 52.1 ± 2.2 kcal/mol, is in good agreement with ΔG298 for adding an H atom to aqueous lumiflavin from electrochemical measurements in the literature, 51.0 kcal/mol, and that from M06-L density functional calculations in the literature, 51.2 kcal/mol, suggesting little, if any, solvent effect on the H atom addition. The proton affinity of lumiflavin deduced from the equilibrium constant for the proton transfer reaction between lumiflavin and 2-picoline is 227.3 ± 2.0 kcal mol(-1). Density functional theory calculations on isomers of protonated lumiflavin provide a basis for assigning the most probable site of protonation as position 1 on the isoalloxazine ring and for estimating the ionization potentials of lumiflavin neutral radicals.

  17. Transport with Feynman propagators

    SciTech Connect

    White, R.H.

    1990-11-06

    Richard Feynman's formulation of quantum electrodynamics suggests a Monte Carlo algorithm for calculating wave propagation. We call this the Sum Over All Paths (SOAP) method. The method is applied to calculate diffraction by double slits of finite width and by a reflection grating. Calculations of reflection by plane and parabolic mirrors of finite aperture and from several figured surfaces are shown. An application to a one-dimensional scattering problem is discussed. A variation of SOAP can be applied to the diffusion equation. 2 refs., 8 figs.

  18. Beam Propagation Experimental Study.

    DTIC Science & Technology

    1982-03-01

    30- -40- -50 I 0 100 200 300 Time (ns) Figure 2. FX-100 diode voltage and current. The gas- insulated coax was charged to 4.2 MV in order to produce...limit the usable gradient. The voltage standoff capability will be further limited by electron bombardment of the insulators , which may lead to flashover ...the low-pressure window for stable propagation has been inferred from measurements of the time delay for the beam arrival at a given axial position. 8

  19. Proton Affinity Calculations with High Level Methods.

    PubMed

    Kolboe, Stein

    2014-08-12

    Proton affinities, stretching from small reference compounds, up to the methylbenzenes and naphthalene and anthracene, have been calculated with high accuracy computational methods, viz. W1BD, G4, G3B3, CBS-QB3, and M06-2X. Computed and the currently accepted reference proton affinities are generally in excellent accord, but there are deviations. The literature value for propene appears to be 6-7 kJ/mol too high. Reported proton affinities for the methylbenzenes seem 4-5 kJ/mol too high. G4 and G3 computations generally give results in good accord with the high level W1BD. Proton affinity values computed with the CBS-QB3 scheme are too low, and the error increases with increasing molecule size, reaching nearly 10 kJ/mol for the xylenes. The functional M06-2X fails markedly for some of the small reference compounds, in particular, for CO and ketene, but calculates methylbenzene proton affinities with high accuracy.

  20. Identity, Affinity, Reality: Making the Case for Affinity Groups in Elementary School

    ERIC Educational Resources Information Center

    Parsons, Julie; Ridley, Kimberly

    2012-01-01

    Affinity groups are places where students build connections and process "ouch" moments from their classes. Children talk about the isolation they sometimes feel. The relationships students gain through race-based affinity groups enable them to feel less alone with their emotions and help them build a stronger sense of self. At the same…

  1. Stepparents' Affinity-Seeking and Affinity-Maintaining Strategies with Stepchildren.

    ERIC Educational Resources Information Center

    Ganong, Lawrence; Coleman, Marilyn; Fine, Mark; Martin, Patricia

    1999-01-01

    Examines the strategies that stepparents use to develop and maintain affinity with stepchildren and the effects that these strategies have on the development of stepparent-stepchildren relationships. Thirty-one affinity-seeking strategies are identified. Results show that dyadic activities worked best, but it is important that stepchildren…

  2. Desertification by front propagation?

    PubMed

    Zelnik, Yuval R; Uecker, Hannes; Feudel, Ulrike; Meron, Ehud

    2017-04-07

    Understanding how desertification takes place in different ecosystems is an important step in attempting to forecast and prevent such transitions. Dryland ecosystems often exhibit patchy vegetation, which has been shown to be an important factor on the possible regime shifts that occur in arid regions in several model studies. In particular, both gradual shifts that occur by front propagation, and abrupt shifts where patches of vegetation vanish at once, are a possibility in dryland ecosystems due to their emergent spatial heterogeneity. However, recent theoretical work has suggested that the final step of desertification - the transition from spotted vegetation to bare soil - occurs only as an abrupt shift, but the generality of this result, and its underlying origin, remain unclear. We investigate two models that detail the dynamics of dryland vegetation using a markedly different functional structure, and find that in both models the final step of desertification can only be abrupt. Using a careful numerical analysis, we show that this behavior is associated with the disappearance of confined spot-pattern domains as stationary states, and identify the mathematical origin of this behavior. Our findings show that a gradual desertification to bare soil due to a front propagation process can not occur in these and similar models, and opens the question of whether these dynamics can take place in nature.

  3. Bolt beam propagation analysis

    NASA Astrophysics Data System (ADS)

    Shokair, I. R.

    BOLT (Beam on Laser Technology) is a rocket experiment to demonstrate electron beam propagation on a laser ionized plasma channel across the geomagnetic field in the ion focused regime (IFR). The beam parameters for BOLT are: beam current I(sub b) = 100 Amps, beam energy of 1--1.5 MeV (gamma =3-4), and a Gaussian beam and channel of radii r(sub b) = r(sub c) = 1.5 cm. The N+1 ionization scheme is used to ionize atomic oxygen in the upper atmosphere. This scheme utilizes 130 nm light plus three IR lasers to excite and then ionize atomic oxygen. The limiting factor for the channel strength is the energy of the 130 nm laser, which is assumed to be 1.6 mJ for BOLT. At a fixed laser energy and altitude (fixing the density of atomic oxygen), the range can be varied by adjusting the laser tuning, resulting in a neutralization fraction axial profile of the form: f(z) = f(sub 0) e(exp minus z)/R, where R is the range. In this paper we consider the propagation of the BOLT beam and calculate the range of the electron beam taking into account the fact that the erosion rates (magnetic and inductive) vary with beam length as the beam and channel dynamically respond to sausage and hose instabilities.

  4. Affine coherent states and Toeplitz operators

    NASA Astrophysics Data System (ADS)

    Hutníková, Mária; Hutník, Ondrej

    2012-06-01

    We study a parameterized family of Toeplitz operators in the context of affine coherent states based on the Calderón reproducing formula (= resolution of unity on L_2( {R})) and the specific admissible wavelets (= affine coherent states in L_2( {R})) related to Laguerre functions. Symbols of such Calderón-Toeplitz operators as individual coordinates of the affine group (= upper half-plane with the hyperbolic geometry) are considered. In this case, a certain class of pseudo-differential operators, their properties and their operator algebras are investigated. As a result of this study, the Fredholm symbol algebras of the Calderón-Toeplitz operator algebras for these particular cases of symbols are described. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’.

  5. Non-affine elasticity in jammed systems

    NASA Astrophysics Data System (ADS)

    Maloney, Craig

    2006-03-01

    Symmetry dictates that perfect crystals should deform homogeneously, or affinely, under external load, and computing the elastic moduli from the underlying interaction potential is then straightforward. For disordered materials no such simple procedure exists, and recent numerical works have demonstrated that non-affine corrections can dramatically reduce the naive expectation for the shear modulus in a broad class of disordered systems and may control rigidity loss in the zero pressure limit in purely repulsive systems, i.e. the unjamming transition (c.f. [O'Hern et. al. PRE 68, 011306 (2003)]). We present numerical results and an analytical framework for the study of these non-affine corrections to the elastic response of disordered packings.

  6. Biomimetic affinity ligands for protein purification.

    PubMed

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  7. Use of Affinity Diagrams as Instructional Tools in Inclusive Classrooms.

    ERIC Educational Resources Information Center

    Haselden, Polly G.

    2003-01-01

    This article describes how the affinity diagram, a tool for gathering information and organizing it into natural groupings, can be used in inclusive classrooms. It discusses how students can be taught to use an affinity diagram, how affinity diagrams can be used to reflect many voices, and how affinity diagrams can be used to plan class projects.…

  8. Cation affinity numbers of Lewis bases.

    PubMed

    Lindner, Christoph; Tandon, Raman; Maryasin, Boris; Larionov, Evgeny; Zipse, Hendrik

    2012-01-01

    Using selected theoretical methods the affinity of a large range of Lewis bases towards model cations has been quantified. The range of model cations includes the methyl cation as the smallest carbon-centered electrophile, the benzhydryl and trityl cations as models for electrophilic substrates encountered in Lewis base-catalyzed synthetic procedures, and the acetyl cation as a substrate model for acyl-transfer reactions. Affinities towards these cationic electrophiles are complemented by data for Lewis-base addition to Michael acceptors as prototypical neutral electrophiles.

  9. New unitary affine-Virasoro constructions

    SciTech Connect

    Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M. ); Yamron, J.P. )

    1990-06-20

    This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g.

  10. On the electron affinity of B2

    SciTech Connect

    Glezakou, Vanda A.; Taylor, Peter

    2009-02-02

    We present the results of high-level ab initio calculations on the electron affinity of B2. Our new best estimate of 1.93±0.03 eV is in agreement with previous calculations as well as the sole existing experimental estimate of 1.8 eV, as derived from quantities with an uncertainty of 0.4 eV. The electron affinity of atomic boron, which is much smaller, is also calculated for comparison, and again found to be in good agreement with experiment. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  11. Negative Electron Affinity Mechanism for Diamond Surfaces

    NASA Technical Reports Server (NTRS)

    Krainsky, I. L.; Asnin, V. M.

    1998-01-01

    The energy distribution of the secondary electrons for chemical vacuum deposited diamond films with Negative Electron Affinity (NEA) was investigated. It was found that while for completely hydrogenated diamond surfaces the negative electron affinity peak in the energy spectrum of the secondary electrons is present for any energy of the primary electrons, for partially hydrogenated diamond surfaces there is a critical energy above which the peak is present in the spectrum. This critical energy increases sharply when hydrogen coverage of the diamond surface diminishes. This effect was explained by the change of the NEA from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surfaces.

  12. Evidence of multi-affinity in the Japanese stock market

    NASA Astrophysics Data System (ADS)

    Katsuragi, Hiroaki

    2000-04-01

    Fluctuations of the Japanese stock market (Tokyo Stock Price Index: TOPIX) are analyzed using a multi-affine analysis method. In the research to date, only some simulated self-affine models have shown multi-affinity. In most experiments using observations of self-affine fractal profiles, multi-affinity has not been found. However, we find evidence of multi-affinity in fluctuations of the Japanese stock market (TOPIX). The qth-order Hurst exponent Hq varies with changes in q. This multi-affinity indicates that there are plural mechanisms that affect the same time scale as stock market price fluctuation dynamics.

  13. ACTS propagation experiment discussion: Ka-band propagation measurements using the ACTS propagation terminal and the CSU-CHILL and Space Communications Technology Center Florida propagation program

    NASA Technical Reports Server (NTRS)

    Bringi, V. N.; Chandrasekar, V.; Mueller, Eugene A.; Turk, Joseph; Beaver, John; Helmken, Henry F.; Henning, Rudy

    1993-01-01

    Papers on Ka-band propagation measurements using the ACTS propagation terminal and the Colorado State University CHILL multiparameter radar and on Space Communications Technology Center Florida Propagation Program are discussed. Topics covered include: microwave radiative transfer and propagation models; NASA propagation terminal status; ACTS channel characteristics; FAU receive only terminal; FAU terminal status; and propagation testbed.

  14. Linear connections with a propagating spin-3 field in gravity

    SciTech Connect

    Baekler, Peter; Boulanger, Nicolas; Hehl, Friedrich W.

    2006-12-15

    We show that Fronsdal's Lagrangian for a free massless spin-3 gauge field in Minkowski spacetime is contained in a general Yang-Mills-like Lagrangian of metric-affine gravity (MAG), the gauge theory of the general affine group in the presence of a metric. Because of the geometric character of MAG, this can best be seen by using Vasiliev's frame formalism for higher-spin gauge fields in which the spin-3 frame is identified with the tracefree nonmetricity one-form associated with the shear generators of GL(n,R). Furthermore, for specific gravitational gauge models in the framework of full nonlinear MAG, exact solutions are constructed, featuring propagating massless and massive spin-3 fields.

  15. Retroelements: propagation and adaptation.

    PubMed

    Hull, R; Covey, S N

    1995-01-01

    Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.

  16. Gauge engineering and propagators

    NASA Astrophysics Data System (ADS)

    Maas, Axel

    2017-03-01

    Beyond perturbation theory gauge-fixing becomes more involved due to the Gribov-Singer ambiguity: The appearance of additional gauge copies requires to define a procedure how to handle them. For the case of Landau gauge the structure and properties of these additional gauge copies will be investigated. Based on these properties gauge conditions are constructed to account for these gauge copies. The dependence of the propagators on the choice of these complete gauge-fixings will then be investigated using lattice gauge theory for Yang-Mills theory. It is found that the implications for the infrared, and to some extent mid-momentum behavior, can be substantial. In going beyond the Yang-Mills case it turns out that the influence of matter can generally not be neglected. This will be briefly discussed for various types of matter.

  17. ACTS mobile propagation campaign

    NASA Technical Reports Server (NTRS)

    Goldhirsh, Julius; Vogel, Wolfhard J.; Torrence, Geoffrey W.

    1994-01-01

    Preliminary results are presented for three propagation measurement campaigns involving a mobile receiving laboratory and 20 GHz transmissions from the Advanced Communications Technology Satellite (ACTS). Four 1994 campaigns were executed during weekly periods in and around Austin, Texas in February and May, in Central Maryland during March, and in Fairbanks, Alaska and environs in June. Measurements tested the following effects at 20 GHz: (1) attenuation due to roadside trees with and without foliage, (2) multipath effects for scenarios in which line-of-sight paths were unshadowed, (3) fades due to terrain and roadside obstacles, (4) fades due to structures in urban environs, (5) single tree attenuation, and (6) effects of fading at low elevation angles (8 deg in Fairbanks, Alaska) and high elevation angles (55 deg in Austin, Texas). Results presented here cover sampled measurements in Austin, Texas for foliage and non-foliage cases and in Central Maryland for non-foliage runs.

  18. Propagation Terminal Design and Measurements

    NASA Technical Reports Server (NTRS)

    Nessel, James

    2015-01-01

    The NASA propagation terminal has been designed and developed by the Glenn Research Center and is presently deployed at over 5 NASA and partner ground stations worldwide collecting information on the effects of the atmosphere on Ka-band and millimeter wave communications links. This lecture provides an overview of the fundamentals and requirements of the measurement of atmospheric propagation effects and, specifically, the types of hardware and digital signal processing techniques employed by current state-of-the-art propagation terminal systems.

  19. Interferometric Propagation Delay

    NASA Technical Reports Server (NTRS)

    Goldstein, Richard

    1999-01-01

    Radar interferometry based on (near) exact repeat passes has lately been used by many groups of scientists, worldwide, to achieve state of the art measurements of topography, glacier and ice stream motion, earthquake displacements, oil field subsidence, lava flows, crop-induced surface decorrelation, and other effects. Variations of tropospheric and ionospheric propagation delays limit the accuracy of all such measurements. We are investigating the extent of this limitation, using data from the Shuttle radar flight, SIR-C, which is sensitive to the troposphere, and the Earth Resources Satellites, ERS-1/2, which are sensitive to both the troposphere and the ionosphere. We are presently gathering statistics of the delay variations over selected, diverse areas to determine the best accuracy possible for repeat track interferometry. The phases of an interferogram depend on both the topography of the scene and variations in propagation delay. The delay variations can be caused by movement of elements in the scene, by changes in tropospheric water vapor and by changes of the charge concentrations in the ionosphere. We plan to separate these causes by using the data from a third satellite visit (three-pass interferometry). The figure gives the geometry of the three-pass observations. The page of the figure is taken to be perpendicular to the spacecraft orbits. The three observational locations are marked on the figure, giving baselines B-12 and B-13, separated by the angle alpha. These parameters are almost constant over the whole scene. However, each pixel has an individual look angle, theta, which is related to the topography, rho is the slant range. A possible spurious time delay is shown. Additional information is contained in the original.

  20. Influence of the galloyl moiety in tea catechins on binding affinity for human serum albumin.

    PubMed

    Minoda, Kanako; Ichikawa, Tatsuya; Katsumata, Tomoharu; Onobori, Ken-ichi; Mori, Taiki; Suzuki, Yukiko; Ishii, Takeshi; Nakayama, Tsutomu

    2010-01-01

    The major catechins of green tea extract are (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECg), and (-)-epigallocatechin gallate (EGCg). Recent research has indicated that catechins form complexes with human serum albumin (HSA) in blood, and differences in their binding affinity toward HSA are believed to modulate their bioavailability. In this study, we kinetically investigated the interaction between the catechins and HSA immobilized on a quartz-crystal microbalance (QCM). The association constants obtained from the frequency changes of QCM revealed interactions of ECg and EGCg with HSA that are 100 times stronger than those of EC and EGC. Furthermore, comparisons of these catechins by native-gel electrophoresis/blotting with redox-cycling staining revealed that, in a phosphate buffer, ECg and EGCg have a higher binding affinity toward HSA than EC and EGC. These observations indicate that catechins with a galloyl moiety have higher binding affinities toward HSA than catechins lacking a galloyl moiety.

  1. On modality and complexity of affine embeddings

    SciTech Connect

    Arzhantsev, I V

    2001-08-31

    Let G be a reductive algebraic group and let H be a reductive subgroup of G. The modality of a G-variety X is the largest number of the parameters in a continuous family of G-orbits in X. A precise formula for the maximum value of the modality over all affine embeddings of the homogeneous space G/H is obtained.

  2. Modern affinity reagents: Recombinant antibodies and aptamers.

    PubMed

    Groff, Katherine; Brown, Jeffrey; Clippinger, Amy J

    2015-12-01

    Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.

  3. Stabilization of the Motion of Affine Systems

    NASA Astrophysics Data System (ADS)

    Babenko, E. A.; Martynyuk, A. A.

    2016-07-01

    Sufficient conditions for the stability of a nonlinear affine system subject to interval initial conditions are established. These conditions are based on new estimates of the norms of the solutions of the systems of perturbed equations of motion. This stabilization method is used to analyze an electromechanical system with permanent magnet

  4. Fan Affinity Laws from a Collision Model

    ERIC Educational Resources Information Center

    Bhattacharjee, Shayak

    2012-01-01

    The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

  5. Vygotsky's and Buber's Pedagogical Perspectives: Some Affinities

    ERIC Educational Resources Information Center

    Bartholo, Roberto; Tunes, Elizabeth; Tacca, Maria Carmen Villela Rosa

    2010-01-01

    The purpose of this paper is to examine the dialogical and creative character of pedagogic work by analyzing the affinities between Martin Buber's "I-Thou relation" and Lev Semenovich Vygotsky's "Zone of Proximal Development". Backed up by empirical studies on the teacher-student relation, we understand that education can only result in students'…

  6. A global/local affinity graph for image segmentation.

    PubMed

    Xiaofang Wang; Yuxing Tang; Masnou, Simon; Liming Chen

    2015-04-01

    Construction of a reliable graph capturing perceptual grouping cues of an image is fundamental for graph-cut based image segmentation methods. In this paper, we propose a novel sparse global/local affinity graph over superpixels of an input image to capture both short- and long-range grouping cues, and thereby enabling perceptual grouping laws, including proximity, similarity, continuity, and to enter in action through a suitable graph-cut algorithm. Moreover, we also evaluate three major visual features, namely, color, texture, and shape, for their effectiveness in perceptual segmentation and propose a simple graph fusion scheme to implement some recent findings from psychophysics, which suggest combining these visual features with different emphases for perceptual grouping. In particular, an input image is first oversegmented into superpixels at different scales. We postulate a gravitation law based on empirical observations and divide superpixels adaptively into small-, medium-, and large-sized sets. Global grouping is achieved using medium-sized superpixels through a sparse representation of superpixels' features by solving a ℓ0-minimization problem, and thereby enabling continuity or propagation of local smoothness over long-range connections. Small- and large-sized superpixels are then used to achieve local smoothness through an adjacent graph in a given feature space, and thus implementing perceptual laws, for example, similarity and proximity. Finally, a bipartite graph is also introduced to enable propagation of grouping cues between superpixels of different scales. Extensive experiments are carried out on the Berkeley segmentation database in comparison with several state-of-the-art graph constructions. The results show the effectiveness of the proposed approach, which outperforms state-of-the-art graphs using four different objective criteria, namely, the probabilistic rand index, the variation of information, the global consistency error, and the

  7. Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model.

    PubMed

    Du, Nan; Knecht, Marc R; Swihart, Mark T; Tang, Zhenghua; Walsh, Tiffany R; Zhang, Aidong

    2015-01-01

    Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.

  8. High-frequency affine mechanics and nonaffine relaxation in a model cytoskeleton.

    PubMed

    Head, David A; Ikebe, Emi; Nakamasu, Akiko; Zhang, Peijuan; Villaruz, Lara Gay; Kinoshita, Suguru; Ando, Shoji; Mizuno, Daisuke

    2014-04-01

    The cytoskeleton is a network of crosslinked, semiflexible filaments, and it has been suggested that it has properties of a glassy state. Here we employ optical-trap-based microrheology to apply forces to a model cytoskeleton and measure the high-bandwidth response at an anterior point. Simulating the highly nonlinear and anisotropic stress-strain propagation assuming affinity, we found that theoretical predictions for the quasistatic response of semiflexible polymers are only realized at high frequencies inaccessible to conventional rheometers. We give a theoretical basis for determining the frequency when both affinity and quasistaticity are valid, and we discuss with experimental evidence that the relaxations at lower frequencies can be characterized by the experimentally obtained nonaffinity parameter.

  9. The impact of antigen density and antibody affinity on antibody-dependent cellular cytotoxicity: relevance for immunotherapy of carcinomas.

    PubMed Central

    Velders, M. P.; van Rhijn, C. M.; Oskam, E.; Fleuren, G. J.; Warnaar, S. O.; Litvinov, S. V.

    1998-01-01

    Antibody-dependent cellular cytotoxicity (ADCC) is considered to be the major mechanism through which tumour cells, upon treatment with anti-tumour MAbs, are eliminated in vivo. However, the relative importance of various parameters that influence the efficacy of ADCC is unclear. Here we present in vitro data on the impact of MAb affinity and antigen density on ADCC, as obtained by comparison of two MAbs against the tumour-associated antigen Ep-CAM. The low-affinity MAb 17-1A (Ka = 5 x 10(7)M(-1)) currently used for therapy, and the high-affinity MAb 323/A3 (Ka = 2 x 10(9) M(-1)), were compared in ADCC experiments against murine and human tumour target cells transfected with the Ep-CAM cDNA under the control of an inducible promoter to enable regulation of the target antigen expression levels. Data obtained from these studies revealed that the high-affinity MAb, in contrast to the low-affinity MAb, could mediate killing of tumour cells with low antigen expression levels. Even at comparable MAb-binding levels, ADCC mediated by the high-affinity MAb was more effective. The kinetics of ADCC was also found to be determined by the level of antigen expression, and by the affinity and the concentration of the MAb used. The efficacy of ADCC with both low- and high-affinity MAbs further depended on adhesive interactions between effector and target cells mediated by CD18. However, at every given MAb concentration these interactions were of less importance for the high-affinity MAb than for the low-affinity MAb. As heterogeneity of a target antigen expression is a common feature of all tumours, and some tumour cells express very low levels of the antigen, the use of high-affinity MAbs in immunotherapy may significantly improve the clinical results obtained to the present date in the treatment of minimal residual disease. PMID:9716030

  10. Join-Graph Propagation Algorithms

    PubMed Central

    Mateescu, Robert; Kask, Kalev; Gogate, Vibhav; Dechter, Rina

    2010-01-01

    The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes. PMID:20740057

  11. Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41

    SciTech Connect

    Gustchina, Elena; Li, Mi; Louis, John M.; Anderson, D.Eric; Lloyd, John; Frisch, Christian; Bewley, Carole A.; Gustchina, Alla; Wlodawer, Alexander; Clore, G.Marius

    2010-12-03

    The conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 is transiently exposed during the fusion process by forming a pre-hairpin intermediate, thus representing an attractive target for the design of fusion inhibitors and neutralizing antibodies. In previous studies we reported a series of broadly neutralizing mini-antibodies derived from a synthetic naive human combinatorial antibody library by panning against a mimetic of the trimeric N-HR coiled coil, followed by affinity maturation using targeted diversification of the CDR-H2 loop. Here we report crystal structures of the N-HR mimetic 5-Helix with two Fabs that represent the extremes of this series: Fab 8066 is broadly neutralizing across a wide panel of B and C type HIV-1 viruses, whereas Fab 8062 is non-neutralizing. The crystal structures reveal important differences in the conformations of the CDR-H2 loops in the complexes that propagate into other regions of the antigen-antibody interface, and suggest that both neutralization properties and affinity for the target can be attributed, at least in part, to the differences in the interactions of the CDR-H2 loops with the antigen. Furthermore, modeling of the complex of an N-HR trimer with three Fabs suggests that the CDR-H2 loop may be involved in close intermolecular contacts between neighboring antibody molecules, and that such contacts may hinder the formation of complexes between the N-HR trimer and more than one antibody molecule depending on the conformation of the bound CDR-H2 loop which is defined by its interactions with antigen. Comparison with the crystal structure of the complex of 5-Helix with another neutralizing monoclonal antibody known as D5, derived using an entirely different antibody library and panning procedure, reveals remarkable convergence in the optimal sequence and conformation of the CDR-H2 loop.

  12. Directed HK propagator.

    PubMed

    Kocia, Lucas; Heller, Eric J

    2015-09-28

    We offer a more formal justification for the successes of our recently communicated "directed Heller-Herman-Kluk-Kay" (DHK) time propagator by examining its performance in one-dimensional bound systems which exhibit at least quasi-periodic motion. DHK is distinguished by its single one-dimensional integral--a vast simplification over the usual 2N-dimensional integral in full Heller-Herman-Kluk-Kay (for an N-dimensional system). We find that DHK accurately captures particular coherent state autocorrelations when its single integral is chosen to lie along these states' fastest growing manifold, as long as it is not perpendicular to their action gradient. Moreover, the larger the action gradient, the better DHK will perform. We numerically examine DHK's accuracy in a one-dimensional quartic oscillator and illustrate that these conditions are frequently satisfied such that the method performs well. This lends some explanation for why DHK frequently seems to work so well and suggests that it may be applicable to systems exhibiting quite strong anharmonicity.

  13. Directed HK propagator

    NASA Astrophysics Data System (ADS)

    Kocia, Lucas; Heller, Eric J.

    2015-09-01

    We offer a more formal justification for the successes of our recently communicated "directed Heller-Herman-Kluk-Kay" (DHK) time propagator by examining its performance in one-dimensional bound systems which exhibit at least quasi-periodic motion. DHK is distinguished by its single one-dimensional integral—a vast simplification over the usual 2N-dimensional integral in full Heller-Herman-Kluk-Kay (for an N-dimensional system). We find that DHK accurately captures particular coherent state autocorrelations when its single integral is chosen to lie along these states' fastest growing manifold, as long as it is not perpendicular to their action gradient. Moreover, the larger the action gradient, the better DHK will perform. We numerically examine DHK's accuracy in a one-dimensional quartic oscillator and illustrate that these conditions are frequently satisfied such that the method performs well. This lends some explanation for why DHK frequently seems to work so well and suggests that it may be applicable to systems exhibiting quite strong anharmonicity.

  14. Optimal Affine-Invariant Point Matching

    NASA Astrophysics Data System (ADS)

    Costa, Mauro S.; Haralick, Robert M.; Phillips, Tsaiyun I.; Shapiro, Linda G.

    1989-03-01

    The affine-transformation matching scheme proposed by Hummel and Wolfson (1988) is very efficient in a model-based matching system, not only in terms of the computational complexity involved, but also in terms of the simplicity of the method. This paper addresses the implementation of the affine-invariant point matching, applied to the problem of recognizing and determining the pose of sheet metal parts. It points out errors that can occur with this method due to quantization, stability, symmetry, and noise problems. By beginning with an explicit noise model which the Hummel and Wolfson technique lacks, we can derive an optimal approach which overcomes these problems. We show that results obtained with the new algorithm are clearly better than the results from the original method.

  15. Affinity Chromatography in Nonionic Detergent Solutions

    NASA Astrophysics Data System (ADS)

    Robinson, Jack B.; Strottmann, James M.; Wick, Donald G.; Stellwagen, Earle

    1980-10-01

    Anionic dye affinity chromatography is commonly unproductive in the presence of nonionic detergents used to extract particulate proteins. Using lactate dehydrogenase as a model protein, Cibacron blue F3GA as a model dye, and Triton X-100 as a model detergent, we find that the dye is encapsulated in nonionic detergent micelles, rendering the dye incapable of ligation with the enzyme. However, the dye can be liberated from the micelles without altering the nonionic detergent concentration by addition of an anionic detergent, such as deoxycholate or sodium dodecyl sulfate, forming mixed anionic/nonionic micelles that displace the anionic dye. Encapsulation of the anionic detergents prevents their activity as protein denaturants. These observations have been successfully translated to the dye affinity chromatography of a detergent extract of brain particulate cyclic nucleotide phosphodiesterase.

  16. Bicarbonate-form anion exchange: affinity, regeneration, and stoichiometry.

    PubMed

    Rokicki, Christopher A; Boyer, Treavor H

    2011-01-01

    Magnetic ion exchange (MIEX) is an effective process for removing dissolved organic carbon (DOC) from natural waters, but its implementation has been limited due to production of waste sodium chloride solution (i.e., brine) from the regeneration process. Chloride is of concern because elevated concentrations can have adverse effects on engineered and natural systems. The goal of this research was to explore the efficacy of using anion exchange resin with bicarbonate as the mobile counter ion, which would produce a non-chloride regeneration solution. It was found that bicarbonate-form MIEX resin had a similar affinity as chloride-form MIEX resin for sulfate, nitrate, DOC, and ultraviolet-absorbing substances. Both bicarbonate-form and chloride-form MIEX resins showed the greatest removal efficiencies as fresh resin, and removal efficiency decreased with multiple regeneration cycles. Nevertheless, sodium bicarbonate solution was as effective as sodium chloride solution at regenerating MIEX resin. Regeneration of the bicarbonate-form MIEX resin was illustrated by sparging carbon dioxide gas in a water/resin slurry. This regeneration process would eliminate the need for the addition of salts such as sodium chloride or sodium bicarbonate. The stoichiometry of the bicarbonate-form resin revealed that the bicarbonate was deprotonating within the resin matrix leading to a mixture of both carbonate and bicarbonate mobile counter ions. This work makes an important contribution to ion exchange applications for water treatment by evaluating the affinity, regeneration, and stoichiometry of bicarbonate-form anion exchange.

  17. Impact of crystalline quality on neuronal affinity of pristine graphene.

    PubMed

    Veliev, Farida; Briançon-Marjollet, Anne; Bouchiat, Vincent; Delacour, Cécile

    2016-04-01

    Due to its outstanding mechanical and electrical properties as well as chemical inertness, graphene has attracted a growing interest in the field of bioelectric interfacing. Herein, we investigate the suitability of pristine, i.e. without a cell adhesive coating, chemical vapor deposition (CVD) grown monolayer graphene to act as a platform for neuronal growth. We study the development of primary hippocampal neurons grown on bare graphene (transferred on glass coverslip) for up to 5 days and show that pristine graphene significantly improves the neurons adhesion and outgrowth at the early stage of culture (1-2 days in vitro). At the later development stage, neurons grown on coating free graphene (untreated with poly-L-lysine) show remarkably well developed neuritic architecture similar to those cultured on conventional poly-L-lysine coated glass coverslips. This exceptional possibility to bypass the adhesive coating allows a direct electrical contact of graphene to the cells and reveals its great potential for chronic medical implants and tissue engineering. Moreover, regarding the controversial results obtained on the neuronal affinity of pristine graphene and its ability to support neuronal growth without the need of polymer or protein coating, we found that the crystallinity of CVD grown graphene plays an important role in neuronal attachment, outgrowth and axonal specification. In particular, we show that the decreasing crystalline quality of graphene tunes the neuronal affinity from highly adhesive to fully repellent.

  18. Negative affinity X-ray photocathodes

    NASA Technical Reports Server (NTRS)

    Vanspeybroeck, L.; Kellogg, E.; Murray, S.; Duckett, S.

    1974-01-01

    A new X-ray image intensifier is described. The device should eventually have a quantum efficiency which is an order of magnitude greater than that of presently available high spatial resolution X-ray detectors, such as microchannel plates. The new intesifier is based upon a GaAs crystal photocathode which is activated to achieve negative electron affinity. Details concerning the detector concept are discussed together with the theoretical relations involved, X-ray data, and optical data.

  19. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture.

  20. Dike Propagation Near Drifts

    SciTech Connect

    NA

    2002-03-04

    The purpose of this Analysis and Model Report (AMR) supporting the Site Recommendation/License Application (SR/LA) for the Yucca Mountain Project is the development of elementary analyses of the interactions of a hypothetical dike with a repository drift (i.e., tunnel) and with the drift contents at the potential Yucca Mountain repository. This effort is intended to support the analysis of disruptive events for Total System Performance Assessment (TSPA). This AMR supports the Process Model Report (PMR) on disruptive events (CRWMS M&O 2000a). This purpose is documented in the development plan (DP) ''Coordinate Modeling of Dike Propagation Near Drifts Consequences for TSPA-SR/LA'' (CRWMS M&O 2000b). Evaluation of that Development Plan and the work to be conducted to prepare Interim Change Notice (ICN) 1 of this report, which now includes the design option of ''Open'' drifts, indicated that no revision to that DP was needed. These analyses are intended to provide reasonable bounds for a number of expected effects: (1) Temperature changes to the waste package from exposure to magma; (2) The gas flow available to degrade waste containers during the intrusion; (3) Movement of the waste package as it is displaced by the gas, pyroclasts and magma from the intruding dike (the number of packages damaged); (4) Movement of the backfill (Backfill is treated here as a design option); (5) The nature of the mechanics of the dike/drift interaction. These analyses serve two objectives: to provide preliminary analyses needed to support evaluation of the consequences of an intrusive event and to provide a basis for addressing some of the concerns of the Nuclear Regulatory Commission (NRC) expressed in the Igneous Activity Issue Resolution Status Report.

  1. Role of the intercalated disc in cardiac propagation and arrhythmogenesis.

    PubMed

    Kleber, Andre G; Saffitz, Jeffrey E

    2014-01-01

    This review article discusses mechanisms underlying impulse propagation in cardiac muscle with specific emphasis on the role of the cardiac cell-to-cell junction, called the "intercalated disc."The first part of this review deals with the role of gap junction channels, formed by connexin proteins, as a determinant of impulse propagation. It is shown that, depending on the underlying structure of the cellular network, decreasing the conductance of gap junction channels (so-called "electrical uncoupling") may either only slow, or additionally stabilize propagation and reverse unidirectional propagation block to bidirectional propagation. This is because the safety factor for propagation increases with decreasing intercellular electrical conductance. The role of heterogeneous connexin expression, which may be present in disease states, is also discussed. The hypothesis that so-called ephaptic impulse transmission plays a role in heart and can substitute for electrical coupling has been revived recently. Whereas ephaptic transmission can be demonstrated in theoretical simulations, direct experimental evidence has not yet been presented. The second part of this review deals with the interaction of three protein complexes at the intercalated disc: (1) desmosomal and adherens junction proteins, (2) ion channel proteins, and (3) gap junction channels consisting of connexins. Recent work has revealed multiple interactions between these three protein complexes which occur, at least in part, at the level of protein trafficking. Such interactions are likely to play an important role in the pathogenesis of arrhythmogenic cardiomyopathy, and may reveal new therapeutic concepts and targets.

  2. Engineering of Bispecific Affinity Proteins with High Affinity for ERBB2 and Adaptable Binding to Albumin

    PubMed Central

    Nilvebrant, Johan; Åstrand, Mikael; Georgieva-Kotseva, Maria; Björnmalm, Mattias; Löfblom, John; Hober, Sophia

    2014-01-01

    The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein. PMID:25089830

  3. ON THE SOURCE OF PROPAGATING SLOW MAGNETOACOUSTIC WAVES IN SUNSPOTS

    SciTech Connect

    Prasad, S. Krishna; Jess, D. B.; Khomenko, Elena

    2015-10-10

    Recent high-resolution observations of sunspot oscillations using simultaneously operated ground- and space-based telescopes reveal the intrinsic connection between different layers of the solar atmosphere. However, it is not clear whether these oscillations are externally driven or generated in situ. We address this question by using observations of propagating slow magnetoacoustic waves along a coronal fan loop system. In addition to the generally observed decreases in oscillation amplitudes with distance, the observed wave amplitudes are also found to be modulated with time, with similar variations observed throughout the propagation path of the wave train. Employing multi-wavelength and multi-instrument data, we study the amplitude variations with time as the waves propagate through different layers of the solar atmosphere. By comparing the amplitude modulation period in different layers, we find that slow magnetoacoustic waves observed in sunspots are externally driven by photospheric p-modes, which propagate upward into the corona before becoming dissipated.

  4. Vibrational photodetachment spectroscopy near the electron affinity of S2

    NASA Astrophysics Data System (ADS)

    Barrick, J. B.; Yukich, J. N.

    2016-02-01

    We have conducted laser photodetachment spectroscopy near the detachment threshold of the electron affinity of S2 in a 1.8-T field. The ions are prepared by dissociative electron attachment to carbonyl sulfide. The experiment is conducted in a Penning ion trap and with a narrow-band, tunable, Ti:sapphire laser. A hybrid model for photodetachment in an ion trap is fit to the data using the appropriate Franck-Condon factors. The observations reveal detachment from and to the first few vibrational levels of the anion and the neutral molecule, respectively. Evaporative cooling of the anion ensemble condenses the thermal distribution to the lowest initial vibrational states. The subsequent detachment spectroscopy yields results consistent with a vibrationally cooled anion population.

  5. Growth factors with heparin binding affinity in human synovial fluid

    SciTech Connect

    Hamerman, D.; Taylor, S.; Kirschenbaum, I.; Klagsbrun, M.; Raines, E.W.; Ross, R.; Thomas, K.A.

    1987-12-01

    Synovial effusions were obtained from the knees of 15 subjects with joint trauma, menisceal or ligamentous injury, or osteoarthritis. Heparin-Sepharose affinity chromatography of these synovial fluids revealed, in general, three major peaks of mitogenic activity as measured by incorporation of /sup 3/H-thymidine into 3T3 cells. Gradient elution patterns showed activities at 0.5M NaCl, which is characteristic of platelet derived growth factor, and at 1.1 M NaCl and 1.6M NaCl, indicative of acidic and basic fibroblast growth factors, respectively. The identities of these mitogenic fractions were confirmed by specific immunologic and receptor-binding assays. The presence of platelet derived, acidic and basic fibroblast growth factors in the synovial fluid may contribute to wound healing in the arthritic joint.

  6. Integrin avidity regulation: are changes in affinity and conformation underemphasized?

    PubMed

    Carman, Christopher V; Springer, Timothy A

    2003-10-01

    Integrins play critical roles in development, wound healing, immunity and cancer. Central to their function is their unique ability to modulate dynamically their adhesiveness through both affinity- and valency-based mechanisms. Recent advances have shed light on the structural basis for affinity regulation and on the signaling mechanisms responsible for both affinity and valency modes of regulation.

  7. Increasing the molecular contacts between maurotoxin and Kv1.2 channel augments ligand affinity.

    PubMed

    M'Barek, Sarrah; Chagot, Benjamin; Andreotti, Nicolas; Visan, Violeta; Mansuelle, Pascal; Grissmer, Stephan; Marrakchi, Mohamed; El Ayeb, Mohamed; Sampieri, François; Darbon, Hervé; Fajloun, Ziad; De Waard, Michel; Sabatier, Jean-Marc

    2005-08-15

    Scorpion toxins interact with their target ion channels through multiple molecular contacts. Because a "gain of function" approach has never been described to evaluate the importance of the molecular contacts in defining toxin affinity, we experimentally examined whether increasing the molecular contacts between a toxin and an ion channel directly impacts toxin affinity. For this purpose, we focused on two scorpion peptides, the well-characterized maurotoxin with its variant Pi1-like disulfide bridging (MTX(Pi1)), used as a molecular template, and butantoxin (BuTX), used as an N-terminal domain provider. BuTX is found to be 60-fold less potent than MTX(Pi1) in blocking Kv1.2 (IC(50) values of 165 nM for BuTX versus 2.8 nM for MTX(Pi1)). Removal of its N-terminal domain (nine residues) further decreases BuTX affinity for Kv1.2 by 5.6-fold, which is in agreement with docking simulation data showing the importance of this domain in BuTX-Kv1.2 interaction. Transfer of the BuTX N-terminal domain to MTX(Pi1) results in a chimera with five disulfide bridges (BuTX-MTX(Pi1)) that exhibits 22-fold greater affinity for Kv1.2 than MTX(Pi1) itself, in spite of the lower affinity of BuTX as compared to MTX(Pi1). Docking experiments performed with the 3-D structure of BuTX-MTX(Pi1) in solution, as solved by (1)H-NMR, reveal that the N-terminal domain of BuTX participates in the increased affinity for Kv1.2 through additional molecular contacts. Altogether, the data indicate that acting on molecular contacts between a toxin and a channel is an efficient strategy to modulate toxin affinity.

  8. A High-Affinity Adenosine Kinase from Anopheles Gambiae

    SciTech Connect

    M Cassera; M Ho; E Merino; E Burgos; A Rinaldo-Matthis; S Almo; V Schramm

    2011-12-31

    Genome analysis revealed a mosquito orthologue of adenosine kinase in Anopheles gambiae (AgAK; the most important vector for the transmission of Plasmodium falciparum in Africa). P. falciparum are purine auxotrophs and do not express an adenosine kinase but rely on their hosts for purines. AgAK was kinetically characterized and found to have the highest affinity for adenosine (K{sub m} = 8.1 nM) of any known adenosine kinase. AgAK is specific for adenosine at the nucleoside site, but several nucleotide triphosphate phosphoryl donors are tolerated. The AgAK crystal structure with a bound bisubstrate analogue Ap{sub 4}A (2.0 {angstrom} resolution) reveals interactions for adenosine and ATP and the geometry for phosphoryl transfer. The polyphosphate charge is partly neutralized by a bound Mg{sup 2+} ion and an ion pair to a catalytic site Arg. The AgAK structure consists of a large catalytic core in a three-layer {alpha}/{beta}/{alpha} sandwich, and a small cap domain in contact with adenosine. The specificity and tight binding for adenosine arise from hydrogen bond interactions of Asn14, Leu16, Leu40, Leu133, Leu168, Phe168, and Thr171 and the backbone of Ile39 and Phe168 with the adenine ring as well as through hydrogen bond interactions between Asp18, Gly64, and Asn68 and the ribosyl 2'- and 3'-hydroxyl groups. The structure is more similar to that of human adenosine kinase (48% identical) than to that of AK from Toxoplasma gondii (31% identical). With this extraordinary affinity for AgAK, adenosine is efficiently captured and converted to AMP at near the diffusion limit, suggesting an important role for this enzyme in the maintenance of the adenine nucleotide pool. mRNA analysis verifies that AgAK transcripts are produced in the adult insects.

  9. Review of aircraft noise propagation

    NASA Technical Reports Server (NTRS)

    Putnam, T. W.

    1975-01-01

    The current state of knowledge about the propagation of aircraft noise was reviewed. The literature on the subject is surveyed and methods for predicting the most important and best understood propagation effects are presented. Available empirical data are examined and the data's general validity is assessed. The methods used to determine the loss of acoustic energy due to uniform spherical spreading, absorption in a homogeneous atmosphere, and absorption due to ground cover are presented. A procedure for determining ground induced absorption as a function of elevation angle between source and receiver is recommended. Other factors that affect propagation, such as refraction and scattering due to turbulence, which were found to be less important for predicting the propagation of aircraft noise, are also evaluated.

  10. Photon propagator for axion electrodynamics

    SciTech Connect

    Itin, Yakov

    2007-10-15

    The axion modified electrodynamics is usually used as a model for description of possible violation of Lorentz invariance in field theory. The low-energy manifestation of Lorentz violation can hopefully be observed in experiments with electromagnetic waves. It justifies the importance of studying how a small axion addition can modify the wave propagation. Although a constant axion does not contribute to the dispersion relation at all, even a slowly varying axion field destroys the light cone structure. In this paper, we study the wave propagation in the axion modified electrodynamics in the framework of the premetric approach. In addition to the modified dispersion relation, we derive the axion generalization of the photon propagator in Feynman and Landau gauge. Our consideration is free of the usual restriction to the constant gradient axion field. It is remarkable that the axion modified propagator is Hermitian. Consequently, the dissipation effects are absent even in the phenomenological model considered here.

  11. Propagation Limitations in Remote Sensing.

    DTIC Science & Technology

    Contents: Multi-sensors and systems in remote sensing ; Radar sensing systems over land; Remote sensing techniques in oceanography; Influence of...propagation media and background; Infrared techniques in remote sensing ; Photography in remote sensing ; Analytical studies in remote sensing .

  12. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani S.

    1992-01-01

    In June 1991, a paper at the fifteenth NASA Propagation Experimenters Meeting (NAPEX 15) was presented outlining the development of a database for propagation models. The database is designed to allow the scientists and experimenters in the propagation field to process their data through any known and accepted propagation model. The architecture of the database also incorporates the possibility of changing the standard models in the database to fit the scientist's or the experimenter's needs. The database not only provides powerful software to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables, and producing impressive and crisp hard copy for presentation and filing.

  13. Reconstruction of nonlinear wave propagation

    DOEpatents

    Fleischer, Jason W; Barsi, Christopher; Wan, Wenjie

    2013-04-23

    Disclosed are systems and methods for characterizing a nonlinear propagation environment by numerically propagating a measured output waveform resulting from a known input waveform. The numerical propagation reconstructs the input waveform, and in the process, the nonlinear environment is characterized. In certain embodiments, knowledge of the characterized nonlinear environment facilitates determination of an unknown input based on a measured output. Similarly, knowledge of the characterized nonlinear environment also facilitates formation of a desired output based on a configurable input. In both situations, the input thus characterized and the output thus obtained include features that would normally be lost in linear propagations. Such features can include evanescent waves and peripheral waves, such that an image thus obtained are inherently wide-angle, farfield form of microscopy.

  14. Propagating plasmons on silver nanowires

    NASA Astrophysics Data System (ADS)

    He, Weidong; Wei, Hong; Li, Zhipeng; Huang, Yingzhou; Fang, Yurui; Li, Ping; Xu, Hongxing

    2010-08-01

    Chemically synthesized Ag nanowires (NWs) can serve as waveguides to support propagating surface plasmons (SPs). By using the propagating SPs on Ag NWs, the surface-enhanced Raman scattering of molecules, located in the nanowire-nanoparticle junction a few microns away from the laser spot on one end of the NW, was excited. The propagating SPs can excite the excitons in quantum dots, and in reverse, the decay of excitons can generate SPs. The direction and polarization of the light emitted through the Ag NW waveguide. The emission polarization depends strongly on the shape of the NW terminals. In branched NW structures, the SPs can be switched between the main NW and the branch NW, by tuning the incident polarization. The light of different wavelength can also be controlled to propagate along different ways. Thus, the branched NW structure can serve as controllable plasmonic router and multiplexer.

  15. Identification of Integrin β Subunit Mutations That Alter Affinity for Extracellular Matrix Ligand*

    PubMed Central

    Kendall, Timmy; Mukai, Leona; Jannuzi, Alison L.; Bunch, Thomas A.

    2011-01-01

    We examined over 50 mutations in the Drosophila βPS integrin subunit that alter integrin function in situ for their ability to bind a soluble monovalent ligand, TWOW-1. Surprisingly, very few of the mutations, which were selected for conditional lethality in the fly, reduce the ligand binding ability of the integrin. The most prevalent class of mutations activates the integrin heterodimer. These findings emphasize the importance of integrin affinity regulation and point out how molecular interactions throughout the integrin molecule are important in keeping the integrin in a low affinity state. Mutations strongly support the controversial deadbolt hypothesis, where the CD loop in the β tail domain acts to restrain the I domain in the inactive, bent conformation. Site-directed mutations in the cytoplasmic domains of βPS and αPS2C reveal different effects on ligand binding from those observed for αIIbβ3 integrins and identify for the first time a cytoplasmic cysteine residue, conserved in three human integrins, as being important in affinity regulation. In the fly, we find that genetic interactions of the βPS mutations with reduction in talin function are consistent with the integrin affinity differences measured in cells. Additionally, these genetic interactions report on increased and decreased integrin functions that do not result in affinity changes in the PS2C integrin measured in cultured cells. PMID:21757698

  16. Affinity improvement by fine tuning of single-chain variable fragment against aflatoxin B1.

    PubMed

    Min, Won-Ki; Na, Kang-In; Yoon, Jung-Hyun; Heo, Yoon-Jee; Lee, Daesang; Kim, Sung-Gun; Seo, Jin-Ho

    2016-10-15

    Aflatoxin B1 (AFB1) produced in Aspergillus flavus is a major hepatocarcinogen found in foods and feed. For effective immunological detection of AFB1 at low concentrations, the development of high affinity antibody for AFB1 is required. Previously, an affinity-maturated single-chain variable fragment containing 6 mutations (scFv-M37) was isolated from an artificial mutagenic library, which showed a 9-fold higher affinity than its wild type scFv. In this study, the effect of the 6 mutated residues on the affinity improvement was characterized using surface plasmon resonance analysis, which identified a deleterious mutation (VH-A110T) located on a framework region of the scFv-M37. The back mutation of VH-A110T resulted in a 3.2-fold affinity improvement, which was attributed to decrease of dissociation rate constant (kd) in interaction between AFB1 and the back mutant scFv. The biophysical analyses using circular dichroism and gel filtration revealed that the back mutation of VH-A110T caused a subtle conformational change of the scFv toward tighter binding to AFB1.

  17. Propagating rifts on midocean ridges

    NASA Astrophysics Data System (ADS)

    Hey, Richard; Duennebier, Frederick K.; Morgan, W. Jason

    1980-07-01

    Spreading center jumps identified west of the Galapagos Islands near 95°W occur in a pattern consistent with the propagating rift hypothesis. A new rift is gradually breaking through the Cocos plate. Each successive jump is slightly longer than the preceding jump. The new spreading center grows at a new azimuth toward the west as the old one dies. The jumps are a manifestation of rift propagation. We extend the analysis of propagating rifts to the case of continuous propagation and predict patterns of magnetic anomalies and bathymetry consistent with the observed patterns. In particular, we correctly predict the trends of fossil spreading centers and V patterns of magnetic anomaly offsets required by the propagating rift hypothesis. Similar V patterns have been observed on many other spreading centers and have been interpreted in various ways. The propagating rift hypothesis appears to offer a simple explanation, consistent with rigid plate tectonics, for each of these patterns. This hypothesis may also have important implications for continental rifting.

  18. Latest European coelacanth shows Gondwanan affinities.

    PubMed

    Cavin, Lionel; Forey, Peter L; Buffetaut, Eric; Tong, Haiyan

    2005-06-22

    The last European fossil occurrence of a coelacanth is from the Mid-Cretaceous of the English Chalk (Turonian, 90 million years ago). Here, we report the discovery of a coelacanth from Late Cretaceous non-marine rocks in southern France. It consists of a left angular bone showing structures that imply close phylogenetic affinities with some extinct Mawsoniidae. The closest relatives are otherwise known from Cretaceous continental deposits of southern continents and suggest that the dispersal of freshwater organisms from Africa to Europe occurred in the Late Cretaceous.

  19. On the electron affinity of Be2

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Partridge, H.

    1984-01-01

    Calculations of the electron affinity (EA) of Be2 using a large Slater-type orbital basis set and extensive correlation based upon a CASSCF reference are reported. The adiabatic EAs are estimated to be 0.44 eV for the 2Sigma sub g(+) state and 0.56 eV for the 2Pi sub u state. The extra electron attaches into an empty bonding orbital, causing a shortening of the bond length and an increase in omega(e). The D(e) of the 2Pi sub u state of Be2 is six times as large as the D(e) of Be2.

  20. On the structure of self-affine convex bodies

    SciTech Connect

    Voynov, A S

    2013-08-31

    We study the structure of convex bodies in R{sup d} that can be represented as a union of their affine images with no common interior points. Such bodies are called self-affine. Vallet's conjecture on the structure of self-affine bodies was proved for d = 2 by Richter in 2011. In the present paper we disprove the conjecture for all d≥3 and derive a detailed description of self-affine bodies in R{sup 3}. Also we consider the relation between properties of self-affine bodies and functional equations with a contraction of an argument. Bibliography: 10 titles.

  1. Affinity filtration coupled with capillary-based affinity purification for the isolation of protein complexes.

    PubMed

    Qureshi, M S; Sheikh, Q I; Hill, R; Brown, P E; Dickman, M J; Tzokov, S B; Rice, D W; Gjerde, D T; Hornby, D P

    2013-08-01

    The isolation of complex macromolecular assemblies at the concentrations required for structural analysis represents a major experimental challenge. Here we present a method that combines the genetic power of site-specific recombination in order to selectively "tag" one or more components of a protein complex with affinity-based rapid filtration and a final step of capillary-based enrichment. This modified form of tandem affinity purification produces highly purified protein complexes at high concentrations in a highly efficient manner. The application of the method is demonstrated for the yeast Arp2/3 heptameric protein complex involved in mediating reorganization of the actin cytoskeleton.

  2. The physical theory and propagation model of THz atmospheric propagation

    NASA Astrophysics Data System (ADS)

    Wang, R.; Yao, J. Q.; Xu, D. G.; Wang, J. L.; Wang, P.

    2011-02-01

    Terahertz (THz) radiation is extensively applied in diverse fields, such as space communication, Earth environment observation, atmosphere science, remote sensing and so on. And the research on propagation features of THz wave in the atmosphere becomes more and more important. This paper firstly illuminates the advantages and outlook of THz in space technology. Then it introduces the theoretical framework of THz atmospheric propagation, including some fundamental physical concepts and processes. The attenuation effect (especially the absorption of water vapor), the scattering of aerosol particles and the effect of turbulent flow mainly influence THz atmosphere propagation. Fundamental physical laws are illuminated as well, such as Lamber-beer law, Mie scattering theory and radiative transfer equation. The last part comprises the demonstration and comparison of THz atmosphere propagation models like Moliere(V5), SARTre and AMATERASU. The essential problems are the deep analysis of physical mechanism of this process, the construction of atmospheric propagation model and databases of every kind of material in the atmosphere, and the standardization of measurement procedures.

  3. Extraction of haemoglobin from human blood by affinity precipitation using a haptoglobin-based stimuli-responsive affinity macroligand.

    PubMed

    Stocker-Majd, Gisela; Hilbrig, Frank; Freitag, Ruth

    2008-06-13

    Affinity precipitation was compared to affinity chromatography and batch adsorption as the final purification step in a protocol for the isolation of haemoglobin from human blood. Haptoglobin was the affinity ligand. The first steps on the process were realized by traditional methods (lyses of red blood cells followed by ammonium sulphate precipitation). For affinity chromatography (and batch adsorption) the ligand was linked to Sepharose, for affinity precipitation to a thermoresponsive polymer, namely poly(N-isopropylacrylamide). Five haptoglobin-poly(N-isopropylacrylamide) bioconjugates (affinity macroligands) were constructed with different polymer: haptoglobin-coupling ratios. Conjugation of haptoglobin to the soluble poly(N-isopropylacrylamide) apparently does not change the interaction thermodynamics with haemoglobin, as the haemoglobin binding constants calculated by a Scatchard analysis for the affinity macroligand were of the same order of magnitude as those described in the literature for the haemoglobin-haptoglobin complex in solution. Two elution protocols were used for haemoglobin release from the various affinity materials, one at pH 2, the other with 5 M urea at pH 11. Both affinity chromatography and affinity precipitation yielded a pure haemoglobin of high quality. Compared to the affinity chromatography, affinity precipitation showed a significantly higher ligand efficiency (ratio of the experimental capacity to the theoretical one). The method thus makes better use of the expensive affinity ligands. As affinity precipitation only requires small temperature changes to bring about precipitation/redissolution of the affinity complexes and a centrifugation step for recovery of the precipitate, the method in addition has advantages in term of scalability and simplicity.

  4. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity.

    PubMed

    Paul, Sinu; Weiskopf, Daniela; Angelo, Michael A; Sidney, John; Peters, Bjoern; Sette, Alessandro

    2013-12-15

    Prediction of HLA binding affinity is widely used to identify candidate T cell epitopes, and an affinity of 500 nM is routinely used as a threshold for peptide selection. However, the fraction (percentage) of peptides predicted to bind with affinities of 500 nM varies by allele. For example, of a large collection of ~30,000 dengue virus-derived peptides only 0.3% were predicted to bind HLA A*0101, whereas nearly 5% were predicted for A*0201. This striking difference could not be ascribed to variation in accuracy of the algorithms used, as predicted values closely correlated with affinity measured in vitro with purified HLA molecules. These data raised the question whether different alleles would also vary in terms of epitope repertoire size, defined as the number of associated epitopes or, alternatively, whether alleles vary drastically in terms of the affinity threshold associated with immunogenicity. To address this issue, strains of HLA transgenic mice with wide (A*0201), intermediate (B*0702), or narrow (A*0101) repertoires were immunized with peptides of varying binding affinity and relative percentile ranking. The results show that absolute binding capacity is a better predictor of immunogenicity, and analysis of epitopes from the Immune Epitope Database revealed that predictive efficacy is increased using allele-specific affinity thresholds. Finally, we investigated the genetic and structural basis of the phenomenon. Although no stringent correlate was defined, on average HLA B alleles are associated with significantly narrower repertoires than are HLA A alleles.

  5. Age-dependent decrease in the affinity of muscarinic M1 receptors in neocortex of rhesus monkeys.

    PubMed Central

    Vannucchi, M G; Goldman-Rakic, P S

    1991-01-01

    In vitro autoradiography on tissue sections and receptor assay in cortical membrane homogenates revealed that pirenzepine high-affinity muscarinic sites (M1) decrease in affinity in the prefrontal cortex and in other cortical areas of aged rhesus monkey (Macaca mulatta). Carbachol competition experiments detected only a single, low-affinity class of sites in old monkeys, while two classes of sites (low and high affinity) were observed in young adults. The change in affinity in the aged monkeys is not accompanied by a decrease in the density of these sites and, further, the age-related decline in the affinity of the M1 site is reversible. In the presence of Mg2+, the M1 muscarinic receptors in the aged monkeys were capable of forming carbachol high-affinity sites. These results provide evidence for age-dependent functional changes in receptor activity in cerebral cortex and indicate that these receptors maintain a degree of plasticity that could be a strategic target for research aimed at treatment of memory disorders in aged humans. Images PMID:1763062

  6. Quantification of hydrophobic interaction affinity of colloids

    NASA Astrophysics Data System (ADS)

    Saini, G.; Nasholm, N.; Wood, B. D.

    2009-12-01

    Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

  7. Affinity-based target deconvolution of safranal

    PubMed Central

    2013-01-01

    Background and the purpose of the study Affinity-based target deconvolution is an emerging method for the identification of interactions between drugs/drug candidates and cellular proteins, and helps to predict potential activities and side effects of a given compound. In the present study, we hypothesized that a part of safranal pharmacological effects, one of the major constituent of Crocus sativus L., relies on its physical interaction with target proteins. Methods Affinity chromatography solid support was prepared by covalent attachment of safranal to agarose beads. After passing tissue lysate through the column, safranal-bound proteins were isolated and separated on SDS-PAGE or two-dimensional gel electrophoresis. Proteins were identified using MALDI-TOF/TOF mass spectrometry and Mascot software. Results and major conclusion Data showed that safranal physically binds to beta actin, cytochrome b-c1 complex sub-unit 1, trifunctional enzyme sub-unit beta and ATP synthase sub-unit alpha and beta. These interactions may explain part of safranal’s pharmacological effects. However, phenotypic and/or biological relevance of these interactions remains to be elucidated by future pharmacological studies. PMID:23514587

  8. Affine conformal vectors in space-time

    NASA Astrophysics Data System (ADS)

    Coley, A. A.; Tupper, B. O. J.

    1992-05-01

    All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.

  9. Ubiquitous Fast Propagating Intensity Disturbances in Solar Chromosphere

    NASA Technical Reports Server (NTRS)

    Kubo, M.; Katsukawa, Y.; Suematsu, Y.; Kano, R.; Bando, T.; Narukage, N.; Ishikawa, R.; Hara, H.; Giono, G.; Winebarger, A.; Kobayashi, K.

    2016-01-01

    High cadence observations by the slit-jaw (SJ) optics system of the sounding rocket experiment "the Chromospheric Lyman Alpha SpectroPolarimeter (CLASP)" reveal ubiquitous intensity disturbances that recurrently propagate in either the chromosphere, transition region, or both at a speed much higher than the sound speed.

  10. Stratospheric constituent response to vertically propagating equatorial waves

    NASA Astrophysics Data System (ADS)

    Salby, Murry L.

    1988-02-01

    Planetary-scale equatorial waves play an important role in the dynamics of the tropical atmosphere. They are believed to be excited in unsteady convective heating in the tropical troposphere. From convective centers in the intertropical convergence zone (ITCZ), equatorial waves propagate vertically into the upper atmosphere where they are eventually absorbed, e.g., through radiative dissipation. A spectrum of vertically propagating Kelvin waves was revealed to be trapped about the equator, radiating vertically out of the tropical troposphere. Two other Kelvin waves were found with phase velocities 2 and 4 times as fast. The ultrafast Kelvin waves move at nearly 120 m/s and are seen to propagate to the highest altitude observed by Nimbus-7 LIMS. Each class has the form of a Kelvin wave, a Gaussian centered on the equator and propagating vertically, and all satisfy the dispersion relationship for equatorial Kelvin waves. These vertically propagating Kelvin waves account for a substantial fraction of the temperature variability in the tropical stratosphere. In combination, they lead to temperature fluctuations in excess of 5K in the upper stratosphere and mesosphere. Because several chemical constituents are photochemically controlled in this region, vertically propagating Kelvin waves are expected to lead to variations in the abundances of such species.

  11. Propagation of dissection in a residually-stressed artery model.

    PubMed

    Wang, Lei; Roper, Steven M; Hill, Nicholas A; Luo, Xiaoyu

    2017-02-01

    This paper studies dissection propagation subject to internal pressure in a residually-stressed two-layer arterial model. The artery is assumed to be infinitely long, and the resultant plane strain problem is solved using the extended finite element method. The arterial layers are modelled using the anisotropic hyperelastic Holzapfel-Gasser-Ogden model, and the tissue damage due to tear propagation is described using a linear cohesive traction-separation law. Residual stress in the arterial wall is determined by an opening angle [Formula: see text] in a stress-free configuration. An initial tear is introduced within the artery which is subject to internal pressure. Quasi-static solutions are computed to determine the critical value of the pressure, at which the dissection starts to propagate. Our model shows that the dissection tends to propagate radially outwards. Interestingly, the critical pressure is higher for both very short and very long tears. The simulations also reveal that the inner wall buckles for longer tears, which is supported by clinical CT scans. In all simulated cases, the critical pressure is found to increase with the opening angle. In other words, residual stress acts to protect the artery against tear propagation. The effect of residual stress is more prominent when a tear is of intermediate length ([Formula: see text]90[Formula: see text] arc length). There is an intricate balance between tear length, wall buckling, fibre orientation, and residual stress that determines the tear propagation.

  12. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

    PubMed

    Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

    2016-08-26

    Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

  13. The geometry of propagating rifts

    NASA Astrophysics Data System (ADS)

    McKenzie, Dan

    1986-03-01

    The kinematics of two different processes are investigated, both of which have been described as rift propagation. Courtillot uses this term to describe the change from distributed to localised extension which occurs during the early development of an ocean basin. The term localisation is instead used here to describe this process, to distinguish it from Hey's type of propagation. Localisation generally leads to rotation of the direction of magnetisation. To Hey propagation means the extension of a rift into the undeformed plate beyond a transform fault. Detail surveys of the Galapagos rift have shown that the propagating and failing rifts are not connected by a single transform fault, but by a zone which is undergoing shear. The principal deformation is simple shear, and the kinematics of this deformation are investigated in some detail. The strike of most of the lineations observed in the area can be produced by such deformation. The mode of extension on the propagating rift appears to be localised for some periods but to be distributed for others. Neither simple kinematic arguments nor stretching of the lithosphere with conservation of crust can account for the observed variations in water depth.

  14. User needs for propagation data

    NASA Technical Reports Server (NTRS)

    Sullivan, Thomas M.

    1993-01-01

    New and refined models of radio signal propagation phenomena are needed to support studies of evolving satellite services and systems. Taking an engineering perspective, applications for propagation measurements and models in the context of various types of analyses that are of ongoing interest are reviewed. Problems that were encountered in the signal propagation aspects of these analyses are reviewed, and potential solutions to these problems are discussed. The focus is on propagation measurements and models needed to support design and performance analyses of systems in the Mobile-Satellite Service (MSS) operating in the 1-3 GHz range. These systems may use geostationary or non-geostationary satellites and Frequency Division Multiple Access (FDMA), Time Division Multiple Access Digital (TDMA), or Code Division Multiple Access (CDMA) techniques. Many of the propagation issues raised in relation to MSS are also pertinent to other services such as broadcasting-satellite (sound) at 2310-2360 MHz. In particular, services involving mobile terminals or terminals with low gain antennas are of concern.

  15. Strategy for affinity maturation of an antibody with high evolvability to (4-hydroxy-3-nitrophenyl) acetyl hapten.

    PubMed

    Furukawa, Koji; Shimizu, Takeyuki; Murakami, Akikazu; Kono, Ryo; Nakagawa, Masatoshi; Sagawa, Takuma; Yamato, Ichiro; Azuma, Takachika

    2007-03-01

    In order to quantitate the contribution of amino acid replacements to an increase in affinity during affinity maturation, we measured thermodynamic parameters of the antigen-antibody interaction for a group of anti-(4-hydroxy-3-nitrophenyl) acetyl monoclonal antibodies whose differences in amino acid sequences had arisen only from somatic hypermutation. We prepared a common ancestor and hypothetical intermediate clones that might occur on the affinity maturation pathway, by employing site-directed mutagenesis. Isothermal calorimetric titration of the antigen-antibody reaction revealed that antibody evolution proceeds in two steps. The first step is driven by a decrease in enthalpy, in which two amino acid replacements in the VL region play an essential role. Further accumulation of amino acid replacements in VH and VL regions during the second step induce a progressive increase in affinity, which is driven by an increase in entropy, which has a cooperative mutational effect.

  16. Wave propagation in ballistic gelatine.

    PubMed

    Naarayan, Srinivasan S; Subhash, Ghatu

    2017-01-23

    Wave propagation characteristics in long cylindrical specimens of ballistic gelatine have been investigated using a high speed digital camera and hyper elastic constitutive models. The induced transient deformation is modelled with strain rate dependent Mooney-Rivlin parameters which are determined by modelling the stress-strain response of gelatine at a range of strain rates. The varying velocity of wave propagation through the gelatine cylinder is derived as a function of prestress or stretch in the gelatine specimen. A finite element analysis is conducted using the above constitutive model by suitably defining the impulse imparted by the polymer bar into the gelatine specimen. The model results are found to capture the experimentally observed wave propagation characteristics in gelatine effectively.

  17. Dynamical Realism and Uncertainty Propagation

    NASA Astrophysics Data System (ADS)

    Park, Inkwan

    In recent years, Space Situational Awareness (SSA) has become increasingly important as the number of tracked Resident Space Objects (RSOs) continues their growth. One of the most significant technical discussions in SSA is how to propagate state uncertainty in a consistent way with the highly nonlinear dynamical environment. In order to keep pace with this situation, various methods have been proposed to propagate uncertainty accurately by capturing the nonlinearity of the dynamical system. We notice that all of the methods commonly focus on a way to describe the dynamical system as precisely as possible based on a mathematical perspective. This study proposes a new perspective based on understanding dynamics of the evolution of uncertainty itself. We expect that profound insights of the dynamical system could present the possibility to develop a new method for accurate uncertainty propagation. These approaches are naturally concluded in goals of the study. At first, we investigate the most dominant factors in the evolution of uncertainty to realize the dynamical system more rigorously. Second, we aim at developing the new method based on the first investigation enabling orbit uncertainty propagation efficiently while maintaining accuracy. We eliminate the short-period variations from the dynamical system, called a simplified dynamical system (SDS), to investigate the most dominant factors. In order to achieve this goal, the Lie transformation method is introduced since this transformation can define the solutions for each variation separately. From the first investigation, we conclude that the secular variations, including the long-period variations, are dominant for the propagation of uncertainty, i.e., short-period variations are negligible. Then, we develop the new method by combining the SDS and the higher-order nonlinear expansion method, called state transition tensors (STTs). The new method retains advantages of the SDS and the STTs and propagates

  18. Wave equations for pulse propagation

    SciTech Connect

    Shore, B.W.

    1987-06-24

    Theoretical discussions of the propagation of pulses of laser radiation through atomic or molecular vapor rely on a number of traditional approximations for idealizing the radiation and the molecules, and for quantifying their mutual interaction by various equations of propagation (for the radiation) and excitation (for the molecules). In treating short-pulse phenomena it is essential to consider coherent excitation phenomena of the sort that is manifest in Rabi oscillations of atomic or molecular populations. Such processes are not adequately treated by rate equations for excitation nor by rate equations for radiation. As part of a more comprehensive treatment of the coupled equations that describe propagation of short pulses, this memo presents background discussion of the equations that describe the field. This memo discusses the origin, in Maxwell's equations, of the wave equation used in the description of pulse propagation. It notes the separation into lamellar and solenoidal (or longitudinal and transverse) and positive and negative frequency parts. It mentions the possibility of separating the polarization field into linear and nonlinear parts, in order to define a susceptibility or index of refraction and, from these, a phase and group velocity. The memo discusses various ways of characterizing the polarization characteristics of plane waves, that is, of parameterizing a transverse unit vector, such as the Jones vector, the Stokes vector, and the Poincare sphere. It discusses the connection between macroscopically defined quantities, such as the intensity or, more generally, the Stokes parameters, and microscopic field amplitudes. The material presented here is a portion of a more extensive treatment of propagation to be presented separately. The equations presented here have been described in various books and articles. They are collected here as a summary and review of theory needed when treating pulse propagation.

  19. Gap soliton propagation in optical fiber gratings

    NASA Astrophysics Data System (ADS)

    Mohideen, U.; Slusher, R. E.; Mizrahi, V.; Erdogan, T.; Kuwata-Gonokami, M.; Lemaire, P. J.; Sipe, J. E.; Martijn de Sterke, C.; Broderick, Neil G. R.

    1995-08-01

    Intense optical pulse propagation in a GeO2 -doped silica glass fiber grating results in nonlinear pulse propagation velocities and increased transmission at wavelengths where the grating reflects light in the linear limit. These nonlinear pulse propagation effects are predicted by numerical simulations of gap soliton propagation. The large linear refractive-index variations used for the fiber gratings in these experiments permit the propagation of gap solitons in short lengths of fiber.

  20. Mepyramine-JNJ7777120-hybrid compounds show high affinity to hH(1)R, but low affinity to hH(4)R.

    PubMed

    Wagner, Eva; Wittmann, Hans-Joachim; Elz, Sigurd; Strasser, Andrea

    2011-11-01

    In literature, a synergism between histamine H(1) and H(4) receptor is discussed. Furthermore, it was shown, that the combined application of mepyramine, a H(1) antagonist and JNJ7777120, a H(4) receptor ligand leads to a synergistic effect in the acute murine asthma model. Thus, the aim of this study was to develop new hybrid ligands, containing one H(1) and one H(4) pharmacophor, connected by an appropriate spacer, in order to address both, H(1)R and H(4)R. Within this study, we synthesized nine hybrid compounds, which were pharmacologically characterized at hH(1)R and hH(4)R. The new compounds revealed (high) affinity to hH(1)R, but showed only low affinity to hH(4)R. Additionally, we performed molecular dynamic studies for some selected compounds at hH(1)R, in order to obtain information about the binding mode of these compounds on molecular level.

  1. The affine cohomology spaces and its applications

    NASA Astrophysics Data System (ADS)

    Fraj, Nizar Ben; Laraiedh, Ismail

    2016-12-01

    We compute the nth cohomology space of the affine Lie superalgebra 𝔞𝔣𝔣(1) on the (1,1)-dimensional real superspace with coefficient in a large class of 𝔞𝔣𝔣(1)-modules M. We apply our results to the module of weight densities and the module of linear differential operators acting on a superspace of weighted densities. This work is the generalization of a result by Basdouri et al. [The linear 𝔞𝔣𝔣(n|1)-invariant differential operators on weighted densities on the superspace ℝ1|n and 𝔞𝔣𝔣(n|1)-relative cohomology, Int. J. Geom. Meth. Mod. Phys. 10 (2013), Article ID: 1320004, 9 pp.

  2. Automatic gesture analysis using constant affine velocity.

    PubMed

    Cifuentes, Jenny; Boulanger, Pierre; Pham, Minh Tu; Moreau, Richard; Prieto, Flavio

    2014-01-01

    Hand human gesture recognition has been an important research topic widely studied around the world, as this field offers the ability to identify, recognize, and analyze human gestures in order to control devices or to interact with computer interfaces. In particular, in medical training, this approach is an important tool that can be used to obtain an objective evaluation of a procedure performance. In this paper, some obstetrical gestures, acquired by a forceps, were studied with the hypothesis that, as the scribbling and drawing movements, they obey the one-sixth power law, an empirical relationship which connects path curvature, torsion, and euclidean velocity. Our results show that obstetrical gestures have a constant affine velocity, which is different for each type of gesture and based on this idea this quantity is proposed as an appropriate classification feature in the hand human gesture recognition field.

  3. The effects of solidification on sill propagation dynamics and geometry

    NASA Astrophysics Data System (ADS)

    Lola, Chanceaux; Thierry, Menand

    2015-04-01

    The effects of solidification on sill propagation dynamics and geometry are studied by means of analogue laboratory experiments. Hot fluid vegetable oil (a magma analogue), that solidifies during its propagation, is injected as a sill in a colder layered gelatine solid (an elastic host rock analogue). The injection flux and temperature are maintained constant during an experiment. In order to vary the importance of solidification and quantify its effect on sill propagation, the injection flux and temperature are systematically varied between each experiment. Depending on the importance of solidification effects, two extreme behaviours for sill propagation dynamics and geometry are observed. When solidification effects are small (high injection temperatures and fluxes), the propagation is continuous and the sill has a regular and smooth surface. Inversely, when solidification effects are important (low injection temperatures and fluxes), sill propagation is discontinuous and occurs by steps. After each propagation step, the sill stalls, thickens progressively by storing hot fluid vegetable oil beneath the partially solidified intrusion, without growing neither in length nor in breadth, and after a pause, the propagation initiates again, soon followed by a new episode of momentary arrest. The geometry of these sills displays folds, ropy structures on their surface, and lobes with imprints of the leading fronts that correspond to each step of surface creation. These experiments show that for a given, constant injected volume, as solidification effects increase, the surface of the sills decreases, their thickness increases, and the number of propagation steps increases. In the same way lower solidification effects promote larger sill surfaces, lower thicknesses, and a lower number of propagation steps. These results have various geological and geophysical implications. Regarding the geometry of sills, 3D seismic studies in sedimentary basins reveal sills with lobate

  4. Dynamic dependence to domain wall propagation through artificial spin ice

    NASA Astrophysics Data System (ADS)

    Burn, D. M.; Chadha, M.; Branford, W. R.

    2017-03-01

    Domain wall propagation dynamics has been studied in nanostructured artificial kagome spin-ice structures. A stripline circuit has been used to provide localized pulsed magnetic fields within the artificial spin-ice (ASI) structure. This provides control of the system through electrically assisted domain wall nucleation events. Synchronization of the pulsed fields with additional global magnetic fields and the use of a focused magneto-optical Kerr effect magnetometer allows our experiments to probe the domain wall transit through an extended ASI structure. We find that the propagation distance depends on the driving field revealing field-driven properties of domain walls below their intrinsic nucleation field.

  5. Effective pinning energy landscape perturbations for propagating magnetic domain walls

    NASA Astrophysics Data System (ADS)

    Burn, D. M.; Atkinson, D.

    2016-10-01

    The interaction between a magnetic domain wall and a pinning site is explored in a planar nanowire using micromagnetics to reveal perturbations of the pinning energetics for propagating domain walls. Numerical simulations in the high damping ’quasi-static’ and low damping ’dynamic’ regimes are compared and show clear differences in de-pinning fields, indicating that dynamical micromagnetic models, which incorporate precessionally limited magnetization processes, are needed to understand domain wall pinning. Differences in the micromagnetic domain wall structure strongly influence the pinning and show periodic behaviour with increasing applied field associated with Walker breakdown. In the propagating regime pinning is complicated.

  6. Effective pinning energy landscape perturbations for propagating magnetic domain walls

    PubMed Central

    Burn, D. M.; Atkinson, D.

    2016-01-01

    The interaction between a magnetic domain wall and a pinning site is explored in a planar nanowire using micromagnetics to reveal perturbations of the pinning energetics for propagating domain walls. Numerical simulations in the high damping ’quasi-static’ and low damping ’dynamic’ regimes are compared and show clear differences in de-pinning fields, indicating that dynamical micromagnetic models, which incorporate precessionally limited magnetization processes, are needed to understand domain wall pinning. Differences in the micromagnetic domain wall structure strongly influence the pinning and show periodic behaviour with increasing applied field associated with Walker breakdown. In the propagating regime pinning is complicated. PMID:27694953

  7. Effective pinning energy landscape perturbations for propagating magnetic domain walls.

    PubMed

    Burn, D M; Atkinson, D

    2016-10-03

    The interaction between a magnetic domain wall and a pinning site is explored in a planar nanowire using micromagnetics to reveal perturbations of the pinning energetics for propagating domain walls. Numerical simulations in the high damping 'quasi-static' and low damping 'dynamic' regimes are compared and show clear differences in de-pinning fields, indicating that dynamical micromagnetic models, which incorporate precessionally limited magnetization processes, are needed to understand domain wall pinning. Differences in the micromagnetic domain wall structure strongly influence the pinning and show periodic behaviour with increasing applied field associated with Walker breakdown. In the propagating regime pinning is complicated.

  8. Simulations of Seismic Wave Propagation on Mars

    NASA Astrophysics Data System (ADS)

    Bozdağ, Ebru; Ruan, Youyi; Metthez, Nathan; Khan, Amir; Leng, Kuangdai; van Driel, Martin; Wieczorek, Mark; Rivoldini, Attilio; Larmat, Carène S.; Giardini, Domenico; Tromp, Jeroen; Lognonné, Philippe; Banerdt, Bruce W.

    2017-03-01

    We present global and regional synthetic seismograms computed for 1D and 3D Mars models based on the spectral-element method. For global simulations, we implemented a radially-symmetric Mars model with a 110 km thick crust (Sohl and Spohn in J. Geophys. Res., Planets 102(E1):1613-1635, 1997). For this 1D model, we successfully benchmarked the 3D seismic wave propagation solver SPECFEM3D_GLOBE (Komatitsch and Tromp in Geophys. J. Int. 149(2):390-412, 2002a; 150(1):303-318, 2002b) against the 2D axisymmetric wave propagation solver AxiSEM (Nissen-Meyer et al. in Solid Earth 5(1):425-445, 2014) at periods down to 10 s. We also present higher-resolution body-wave simulations with AxiSEM down to 1 s in a model with a more complex 1D crust, revealing wave propagation effects that would have been difficult to interpret based on ray theory. For 3D global simulations based on SPECFEM3D_GLOBE, we superimposed 3D crustal thickness variations capturing the distinct crustal dichotomy between Mars' northern and southern hemispheres, as well as topography, ellipticity, gravity, and rotation. The global simulations clearly indicate that the 3D crust speeds up body waves compared to the reference 1D model, whereas it significantly changes surface waveforms and their dispersive character depending on its thickness. We also perform regional simulations with the solver SES3D (Fichtner et al. Geophys. J. Int. 179:1703-1725, 2009) based on 3D crustal models derived from surface composition, thereby addressing the effects of various distinct crustal features down to 2 s. The regional simulations confirm the strong effects of crustal variations on waveforms. We conclude that the numerical tools are ready for examining more scenarios, including various other seismic models and sources.

  9. Prolactin-binding components in rabbit mammary gland: characterization by partial purification and affinity labeling

    SciTech Connect

    Katoh, M.; Djiane, J.; Kelly, P.A.

    1985-06-01

    The molecular characteristics of the PRL receptor isolated from rabbit mammary gland microsomes were investigated. Two approaches were employed: 1) affinity purification of PRL receptors and direct electrophoretic analysis, and 2) affinity cross-linking of microsomal receptors with (/sup 125/I)ovine PRL ((/sup 125/I)oPRL). PRL receptors were solubilized from mammary microsomes with 3-((3-cholamidopropyl)dimethylammonio)1-propane sulfonate and purified using an oPRL agarose affinity column. Sodium dodecylsulfate-polyacrylamide gel electrophoresis and silver staining of the gel revealed at least nine bands, including a 32,000 mol wt band which was most intensively labeled with /sup 125/I using the chloramine-T method. Covalent labeling of PRL receptors with (/sup 125/I)oPRL was performed using N-hydroxysuccinimidyl-4-azido benzoate, disuccinimidyl suberate, or ethylene glycol bis (succinimidyl succinate). A single band of 59,000 mol wt was produced by all three cross-linkers when sodium dodecylsulfate-polyacrylamide gel electrophoresis was performed under reducing conditions. Assuming 1:1 binding of hormone and binding subunit and by subtracting the mol wt of (/sup 125/I)oPRL, which was estimated from the migration distance on the gel, the mol wt of the binding subunit was calculated as 32,000. In the absence of dithiothreitol during electrophoresis, only one major hormone-receptor complex band was observed. The same mol wt binding components were also detected in microsomal fractions of rabbit kidney, ovary, and adrenal. A slightly higher mol wt binding subunit was observed in rat liver microsomes. Rabbit liver microsomes revealed five (/sup 125/I)oPRL-binding components, three of which were considered to be those of a GH receptor. Moreover, affinity labeling of detergent-solubilized and affinity purified mammary PRL receptors showed a similar major binding subunit.

  10. Propagators in polymer quantum mechanics

    NASA Astrophysics Data System (ADS)

    Flores-González, Ernesto; Morales-Técotl, Hugo A.; Reyes, Juan D.

    2013-09-01

    Polymer Quantum Mechanics is based on some of the techniques used in the loop quantization of gravity that are adapted to describe systems possessing a finite number of degrees of freedom. It has been used in two ways: on one hand it has been used to represent some aspects of the loop quantization in a simpler context, and, on the other, it has been applied to each of the infinite mechanical modes of other systems. Indeed, this polymer approach was recently implemented for the free scalar field propagator. In this work we compute the polymer propagators of the free particle and a particle in a box; amusingly, just as in the non polymeric case, the one of the particle in a box may be computed also from that of the free particle using the method of images. We verify the propagators hereby obtained satisfy standard properties such as: consistency with initial conditions, composition and Green's function character. Furthermore they are also shown to reduce to the usual Schrödinger propagators in the limit of small parameter μ0, the length scale introduced in the polymer dynamics and which plays a role analog of that of Planck length in Quantum Gravity.

  11. Microwave Propagation in Dielectric Fluids.

    ERIC Educational Resources Information Center

    Lonc, W. P.

    1980-01-01

    Describes an undergraduate experiment designed to verify quantitatively the effect of a dielectric fluid's dielectric constant on the observed wavelength of microwave radiation propagating through the fluid. The fluid used is castor oil, and results agree with the expected behavior within 5 percent. (Author/CS)

  12. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: Implications for WT1-based cancer therapeutics

    SciTech Connect

    Borbulevych, Oleg Y.; Do, Priscilla; Baker, Brian M.

    2010-09-07

    Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex.

  13. Smooth affine shear tight frames: digitization and applications

    NASA Astrophysics Data System (ADS)

    Zhuang, Xiaosheng

    2015-08-01

    In this paper, we mainly discuss one of the recent developed directional multiscale representation systems: smooth affine shear tight frames. A directional wavelet tight frame is generated by isotropic dilations and translations of directional wavelet generators, while an affine shear tight frame is generated by anisotropic dilations, shears, and translations of shearlet generators. These two tight frames are actually connected in the sense that the affine shear tight frame can be obtained from a directional wavelet tight frame through subsampling. Consequently, an affine shear tight frame indeed has an underlying filter bank from the MRA structure of its associated directional wavelet tight frame. We call such filter banks affine shear filter banks, which can be designed completely in the frequency domain. We discuss the digitization of affine shear filter banks and their implementations: the forward and backward digital affine shear transforms. Redundancy rate and computational complexity of digital affine shear transforms are also investigated in this paper. Numerical experiments and comparisons in image/video processing show the advantages of digital affine shear transforms over many other state-of-art directional multiscale representation systems.

  14. Structure of Propagating and Attached Hydrocarbon Flames

    NASA Technical Reports Server (NTRS)

    Takahashi, Fumiaki; Katta, Viswanath

    2004-01-01

    Direct numerical simulations with C3-chemistry and radiative heat-loss models have been performed to reveal the internal structure of propagating and attached flames in an axisymmetric fuel jet of methane, ethane, ethylene, acetylene, or propane in air under normal and zero gravity. Observations of the flames were also made at the NASA Glenn 2.2-Second Drop Tower. In computations, the fuel issued into quasi-quiescent air for a fixed mixing time before it was ignited along the centerline at stoichiometry. The edge of the flame propagated through a flammable layer at the laminar flame speed of the stoichiometric fuel-air mixture independent of gravity. For all cases, a peak reactivity spot, i.e., reaction kernel, was formed in the flame base, thereby holding a trailing diffusion flame. The location of the reaction kernel in the attached flames depended inversely on the reactivity. The reaction-kernel correlations between the reactivity and the velocity were developed further using variables related to local Damkahler and Peclet numbers.

  15. Noncompetitive affinity assays of glucagon and amylin using mirror-image aptamers as affinity probes.

    PubMed

    Yi, Lian; Wang, Xue; Bethge, Lucas; Klussmann, Sven; Roper, Michael G

    2016-03-21

    The ability to detect picomolar concentrations of glucagon and amylin using fluorescently labeled mirror-image aptamers, so-called Spiegelmers, is demonstrated. Spiegelmers rival the specificity of antibodies and overcome the problem of biostability of natural aptamers in a biological matrix. Using Spiegelmers as affinity probes, noncompetitive capillary electrophoresis affinity assays of glucagon and murine amylin were developed and optimized. The detection limit for glucagon was 6 pM and for amylin was 40 pM. Glucagon-like peptide-1 and -2 did not interfere with the glucagon assay, while the amylin assay showed cross-reactivity to calcitonin gene related peptide. The developed assays were combined with a competitive immunoassay for insulin to measure glucagon, amylin, and insulin secretion from batches of islets after incubation with different glucose concentrations. The development of these assays is an important step towards incorporation into an online measurement system for monitoring dynamic secretion from single islets.

  16. Laser-induced propagation and destruction of amyloid beta fibrils.

    PubMed

    Yagi, Hisashi; Ozawa, Daisaku; Sakurai, Kazumasa; Kawakami, Toru; Kuyama, Hiroki; Nishimura, Osamu; Shimanouchi, Toshinori; Kuboi, Ryoichi; Naiki, Hironobu; Goto, Yuji

    2010-06-18

    The amyloid deposition of amyloid beta (Abeta) peptides is a critical pathological event in Alzheimer disease (AD). Preventing the formation of amyloid deposits and removing preformed fibrils in tissues are important therapeutic strategies against AD. Previously, we reported the destruction of amyloid fibrils of beta(2)-microglobulin K3 fragments by laser irradiation coupled with the binding of amyloid-specific thioflavin T. Here, we studied the effects of a laser beam on Abeta fibrils. As was the case for K3 fibrils, extensive irradiation destroyed the preformed Abeta fibrils. However, irradiation during spontaneous fibril formation resulted in only the partial destruction of growing fibrils and a subsequent explosive propagation of fibrils. The explosive propagation was caused by an increase in the number of active ends due to breakage. The results not only reveal a case of fragmentation-induced propagation of fibrils but also provide insights into therapeutic strategies for AD.

  17. Asymmetric light propagation in chirped photonic crystal waveguides.

    PubMed

    Kurt, H; Yilmaz, D; Akosman, A E; Ozbay, E

    2012-08-27

    We report numerical and experimental investigations of asymmetric light propagation in a newly designed photonic structure that is formed by creating a chirped photonic crystal (PC) waveguide. The use of a non-symmetric distribution of unit cells of PC ensures the obtaining of asymmetric light propagation. Properly designing the spatial modulation of a PC waveguide inherently modifies the band structure. That in turn induces asymmetry for the light's followed path. The investigation of the transmission characteristics of this structure reveals optical diode like transmission behavior. The amount of power collected at the output of the waveguide centerline is different for the forward and backward propagation directions in the designed configuration. The advantageous properties of the proposed approach are the linear optic concept, compact configuration and compatibility with the integrated photonics. These features are expected to hold great potential for implementing practical optical rectifier-type devices.

  18. Seismotectonics of mid-ocean ridge propagation

    NASA Astrophysics Data System (ADS)

    Floyd, Jacqueline Suzanne

    This dissertation investigates the rifting-spreading transition of two propagating mid-ocean spreading centers within actively rifting lithosphere, Woodlark Basin and Hess Deep. Hess Deep is a 5.4 km-deep oceanic rift basin at the westernmost tip of the Galapagos Spreading Center where it meets the East Pacific Rise at the Galapagos Triple Junction. Hydroacoustic seismicity data recorded over 200 earthquakes in Hess Deep that reveal earthquake and deformation patterns that are similar to those found in the process zone of laboratory-scale propagating tensile cracks. Seismicity and deformation patterns observed in Hess Deep are consistent with those from crack tip process zones Process zone deformation releases large crack tip stresses predicted by theoretical fracture mechanics and allows stable propagation to occur; thus, viscous suction or other forces are not required to balance the crack tip stress as proposed by previous investigators. The western Woodlark Basin of Papua New Guinea is the site of a major low-angle detachment fault immediately ahead of the westward propagating spreading center. We present the results of two studies of this fault: one using reflection seismology to image the fault zone velocity structure and composition, and one using deep crustal refraction seismology to image the large-scale velocity structure of the fault and surrounding crust. Results from genetic algorithm inversion of seismic reflection data show that the fault contains a frictionally weak fault gouge layer and fluids, while results from seismic tomography show that the fault is a major rift boundary between the northern and southern rift margins of the western Woodlark Basin. We conclude that favorable conditions exist for frictional slip at angles of 30° or less and that this will be the last fault to form before the crust completely rifts apart to create new oceanic crust and lithosphere. The morphology of the rifting-spreading transitions in Woodlark Basin and Hess

  19. Investigating the Affinities and Persistence of VX Nerve Agent in Environmental Matrices

    SciTech Connect

    Love, A H; Vance, A L; Reynolds, J G; Davisson, M L

    2004-03-09

    Laboratory experiments were conducted to determine environmental variables that affect the affinities and persistence of the nerve agent O-ethyl S-(2-diisopropylaminoethyl) methylphosphonothiolate (VX) at dilute concentrations in environmental matrices. Quantitative analyses of VX and its degradation products were performed using LC-MS. Batch hydrolysis experiments demonstrated an increasing hydrolysis rate as pH increased, as shown in previous studies, but also indicated that dissolved aqueous constituents can cause significant differences in the absolute hydrolysis rate. Adsorption isotherms from batch aqueous experiments revealed that VX has a high affinity for hydrophobic organics, a moderate affinity for montmorillonite clay, and a very low affinity for an iron-oxyhydroxide soil mineral, goethite. The adsorption on goethite was increased with the presence of dissolved organic matter in solution. VX degraded rapidly when dried onto goethite, when an inner-sphere complex was forced. No enhanced degradation occurred with goethite in small amounts water. These results suggest that aqueous conditions have important controls on VX adsorption and degradation in the environment and a more mechanistic understanding of these controls is needed in order to enable accurate predictions of its long-term fate and persistence.

  20. Investigating the affinities and persistence of VX nerve agent in environmental matrices.

    PubMed

    Love, Adam H; Vance, Andrew L; Reynolds, John G; Davisson, M Lee

    2004-12-01

    Laboratory experiments were conducted to determine environmental variables that affect the affinities and persistence of the nerve agent O-ethyl S-(2-diisopropylaminoethyl) methylphosphonothiolate (VX) at dilute concentrations in environmental matrices. Quantitative analyses of VX and its degradation products were performed using LC-MS. Batch hydrolysis experiments demonstrated an increasing hydrolysis rate as pH increased, as shown in previous studies, but also indicated that dissolved aqueous constituents can cause significant differences in the absolute hydrolysis rate. Adsorption isotherms from batch aqueous experiments revealed that VX has a high affinity for hydrophobic organics, a moderate affinity for montmorillonite clay, and a very low affinity for an iron-oxyhydroxide soil mineral, goethite. The adsorption on goethite was increased with the presence of dissolved organic matter in solution. VX degraded rapidly when dried onto goethite, when specific adsorption was forced. No enhanced degradation occurred with goethite in small amounts of water. These results suggest that aqueous conditions have important controls on VX adsorption and degradation in the environment and a more mechanistic understanding of these controls is needed in order to enable accurate predictions of its long-term fate and persistence.

  1. Affinity improvement of a therapeutic antibody to methamphetamine and amphetamine through structure-based antibody engineering.

    PubMed

    Thakkar, Shraddha; Nanaware-Kharade, Nisha; Celikel, Reha; Peterson, Eric C; Varughese, Kottayil I

    2014-01-14

    Methamphetamine (METH) abuse is a worldwide threat, without any FDA approved medications. Anti-METH IgGs and single chain fragments (scFvs) have shown efficacy in preclinical studies. Here we report affinity enhancement of an anti-METH scFv for METH and its active metabolite amphetamine (AMP), through the introduction of point mutations, rationally designed to optimize the shape and hydrophobicity of the antibody binding pocket. The binding affinity was measured using saturation binding technique. The mutant scFv-S93T showed 3.1 fold enhancement in affinity for METH and 26 fold for AMP. The scFv-I37M and scFv-Y34M mutants showed enhancement of 94, and 8 fold for AMP, respectively. Structural analysis of scFv-S93T:METH revealed that the substitution of Ser residue by Thr caused the expulsion of a water molecule from the cavity, creating a more hydrophobic environment for the binding that dramatically increases the affinities for METH and AMP.

  2. Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling

    PubMed Central

    2015-01-01

    Small molecules that increase the oxygen affinity of human hemoglobin may reduce sickling of red blood cells in patients with sickle cell disease. We screened 38 700 compounds using small molecule microarrays and identified 427 molecules that bind to hemoglobin. We developed a high-throughput assay for evaluating the ability of the 427 small molecules to modulate the oxygen affinity of hemoglobin. We identified a novel allosteric effector of hemoglobin, di(5-(2,3-dihydro-1,4-benzodioxin-2-yl)-4H-1,2,4-triazol-3-yl)disulfide (TD-1). TD-1 induced a greater increase in oxygen affinity of human hemoglobin in solution and in red blood cells than did 5-hydroxymethyl-2-furfural (5-HMF), N-ethylmaleimide (NEM), or diformamidine disulfide. The three-dimensional structure of hemoglobin complexed with TD-1 revealed that monomeric units of TD-1 bound covalently to β-Cys93 and β-Cys112, as well as noncovalently to the central water cavity of the hemoglobin tetramer. The binding of TD-1 to hemoglobin stabilized the relaxed state (R3-state) of hemoglobin. TD-1 increased the oxygen affinity of sickle hemoglobin and inhibited in vitro hypoxia-induced sickling of red blood cells in patients with sickle cell disease without causing hemolysis. Our study indicates that TD-1 represents a novel lead molecule for the treatment of patients with sickle cell disease. PMID:25061917

  3. Studies toward bivalent κ opioids derived from salvinorin A: heteromethylation of the furan ring reduces affinity.

    PubMed

    Munro, Thomas A; Xu, Wei; Ho, Douglas M; Liu-Chen, Lee-Yuan; Cohen, Bruce M

    2013-12-20

    The recent crystal structure of the κ-opioid receptor (κ-OR) revealed, unexpectedly, that the antagonist JDTic is a bivalent ligand: in addition to the orthosteric pocket occupied by morphinans, JDTic also occupies a distinct (allotopic) pocket. Mutagenesis data suggest that salvinorin A (1) also binds to this allotopic pocket, adjacent to the aspartate residue that anchors the basic nitrogen atom of classical opiates (Asp138). It has been suggested that an H-bond donor appended to 1 might interact with Asp138, increasing affinity. Such a bivalent ligand might also possess altered functional selectivity. Based on modeling and known N-furanylmethyl opioid antagonists, we appended H-bond donors to the furan ring of 1. (Dimethylamino)methyl groups at C-15 or C-16 abolished affinity for κ-OR. Hydroxymethylation at C-16 was tolerated, but 15,16-bis-hydroxymethylation was not. Since allosteric modulators may go undetected in binding assays, we also tested these and other low-affinity derivatives of 1 for allosteric modulation of dynorphin A in the [(35)S]GTPγS assay. No modulation was detected. As an alternative attachment point for bivalent derivatives, we prepared the 2-(hydroxyethoxy)methyl ether, which retained high affinity for κ-OR. We discuss alternative design strategies for linked, fused or merged bivalent derivatives of 1.

  4. Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation

    PubMed Central

    Kepler, Thomas B.; Munshaw, Supriya; Wiehe, Kevin; Zhang, Ruijun; Yu, Jae-Sung; Woods, Christopher W.; Denny, Thomas N.; Tomaras, Georgia D.; Alam, S. Munir; Moody, M. Anthony; Kelsoe, Garnett; Liao, Hua-Xin; Haynes, Barton F.

    2014-01-01

    Affinity maturation of the antibody response is a fundamental process in adaptive immunity during which B-cells activated by infection or vaccination undergo rapid proliferation accompanied by the acquisition of point mutations in their rearranged immunoglobulin (Ig) genes and selection for increased affinity for the eliciting antigen. The rate of somatic hypermutation at any position within an Ig gene is known to depend strongly on the local DNA sequence, and Ig genes have region-specific codon biases that influence the local mutation rate within the gene resulting in increased differential mutability in the regions that encode the antigen-binding domains. We have isolated a set of clonally related natural Ig heavy chain–light chain pairs from an experimentally infected influenza patient, inferred the unmutated ancestral rearrangements and the maturation intermediates, and synthesized all the antibodies using recombinant methods. The lineage exhibits a remarkably uniform rate of improvement of the effective affinity to influenza hemagglutinin (HA) over evolutionary time, increasing 1000-fold overall from the unmutated ancestor to the best of the observed antibodies. Furthermore, analysis of selection reveals that selection and mutation bias were concordant even at the level of maturation to a single antigen. Substantial improvement in affinity to HA occurred along mutationally preferred paths in sequence space and was thus strongly facilitated by the underlying local codon biases. PMID:24795717

  5. Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation.

    PubMed

    Kepler, Thomas B; Munshaw, Supriya; Wiehe, Kevin; Zhang, Ruijun; Yu, Jae-Sung; Woods, Christopher W; Denny, Thomas N; Tomaras, Georgia D; Alam, S Munir; Moody, M Anthony; Kelsoe, Garnett; Liao, Hua-Xin; Haynes, Barton F

    2014-01-01

    Affinity maturation of the antibody response is a fundamental process in adaptive immunity during which B-cells activated by infection or vaccination undergo rapid proliferation accompanied by the acquisition of point mutations in their rearranged immunoglobulin (Ig) genes and selection for increased affinity for the eliciting antigen. The rate of somatic hypermutation at any position within an Ig gene is known to depend strongly on the local DNA sequence, and Ig genes have region-specific codon biases that influence the local mutation rate within the gene resulting in increased differential mutability in the regions that encode the antigen-binding domains. We have isolated a set of clonally related natural Ig heavy chain-light chain pairs from an experimentally infected influenza patient, inferred the unmutated ancestral rearrangements and the maturation intermediates, and synthesized all the antibodies using recombinant methods. The lineage exhibits a remarkably uniform rate of improvement of the effective affinity to influenza hemagglutinin (HA) over evolutionary time, increasing 1000-fold overall from the unmutated ancestor to the best of the observed antibodies. Furthermore, analysis of selection reveals that selection and mutation bias were concordant even at the level of maturation to a single antigen. Substantial improvement in affinity to HA occurred along mutationally preferred paths in sequence space and was thus strongly facilitated by the underlying local codon biases.

  6. Crystallographic structure of Ni-Co coating on the affinity adsorption of histidine-tagged protein.

    PubMed

    Chang, Yaw-Jen; Chen, Sheng-Zheng; Ho, Ching-Yuan

    2015-04-01

    The principle of immobilized metal affinity chromatography (IMAC) has been recently implemented for protein microarrays for the study of protein abundance and function. Ni-Co film fabricated by electrodeposition is a novel microarray surface in an alloy type for immobilizing histidine-tagged proteins based on IMAC. In this paper, the effects of crystallographic structures and surface properties of Ni-Co coatings, with and without the annealing process, on the immobilization of histidine-tagged proteins were systematically investigated. The experimental results reveal that the stronger hcp texture, due to a higher Co content, results in better affinity adsorption for histidine-tagged biotin. Nevertheless, the allotropic phase transformation from hcp to fcc, due to the annealing process, leads to the decrease of affinity adsorption. The wettability property and the surface roughness of Ni-Co coating are, however, not important factors. Obviously, the crystallographic structure of Ni-Co coating is the dominant factor for the specific affinity adsorption of histidine-tagged protein.

  7. Mechanism of high affinity inhibition of the human urate transporter URAT1

    PubMed Central

    Tan, Philip K.; Ostertag, Traci M.; Miner, Jeffrey N.

    2016-01-01

    Gout is caused by elevated serum urate levels, which can be treated using inhibitors of the uric acid transporter, URAT1. We exploited affinity differences between the human and rat transporters to map inhibitor binding sites in URAT1. Human-rat transporter chimeras revealed that human URAT1 serine-35, phenylalanine-365 and isoleucine-481 are necessary and sufficient to provide up to a 100-fold increase in affinity for inhibitors. Moreover, serine-35 and phenylalanine-365 are important for high-affinity interaction with the substrate urate. A novel URAT1 binding assay provides support for direct interaction with these amino acids; thus, current clinically important URAT1 inhibitors likely bind the same site in URAT1. A structural model suggests that these three URAT1 residues are in close proximity potentially projecting within the channel. Our results indicate that amino acids from several transmembrane segments functionally cooperate to form a high-affinity URAT1 inhibitor binding site that, when occupied, prevents substrate interactions. PMID:27713539

  8. Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies

    PubMed Central

    Wang, Shenshen; Mata-Fink, Jordi; Kriegsman, Barry; Hanson, Melissa; Irvine, Darrell J.; Eisen, Herman N.; Burton, Dennis R.; Wittrup, K. Dane; Kardar, Mehran; Chakraborty, Arup K.

    2015-01-01

    Summary Generation of potent antibodies by a mutation-selection process called affinity maturation is a key component of effective immune responses. Antibodies that protect against highly mutable pathogens must neutralize diverse strains. Developing effective immunization strategies to drive their evolution requires understanding how affinity maturation happens in an enviroment where variants of the same antigen are present. We present an in silico model of affinity maturation driven by antigen variants which reveals that induction of cross-reactive antibodies often occurs with low probability because conflicting selection forces, imposed by different antigen variants, can frustrate affinity maturation. We describe how variables such as temporal pattern of antigen administration influence the outcome of this frustrated evolutionary process. Our calculations predict, and experiments in mice with variant gp120 constructs of the HIV envelope protein confirm, that sequential immunization with antigen variants is preferred over a cocktail for induction of cross-reactive antibodies focused on the shared CD4 binding site epitope. PMID:25662010

  9. Effects of shear rate on propagation of blood clotting determined using microfluidics and numerical simulations.

    PubMed

    Runyon, Matthew K; Kastrup, Christian J; Johnson-Kerner, Bethany L; Ha, Thuong G Van; Ismagilov, Rustem F

    2008-03-19

    This paper describes microfluidic experiments with human blood plasma and numerical simulations to determine the role of fluid flow in the regulation of propagation of blood clotting. We demonstrate that propagation of clotting can be regulated by different mechanisms depending on the volume-to-surface ratio of a channel. In small channels, propagation of clotting can be prevented by surface-bound inhibitors of clotting present on vessel walls. In large channels, where surface-bound inhibitors are ineffective, propagation of clotting can be prevented by a shear rate above a threshold value, in agreement with predictions of a simple reaction-diffusion mechanism. We also demonstrate that propagation of clotting in a channel with a large volume-to-surface ratio and a shear rate below a threshold shear rate can be slowed by decreasing the production of thrombin, an activator of clotting. These in vitro results make two predictions, which should be experimentally tested in vivo. First, propagation of clotting from superficial veins to deep veins may be regulated by shear rate, which might explain the correlation between superficial thrombosis and the development of deep vein thrombosis (DVT). Second, nontoxic thrombin inhibitors with high binding affinities could be locally administered to prevent recurrent thrombosis after a clot has been removed. In addition, these results demonstrate the utility of simplified mechanisms and microfluidics for generating and testing predictions about the dynamics of complex biochemical networks.

  10. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  11. Dynamic crack propagation through nanoporous media

    NASA Astrophysics Data System (ADS)

    Nguyen, Thao; Wilkerson, Justin

    2015-06-01

    The deformation and failure of nanoporous metals may be considerably different than that of more traditional bulk porous metals. The length scales in traditional bulk porous metals are typically large enough for classic plasticity and buckling to be operative. However, the extremely small length scales associated with nanoporous metals may inhibit classic plasticity mechanisms. Here, we motivate an alternative nanovoid growth mechanism mediated by dislocation emission. Following an approach similar to Lubarda and co-workers, we make use of stability arguments applied to the analytic solutions of the elastic interactions of dislocations and voids to derive a simple stress-based criterion for emission activation. We then propose a dynamic nanovoid growth law that is motivated by the kinetics of dislocation emission. The resulting failure model is implemented into a commercial finite element software to simulate dynamic crack growth. The simulations reveal that crack propagation through a nanoporous media proceeds at somewhat faster velocities than through the more traditional bulk porous metal.

  12. Stress analysis of fracture of atherosclerotic plaques: crack propagation modeling.

    PubMed

    Rezvani-Sharif, Alireza; Tafazzoli-Shadpour, Mohammad; Kazemi-Saleh, Davood; Sotoudeh-Anvari, Maryam

    2016-12-09

    Traditionally, the degree of luminal obstruction has been used to assess the vulnerability of atherosclerotic plaques. However, recent studies have revealed that other factors such as plaque morphology, material properties of lesion components and blood pressure may contribute to the fracture of atherosclerotic plaques. The aim of this study was to investigate the mechanism of fracture of atherosclerotic plaques based on the mechanical stress distribution and fatigue analysis by means of numerical simulation. Realistic models of type V plaques were reconstructed based on histological images. Finite element method was used to determine mechanical stress distribution within the plaque. Assuming that crack propagation initiated at the sites of stress concentration, crack propagation due to pulsatile blood pressure was modeled. Results showed that crack propagation considerably changed the stress field within the plaque and in some cases led to initiation of secondary cracks. The lipid pool stiffness affected the location of crack formation and the rate and direction of crack propagation. Moreover, increasing the mean or pulse pressure decreased the number of cycles to rupture. It is suggested that crack propagation analysis can lead to a better recognition of factors involved in plaque rupture and more accurate determination of vulnerable plaques.

  13. Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria

    PubMed Central

    Pramana, Setia; Conte, Ianina; Brown, Biobele J.; Orimadegun, Adebola E.; Ajetunmobi, Wasiu A.; Afolabi, Nathaniel K.; Akinkunmi, Francis; Omokhodion, Samuel; Akinbami, Felix O.; Shokunbi, Wuraola A.; Kampf, Caroline; Pawitan, Yudi; Uhlén, Mathias; Sodeinde, Olugbemiro; Schwenk, Jochen M.; Wahlgren, Mats; Fernandez-Reyes, Delmiro; Nilsson, Peter

    2014-01-01

    Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria. PMID:24743550

  14. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition.

    PubMed

    Taylor, Martin S; LaCava, John; Mita, Paolo; Molloy, Kelly R; Huang, Cheng Ran Lisa; Li, Donghui; Adney, Emily M; Jiang, Hua; Burns, Kathleen H; Chait, Brian T; Rout, Michael P; Boeke, Jef D; Dai, Lixin

    2013-11-21

    LINE-1s are active human DNA parasites that are agents of genome dynamics in evolution and disease. These streamlined elements require host factors to complete their life cycles, whereas hosts have developed mechanisms to combat retrotransposition's mutagenic effects. As such, endogenous L1 expression levels are extremely low, creating a roadblock for detailed interactomic analyses. Here, we describe a system to express and purify highly active L1 RNP complexes from human suspension cell culture and characterize the copurified proteome, identifying 37 high-confidence candidate interactors. These data sets include known interactors PABPC1 and MOV10 and, with in-cell imaging studies, suggest existence of at least three types of compositionally and functionally distinct L1 RNPs. Among the findings, UPF1, a key nonsense-mediated decay factor, and PCNA, the polymerase-delta-associated sliding DNA clamp, were identified and validated. PCNA interacts with ORF2p via a PIP box motif; mechanistic studies suggest that this occurs during or immediately after target-primed reverse transcription.

  15. Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.

    PubMed

    Bachmann, Julie; Burté, Florence; Pramana, Setia; Conte, Ianina; Brown, Biobele J; Orimadegun, Adebola E; Ajetunmobi, Wasiu A; Afolabi, Nathaniel K; Akinkunmi, Francis; Omokhodion, Samuel; Akinbami, Felix O; Shokunbi, Wuraola A; Kampf, Caroline; Pawitan, Yudi; Uhlén, Mathias; Sodeinde, Olugbemiro; Schwenk, Jochen M; Wahlgren, Mats; Fernandez-Reyes, Delmiro; Nilsson, Peter

    2014-04-01

    Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.

  16. Affine connection form of Regge calculus

    NASA Astrophysics Data System (ADS)

    Khatsymovsky, V. M.

    2016-12-01

    Regge action is represented analogously to how the Palatini action for general relativity (GR) as some functional of the metric and a general connection as independent variables represents the Einstein-Hilbert action. The piecewise flat (or simplicial) spacetime of Regge calculus is equipped with some world coordinates and some piecewise affine metric which is completely defined by the set of edge lengths and the world coordinates of the vertices. The conjugate variables are the general nondegenerate matrices on the three-simplices which play the role of a general discrete connection. Our previous result on some representation of the Regge calculus action in terms of the local Euclidean (Minkowsky) frame vectors and orthogonal connection matrices as independent variables is somewhat modified for the considered case of the general linear group GL(4, R) of the connection matrices. As a result, we have some action invariant w.r.t. arbitrary change of coordinates of the vertices (and related GL(4, R) transformations in the four-simplices). Excluding GL(4, R) connection from this action via the equations of motion we have exactly the Regge action for the considered spacetime.

  17. [Separation of osteoclasts by lectin affinity chromatography].

    PubMed

    Itokazu, M; Tan, A; Tanaka, S

    1991-09-01

    Newborn rat calvaria bone cells obtained by digestion were fractionated on columns of wheat-germ agglutinin (WGA) sepharose 6MB for osteoclast isolation. The initial nonspecific binding cells which were passed through the WGA sepharose column by a buffer acquired a high enzyme activity of alkaline phosphatase, but not that of acid phosphatase. However, elution of cells using a buffer with the addition of N-acetyl-D-glucosamine resulted in a high acid phosphatase activity but no alkaline phosphatase activity. The former WGA binding negative fraction enriched osteoblasts averaging 30 microns in size. The latter WGA binding positive fraction enriched osteoclasts ranging from 20 microns to 60 microns in size. The electron-microscope clearly demonstrated the cellular details of osteoclasts. Isolated cell counts showed a ratio of six to four. These results indicate that our method of osteoclast isolation is simple and useful in lectin affinity chromatography because all cells have sugar moieties on their surface and the binding of osteoclasts can be reversed by the addition of specific lectin-binding sugars to the eluting buffer.

  18. Prostate Cancer and Bone: The Elective Affinities

    PubMed Central

    2014-01-01

    The onset of metastases dramatically changes the prognosis of prostate cancer patients, determining increased morbidity and a drastic fall in survival expectancy. Bone is a common site of metastases in few types of cancer, and it represents the most frequent metastatic site in prostate cancer. Of note, the prevalence of tumor relapse to the bone appears to be increasing over the years, likely due to a longer overall survival of prostate cancer patients. Bone tropism represents an intriguing challenge for researchers also because the preference of prostate cancer cells for the bone is the result of a sequential series of targetable molecular events. Many factors have been associated with the peculiar ability of prostate cancer cells to migrate in bone marrow and to determine mixed osteoblastic/osteolytic lesions. As anticipated by the success of current targeted therapy aimed to block bone resorption, a better understanding of molecular affinity between prostate cancer and bone microenvironment will permit us to cure bone metastasis and to improve prognosis of prostate cancer patients. PMID:24971315

  19. Multiplexed protein profiling by sequential affinity capture

    PubMed Central

    Ayoglu, Burcu; Birgersson, Elin; Mezger, Anja; Nilsson, Mats; Uhlén, Mathias; Nilsson, Peter

    2016-01-01

    Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off‐target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi‐automated sequential capture assay. This novel bead‐based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read‐out by a secondary capture bead array. We demonstrate in a proof‐of‐concept setting that target detection via two sequential affinity interactions reduced off‐target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA‐based signal amplification, and demonstrate the applicability of the dual capture bead‐based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond. PMID:26935855

  20. Cambrian trilobites with Siberian affinities, southwestern Alaska

    SciTech Connect

    Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

    1985-02-01

    Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

  1. Affinity of guanosine derivatives for polycytidylate revisited

    NASA Technical Reports Server (NTRS)

    Kanavarioti, A.; Hurley, T. B.; Baird, E. E.

    1995-01-01

    Evidence is presented for complexation of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) with polycytidylate (poly(C)) at pH 8.0 and 23 degrees C in the presence of 1.0 M NaCl2 and 0.2 M MgCl2 in water. The association of 2-MeImpG with poly(C) was investigated using UV-vis spectroscopy as well as by monitoring the kinetics of the nucleophilic substitution reaction of the imidazole moiety by amines. The results of both methods are consistent with moderately strong poly(C) 2-MeImpG complexation and the spectrophotometric measurements allowed the construction of a binding isotherm with a concentration of 2-MeImpG equal to 5.55 +/- 0.15 mM at half occupancy. UV spectroscopy was employed to establish the binding of other guanosine derivatives on poly(C). These derivatives are guanosine 5'-monophosphate (5'GMP), guanosine 5'-monophosphate imidazolide (ImpG), and guanosine 5'-monophosphate morpholidate (morpG). Within experimental error these guanosine derivatives exhibit the same affinity for poly(C) as 2-MeImpG.

  2. Macroporous chitin affinity membranes for lysozyme separation.

    PubMed

    Ruckenstein, E; Zeng, X

    1997-12-20

    Macroporous chitin membranes with high, controlled porosity and good mechanical properties have been prepared using a technique developed in this laboratory based on silica particles as porogen. They were employed for the affinity separation of lysozyme. Chitin membranes (1 mm thickness) can be operated at high fluxes (>/=1.1 mL/min/cm(2)) corresponding to pressure drops >/=2 psi. Their adsorption capacity for lysozyme ( approximately 50 mg/mL membrane) is by an order of magnitude higher than that of the chitin beads employed in column separation. In a binary mixture of lysozyme and ovalbumin, the membranes showed very high selectivity towards lysozyme. The effect of some important operation parameters, such as the flow rates during loading and elution were investigated. Lysozyme of very high purity (>98%) was obtained from a mixture of lysozyme and ovalbumin, and from egg white. The results indicate that the macroporous chitin membranes can be used for the separation, purification, and recovery of lysozyme at large scale. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 610-617, 1997.

  3. Phosphorylation of a chloroplast RNA-binding protein changes its affinity to RNA.

    PubMed Central

    Lisitsky, I; Schuster, G

    1995-01-01

    An RNA-binding protein of 28 kDa (28RNP) was previously isolated from spinach chloroplasts and found to be required for 3' end-processing of chloroplast mRNAs. The amino acid sequence of 28RNP revealed two approximately 80 amino-acid RNA-binding domains, as well as an acidic- and glycine-rich amino terminal domain. Upon analysis of the RNA-binding properties of the 'native' 28RNP in comparison to the recombinant bacterial expressed protein, differences were detected in the affinity to some chloroplastic 3' end RNAs. It was suggested that post-translational modification can modulate the affinity of the 28RNP in the chloroplast to different RNAs. In order to determine if phosphorylation accounts for this post-translational modification, we examined if the 28RNP is a phosphoprotein and if it can serve as a substrate for protein kinases. It was found that the 28RNP was phosphorylated when intact chloroplasts were metabolically labeled with [32P] orthophosphate, and that recombinant 28RNP served as an excellent substrate in vitro for protein kinase isolated from spinach chloroplasts or recombinant alpha subunit of maize casein kinase II. The 28RNP was apparently phosphorylated at one site located in the acidic domain at the N-terminus of the protein. Site-directed mutagenesis of the serines in that region revealed that the phosphorylation of the protein was eliminated when serine number 22 from the N-terminus was changed to tryptophan. RNA-binding analysis of the phosphorylated 28RNP revealed that the affinity of the phosphorylated protein was reduced approximately 3-4-fold in comparison to the non-phosphorylated protein. Therefore, phosphorylation of the 28RNP modulates its affinity to RNA and may play a significant role in its biological function in the chloroplast. Images PMID:7630729

  4. Germinal center reaction: antigen affinity and presentation explain it all.

    PubMed

    Oropallo, Michael A; Cerutti, Andrea

    2014-07-01

    The selection and expansion of B cells undergoing affinity maturation in the germinal center is a hallmark of humoral immunity. A recent paper in Nature provides new insights into the relationships between the affinity of the immunoglobulin receptor for antigen, the ability of B cells to present antigen to T cells, and the processes of selection, mutation, and clonal expansion in the germinal center.

  5. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  6. Tending to Change: Toward a Situated Model of Affinity Spaces

    ERIC Educational Resources Information Center

    Bommarito, Dan

    2014-01-01

    The concept of affinity spaces, a theoretical construct used to analyze literate activity from a spatial perspective, has gained popularity among scholars of literacy studies and, particularly, video-game studies. This article seeks to expand current notions of affinity spaces by identifying key assumptions that have limited researchers'…

  7. Sound propagation in choked ducts

    NASA Technical Reports Server (NTRS)

    Hersh, A. S.; Liu, C. Y.

    1976-01-01

    The linearized equations describing the propagation of sound in variable area ducts containing flow are shown to be singular when the duct mean flow is sonic. The singularity is removed when previously ignored nonlinear terms are retained. The results of a numerical study, for the case of plane waves propagating in a one-dimensional converging-diverging duct, show that the sound field is adequately described by the linearized equations only when the axial mean flow Mach number at the duct throat M sub th 0.6. For M sub th 0.6, the numerical results showed that acoustic energy flux was not conserved. An attempt was made to extend the study to include the nonlinear behavior of the sound field. Meaningful results were not obtained due, primarily, to numerical difficulties.

  8. Exact propagators in harmonic superspace

    NASA Astrophysics Data System (ADS)

    Kuzenko, Sergei M.

    2004-10-01

    Within the background field formulation in harmonic superspace for quantum N = 2 super-Yang-Mills theories, the propagators of the matter, gauge and ghost superfields possess a complicated dependence on the SU(2) harmonic variables via the background vector multiplet. This dependence is shown to simplify drastically in the case of an on-shell vector multiplet. For a covariantly constant background vector multiplet, we exactly compute all the propagators. In conjunction with the covariant multi-loop scheme developed in arxiv:hep-th/0302205, these results provide an efficient (manifestly N = 2 supersymmetric) technical setup for computing multi-loop quantum corrections to effective actions in N = 2 supersymmetric gauge theories, including the N = 4 super-Yang-Mills theory.

  9. Atmospheric propagation of THz radiation.

    SciTech Connect

    Wanke, Michael Clement; Mangan, Michael A.; Foltynowicz, Robert J.

    2005-11-01

    In this investigation, we conduct a literature study of the best experimental and theoretical data available for thin and thick atmospheres on THz radiation propagation from 0.1 to 10 THz. We determined that for thick atmospheres no data exists beyond 450 GHz. For thin atmospheres data exists from 0.35 to 1.2 THz. We were successful in using FASE code with the HITRAN database to simulate the THz transmission spectrum for Mauna Kea from 0.1 to 2 THz. Lastly, we successfully measured the THz transmission spectra of laboratory atmospheres at relative humidities of 18 and 27%. In general, we found that an increase in the water content of the atmosphere led to a decrease in the THz transmission. We identified two potential windows in an Albuquerque atmosphere for THz propagation which were the regions from 1.2 to 1.4 THz and 1.4 to 1.6 THz.

  10. Fracture propagation, pipe deformation study

    SciTech Connect

    Aloe, A.; Di Candia, A.; Bramante, M.

    1983-04-15

    Shear fracture propagation has become an important research subject connected with design aspects of gas pipelines. Difficulties involved in predicting safe service conditions from pure theoretical studies require 1:1 scale experiments. Through these tests, semiempirical design criteria was formulated where the minimum level of material quality, indicated by Charpy V energy in the ductile range, is determined as a function of pipe geometry and hoop stress. Disagreements exist among these criteria. Different arrest energy predictions at high hoop stresses and different effects ascribed to the thickness have called for further research in the field. Some interesting indications were obtained about shape and size of the plastic zone ahead of the propagating crack. Burst tests have been conducted and are discussed.

  11. Special Topics in HF Propagation

    DTIC Science & Technology

    1979-11-01

    data for the prediction of auroral absorption experienced by high-frequency radio waves: Basler (1965), Gorbushina et al. (1969), Agy (1970), Vargas ...Thomas (1959), Studies in polar blackout morphology, URSI-AGI, Com- mittee Report. Vargas -Vila, R. (1972), Auroral absorption predictions for high...cuide wa]ls in mho/m permeability of the propagation medium in henry /m E. permittivity of the propagat.on medium iiu fa-ad/m. For TE. modes, thi-s

  12. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Chuong

    1995-01-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self explanatory.

  13. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Choung

    1994-01-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self-explanatory; however, a sample run of the CCIR rain attenuation model is presented.

  14. A database for propagation models

    NASA Astrophysics Data System (ADS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Chuong

    1995-08-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self explanatory.

  15. UHF Radiowave Propagation through Forests

    DTIC Science & Technology

    1982-09-01

    sde It nece sary and Identify b block number) " A model for UHF radiowave propagation thzough a forest of tree trunks, branches, and leaves is...all having prescribed location and orientation statistics. Tree trunks are modelled as infinitely-long, circular, lossy-di- electric cylinders...results. An anisotropic half-space model of the forest is developed based upon the effective dyadic susceptibility and the direct-, reflected-, and

  16. GOES dynamic propagation of attitude

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis; Seidewitz, ED; Chu, Don; Rowe, John N.

    1988-01-01

    The spacecraft in the next series of Geostationary Operational Environmental Satellites (GOES-Next) are Earth pointing and have 5-year mission lifetimes. Because gyros can be depended on only for a few years of continuous use, they will be turned off during routine operations. This means attitude must, at times, be determined without benefit of gyros and, often, using only Earth sensor data. To minimize the interruption caused by dumping angular momentum, these spacecraft have been designed to reduce the environmental torque acting on them and incorporate an adjustable solar trim tab for fine adjustment. A new support requirement for GOES-Next is that of setting the solar trim tab. Optimizing its setting requires an estimate of the unbalanced torque on the spacecraft. These two requirements, determining attitude without gyros and estimating the external torque, are addressed by replacing or supplementing the gyro propagation with a dynamic one, that is, one that integrates the rigid body equations of motion. By processing quarter-orbit or longer batches, this approach takes advantage of roll-yaw coupling to observe attitude completely without Sun sensor data. Telemetered momentum wheel speeds are used as observations of the unbalanced external torques. GOES-Next provides a unique opportunity to study dynamic attitude propagation. The geosynchronous altitude and adjustable trim tab minimize the external torque and its uncertainty, making long-term dynamic propagation feasible. This paper presents the equations for dynamic propagation, an analysis of the environmental torques, and an estimate of the accuracies obtainable with the proposed method.

  17. Camelid VHH affinity ligands enable separation of closely related biopharmaceuticals

    PubMed Central

    Pabst, Timothy M.; Wendeler, Michaela; Wang, Xiangyang; Bezemer, Sandra; Hermans, Pim

    2016-01-01

    Abstract Interest in new and diverse classes of molecules such as recombinant toxins, enzymes, and blood factors continues to grow for use a biotherapeutics. Compared to monoclonal antibodies, these novel drugs typically lack a commercially available affinity chromatography option, which leads to greater process complexity, longer development timelines, and poor platformability. To date, for both monoclonal antibodies and novel molecules, affinity chromatography has been mostly reserved for separation of process‐related impurities such as host cell proteins and DNA. Reports of affinity purification of closely related product variants and modified forms are much rarer. In this work we describe custom affinity chromatography development using camelid VHH antibody fragments as "tunable" immunoaffinity ligands for separation of product‐related impurities. One example demonstrates high selectivity for a recombinant immunotoxin where no binding was observed for an undesired deamidated species. Also discussed is affinity purification of a coagulation factor through specific recognition of the gamma‐carboxylglutamic acid domain. PMID:27677057

  18. Affinity Monolith-Integrated Microchips for Protein Purification and Concentration.

    PubMed

    Gao, Changlu; Sun, Xiuhua; Wang, Huaixin; Qiao, Wei; Hu, Bo

    2016-01-01

    Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture.

  19. Optimal T-cell receptor affinity for inducing autoimmunity

    PubMed Central

    Koehli, Sabrina; Naeher, Dieter; Galati-Fournier, Virginie; Zehn, Dietmar; Palmer, Ed

    2014-01-01

    T-cell receptor affinity for self-antigen has an important role in establishing self-tolerance. Three transgenic mouse strains expressing antigens of variable affinity for the OVA transgenic-I T-cell receptor were generated to address how TCR affinity affects the efficiency of negative selection, the ability to prime an autoimmune response, and the elimination of the relevant target cell. Mice expressing antigens with an affinity just above the negative selection threshold exhibited the highest risk of developing experimental autoimmune diabetes. The data demonstrate that close to the affinity threshold for negative selection, sufficient numbers of self-reactive T cells escape deletion and create an increased risk for the development of autoimmunity. PMID:25411315

  20. Detection of protein-protein interactions using tandem affinity purification.

    PubMed

    Goodfellow, Ian; Bailey, Dalan

    2014-01-01

    Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.

  1. Affinity Regulates Spatial Range of EGF Receptor Autocrine Ligand Binding

    SciTech Connect

    Dewitt, Ann; Iida, Tomoko; Lam, Ho-Yan; Hill, Virginia; Wiley, H S.; Lauffenburger, Douglas A.

    2002-08-08

    Proper spatial localization of EGFR signaling activated by autocrine ligands represents a critical factor in embryonic development as well as tissue organization and function, and ligand/receptor binding affinity is among the molecular and cellular properties suggested to play a role in governing this localization. The authors employ a computational model to predict how receptor-binding affinity affects local capture of autocrine ligand vis-a-vis escape to distal regions, and provide experimental test by constructing cell lines expressing EGFR along with either wild-type EGF or a low-affinity mutant, EGF{sup L47M}. The model predicts local capture of a lower affinity autocrine ligand to be less efficient when the ligand production rate is small relative to receptor appearance rate. The experimental data confirm this prediction, demonstrating that cells can use ligand/receptor binding affinity to regulate ligand spatial distribution when autocrine ligand production is limiting for receptor signaling.

  2. Generation of metastatic melanoma specific antibodies by affinity purification

    PubMed Central

    Schütz, Birgit; Koppensteiner, Anita; Schörghofer, David; Kinslechner, Katharina; Timelthaler, Gerald; Eferl, Robert; Hengstschläger, Markus; Missbichler, Albert; Hundsberger, Harald; Mikula, Mario

    2016-01-01

    Melanoma is the most aggressive type of skin cancer and one of the most frequent tumours in young adults. Identification of primary tumours prone to develop metastasis is of paramount importance for further patient stratification. However, till today, no markers exist that are routinely used to predict melanoma progression. To ameliorate this problem, we generated antiserum directed against metastatic melanoma tissue lysate and applied a novel approach to purify the obtained serum via consecutive affinity chromatography steps. The established antibody, termed MHA-3, showed high reactivity against metastatic melanoma cell lines both in vitro and in vivo. We also tested MHA-3 on 227 melanoma patient samples and compared staining with the melanoma marker S100b. Importantly, MHA-3 was able to differentiate between metastatic and non-metastatic melanoma samples. By proteome analysis we identified 18 distinct antigens bound by MHA-3. Combined expression profiling of all identified proteins revealed a significant survival difference in melanoma patients. In conclusion, we developed a polyclonal antibody, which is able to detect metastatic melanoma on paraffin embedded sections. Hence, we propose that this antibody will represent a valuable additional tool for precise melanoma diagnosis. PMID:27853253

  3. Human whole-blood oxygen affinity: effect of temperature.

    PubMed

    Zwart, A; Kwant, G; Oeseburg, B; Zijlstra, W G

    1984-08-01

    phe effect of temperature changes on human whole-blood O2 affinity was measured in the blood of six healthy donors over almost the entire O2 saturation (SO2) range (1-99%). The results showed that temperature has no influence on the shape of the O2 dissociation curve, implying that the temperature coefficient (delta log PO2/delta T) is independent of SO2. Simultaneous measurements of the total (proton) Haldane factor (delta[HbH]/[delta HbO2]) at the five temperatures under study (22, 27, 32, 37, and 42 degrees C) revealed that this factor depends on temperature. The liberation of protons from hemoglobin appeared to be linear with respect to changes in SO2. We therefore conclude that the (proton) Bohr factor (H+ factor) is dependent on temperature over the entire SO2 range in the same way as previously described for SO2 = 50%. The exothermic oxygenation reaction in whole blood was accompanied by a heat evolution (delta HO2) of 42.7 kJ/mol (monomeric) hemoglobin.

  4. Jet propagation through energetic materials

    SciTech Connect

    Pincosy, P; Poulsen, P

    2004-01-08

    In applications where jets propagate through energetic materials, they have been observed to become sufficiently perturbed to reduce their ability to effectively penetrate subsequent material. Analytical calculations of the jet Bernoulli flow provides an estimate of the onset and extent of such perturbations. Although two-dimensional calculations show the back-flow interaction pressure pulses, the symmetry dictates that the flow remains axial. In three dimensions the same pressure impulses can be asymmetrical if the jet is asymmetrical. The 3D calculations thus show parts of the jet having a significant component of radial velocity. On the average the downstream effects of this radial flow can be estimated and calculated by a 2D code by applying a symmetrical radial component to the jet at the appropriate position as the jet propagates through the energetic material. We have calculated the 3D propagation of a radio graphed TOW2 jet with measured variations in straightness and diameter. The resultant three-dimensional perturbations on the jet result in radial flow, which eventually tears apart the coherent jet flow. This calculated jet is compared with jet radiographs after passage through the energetic material for various material thickness and plate thicknesses. We noted that confinement due to a bounding metal plate on the energetic material extends the pressure duration and extent of the perturbation.

  5. Turbofan Acoustic Propagation and Radiation

    NASA Technical Reports Server (NTRS)

    Eversman, Walter

    2000-01-01

    This document describes progress in the development of finite element codes for the prediction of near and far field acoustic radiation from the inlet and aft fan ducts of turbofan engines. The report consists of nine papers which have appeared in archival journals and conference proceedings, or are presently in review for publication. Topics included are: 1. Aft Fan Duct Acoustic Radiation; 2. Mapped Infinite Wave Envelope Elements for Acoustic Radiation in a Uniformly Moving Medium; 3. A Reflection Free Boundary Condition for Propagation in Uniform Flow Using Mapped Infinite Wave Envelope Elements; 4. A Numerical Comparison Between Multiple-Scales and FEM Solution for Sound Propagation in Lined Flow Ducts; 5. Acoustic Propagation at High Frequencies in Ducts; 6. The Boundary Condition at an Impedance Wall in a Nonuniform Duct with Potential Flow; 7. A Reverse Flow Theorem and Acoustic Reciprocity in Compressible Potential Flows; 8. Reciprocity and Acoustics Power in One Dimensional Compressible Potential Flows; and 9. Numerical Experiments on Acoustic Reciprocity in Compressible Potential Flows.

  6. Sound Propagation in the Atmosphere

    NASA Astrophysics Data System (ADS)

    Attenborough, Keith

    Propagation of sound close to the ground outdoors involves geometric spreading, air absorption, interaction with the ground, barriers, vegetation and refraction associated with wind and temperature gradients. After a brief survey of historical aspects of the study of outdoor sound and its applications, this chapter details the physical principles associated with various propagation effects, reviews data that demonstrate them and methods for predicting them. The discussion is concerned primarily with the relatively short ranges and spectra of interest when predicting and assessing community noise rather than the frequencies and long ranges of concern, for example, in infrasonic global monitoring or used for remote sensing of the atmosphere. Specific phenomena that are discussed include spreading losses, atmospheric absorption, diffraction by barriers and buildings, interaction of sound with the ground (ground waves, surface waves, ground impedance associated with porosity and roughness, and elasticity effects), propagation through crops, shrubs and trees, wind and temperature gradient effects, shadow zones and incoherence due to atmospheric turbulence. The chapter concludes by suggesting a few areas that require further research.

  7. Transequatorial Propagation and Depletion Precursors

    NASA Astrophysics Data System (ADS)

    Miller, E. S.; Bust, G. S.; Kaeppler, S. R.; Frissell, N. A.; Paxton, L. J.

    2014-12-01

    The bottomside equatorial ionosphere in the afternoon and evening sector frequently evolves rapidly from smoothly stratified to violently unstable with large wedges of depleted plasma growing through to the topside on timescales of a few tens of minutes. These depletions have numerous practical impacts on radio propagation, including amplitude scintillation, field-aligned irregularity scatter, HF blackouts, and long-distance transequatorial propagation at frequencies above the MUF. Practical impacts notwithstanding, the pathways and conditions under which depletions form remain a topic of vigorous inquiry some 80 years after their first report. Structuring of the pre-sunset ionosphere---morphology of the equatorial anomalies and long-wavelength undulations of the isodensity contours on the bottomside---are likely to hold some clues to conditions that are conducive to depletion formation. The Conjugate Depletion Experiment is an upcoming transequatorial forward-scatter HF/VHF experiment to investigate pre-sunset undulations and their connection with depletion formation. We will present initial results from the Conjugate Depletion Experiment, as well as a companion analysis of a massive HF propagation data set.

  8. Calculations of precursor propagation in dispersive dielectrics.

    SciTech Connect

    Bacon, Larry Donald

    2003-08-01

    The present study is a numerical investigation of the propagation of electromagnetic transients in dispersive media. It considers propagation in water using Debye and composite Rocard-Powles-Lorentz models for the complex permittivity. The study addresses this question: For practical transmitted spectra, does precursor propagation provide any features that can be used to advantage over conventional signal propagation in models of dispersive media of interest? A companion experimental study is currently in progress that will attempt to measure the effects studied here.

  9. Confining crack propagation in defective graphene.

    PubMed

    López-Polín, Guillermo; Gómez-Herrero, Julio; Gómez-Navarro, Cristina

    2015-03-11

    Crack propagation in graphene is essential to understand mechanical failure in 2D materials. We report a systematic study of crack propagation in graphene as a function of defect content. Nanoindentations and subsequent images of graphene membranes with controlled induced defects show that while tears in pristine graphene span microns length, crack propagation is strongly reduced in the presence of defects. Accordingly, graphene oxide exhibits minor crack propagation. Our work suggests controlled defect creation as an approach to avoid catastrophic failure in graphene.

  10. Chasing polys: Interdisciplinary affinity and its connection to physics identity

    NASA Astrophysics Data System (ADS)

    Scott, Tyler D.

    This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity

  11. Enzyme- and affinity biomolecule-mediated polymerization systems for biological signal amplification and cell screening.

    PubMed

    Malinowska, Klara H; Nash, Michael A

    2016-06-01

    Enzyme-mediated polymerization and polymerization-based signal amplification have emerged as two closely related techniques that are broadly applicable in the nanobio sciences. We review recent progress on polymerization systems mediated by biological molecules (e.g., affinity molecules and enzymes), and highlight newly developed formats and configurations of these systems to perform such tasks as non-instrumented biodetection, synthesis of core-shell nanomaterials, isolation of rare cells, and high-throughput screening. We discuss useful features of biologically mediated polymerization systems, such as multiple mechanisms of amplification (e.g., enzymatic, radical chain propagation), and the ability to localize structures at interfaces and at cell surfaces with microscopic spatial confinement. We close with a perspective on desirable improvements that need to be addressed to adapt these molecular systems to future applications.

  12. Japanese propagation experiments with ETS-5

    NASA Technical Reports Server (NTRS)

    Ikegami, Tetsushi

    1989-01-01

    Propagation experiments for maritime, aeronautical, and land mobile satellite communications were performed using Engineering Test Satellite-Five (ETS-5). The propagation experiments are one of major mission of Experimental Mobile Satellite System (EMSS) which is aimed for establishing basic technology for future general mobile satellite communication systems. A brief introduction is presented for the experimental results on propagation problems of ETS-5/EMSS.

  13. Understanding and Predicting Urban Propagation Losses

    DTIC Science & Technology

    2009-09-01

    available, the vast variety of physical cond Propagation Loss Tool will also be entered into a variety of examples, to test a few of the propagation loss...Model for Urban Areas. Rep. Silva, Junior, Edgar, and Gilberto A. Carrijo. "A Vectorial Istanbul: Bogazici University. Analysis of UHF Propagation

  14. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  15. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  16. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  17. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  18. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation. [Amdt. 195-45, 56 FR 26926, June 12, 1991]...

  19. Affinity capillary electrophoresis: the theory of electromigration.

    PubMed

    Dubský, Pavel; Dvořák, Martin; Ansorge, Martin

    2016-12-01

    We focus on the state-of-the-art theory of electromigration under single and multiple complexation equilibrium. Only 1:1 complexation stoichiometry is discussed because of its unique status in the field of affinity capillary electrophoresis (ACE). First, we summarize the formulas for the effective mobility in various ACE systems as they appeared since the pioneering days in 1992 up to the most recent theories till 2015. Disturbing phenomena that do not alter the mobility of the analyte directly but cause an unexpected peak broadening have been studied only recently and are also discussed in this paper. Second, we turn our attention to the viscosity effects in ACE. Change in the background electrolyte viscosity is unavoidable in ACE but numerous observations scattered throughout the literature have not been reviewed previously. This leads to an uncritical employment of correction factors that may or may not be appropriate in practice. Finally, we consider the ionic strength effects in ACE, too. Limitations of the current theories are also discussed and the tasks identified where open problems still prevail. Graphical Abstract A weak base (A) undergoes an acidic-basic equilibria (in blue) and migrates with an electrophoretic mobility of [Formula: see text]. Simultaneously, it interacts with a selector (sel) while the analyte-selector complex migrates with an electrophoretic mobility of [Formula: see text]. The strength of the interaction (in orange) is governed by the binding constant, K A , and the concentration of the selector, c sel . This all gives the analyte an effective mobility of [Formula: see text] and moves it out of the zero position (EOF; right top insert). The interaction of the positively charged analyte with the neutral selector slows down the analyte with increasing selector concentration (right bottom insert).

  20. The mammalian profilin isoforms display complementary affinities for PIP2 and proline-rich sequences.

    PubMed

    Lambrechts, A; Verschelde, J L; Jonckheere, V; Goethals, M; Vandekerckhove, J; Ampe, C

    1997-02-03

    We present a study on the binding properties of the bovine profilin isoforms to both phosphatidylinositol 4,5-bisphosphate (PIP2) and proline-rich peptides derived from vasodilator-stimulated phosphoprotein (VASP) and cyclase-associated protein (CAP). Using microfiltration, we show that compared with profilin II, profilin I has a higher affinity for PIP2. On the other hand, fluorescence spectroscopy reveals that proline-rich peptides bind better to profilin II. At micromolar concentrations, profilin II dimerizes upon binding to proline-rich peptides. Circular dichroism measurements of profilin II reveal a significant conformational change in this protein upon binding of the peptide. We show further that PIP2 effectively competes for binding of profilin I to poly-L-proline, since this isoform, but not profilin II, can be eluted from a poly-L-proline column with PIP2. Using affinity chromatography on either profilin isoform, we identified profilin II as the preferred ligand for VASP in bovine brain extracts. The complementary affinities of the profilin isoforms for PIP2 and the proline-rich peptides offer the cell an opportunity to direct actin assembly at different subcellular localizations through the same or different signal transduction pathways.

  1. Genetic and functional diversity of propagating cells in glioblastoma.

    PubMed

    Piccirillo, Sara G M; Colman, Sue; Potter, Nicola E; van Delft, Frederik W; Lillis, Suzanne; Carnicer, Maria-Jose; Kearney, Lyndal; Watts, Colin; Greaves, Mel

    2015-01-13

    Glioblastoma (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three) that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo.

  2. Preorganized Peptide Scaffolds as Mimics of Phosphorylated Proteins Binding Sites with a High Affinity for Uranyl.

    PubMed

    Starck, Matthieu; Sisommay, Nathalie; Laporte, Fanny A; Oros, Stéphane; Lebrun, Colette; Delangle, Pascale

    2015-12-07

    Cyclic peptides with two phosphoserines and two glutamic acids were developed to mimic high-affinity binding sites for uranyl found in proteins such as osteopontin, which is believed to be a privileged target of this ion in vivo. These peptides adopt a β-sheet structure that allows the coordination of the latter amino acid side chains in the equatorial plane of the dioxo uranyl cation. Complementary spectroscopic and analytical methods revealed that these cyclic peptides are efficient uranyl chelating peptides with a large contribution from the phosphorylated residues. The conditional affinity constants were measured by following fluorescence tryptophan quenching and are larger than 10(10) at physiological pH. These compounds are therefore promising models for understanding uranyl chelation by proteins, which is relevant to this actinide ion toxicity.

  3. Pre-Yield Non-Affine Fluctuations and A Hidden Critical Point in Strained Crystals

    PubMed Central

    Das, Tamoghna; Ganguly, Saswati; Sengupta, Surajit; Rao, Madan

    2015-01-01

    A crystalline solid exhibits thermally induced localised non-affine droplets in the absence of external stress. Here we show that upon an imposed shear, the size of these droplets grow until they percolate at a critical strain, well below the value at which the solid begins to yield. This critical point does not manifest in most thermodynamic or mechanical properties, but is hidden and reveals itself in the onset of inhomogeneities in elastic moduli, marked changes in the appearance and local properties of non-affine droplets and a sudden enhancement in defect pair concentration. Slow relaxation of stress and an-elasticity appear as observable dynamical consequences of this hidden criticality. Our results may be directly verified in colloidal crystals with video microscopy techniques but are expected to have more general validity. PMID:26039380

  4. Studies on the binding affinity of anticancer drug mitoxantrone to chromatin, DNA and histone proteins

    PubMed Central

    Hajihassan, Zahra; Rabbani-Chadegani, Azra

    2009-01-01

    Mitoxantrone is a potent antitumor drug, widely used in the treatment of various cancers. In the present study, we have investigated and compared the affinity of anticancer drug, mitoxantrone, to EDTA-soluble chromatin (SE-chromatin), DNA and histones employing UV/Vis, fluorescence, CD spectroscopy, gel electrophoresis and equilibrium dialysis techniques. The results showed that the interaction of mitoxantrone with SE-chromatin proceeds into compaction/aggregation as revealed by reduction in the absorbencies at 608 and 260 nm (hypochromicity) and disappearance of both histones and DNA on the gels. Mitoxantrone interacts strongly with histone proteins in solution making structural changes in the molecule as shown by CD and fluorescence analysis. The binding isotherms demonstrate a positive cooperative binding pattern for the chromatin- mitoxantrone interaction. It is suggested higher binding affinity of mitoxantrone to chromatin compared to DNA implying that the histone proteins may play an important role in the chromatin- mitoxantrone interaction process. PMID:19284573

  5. Effects of acid diffusibility and affinity to cellulose on strength loss of polycarboxylic acid crosslinked fabrics.

    PubMed

    Ji, Bolin; Zhao, Cunyi; Yan, Kelu; Sun, Gang

    2016-06-25

    1,2,3,4-Butanetetracarboxylic acid (BTCA) imparts good anti-wrinkle property to cotton fabrics and results in significant strength loss due to cross-linking and acid degradation of cellulose simultaneously. However, benzophenone-3,3',4,4'- tetracarboxylic acid (BPTCA), an aromatic acid, crosslinks cellulose effectively but causes less strength loss to the products under similar conditions. The difference in damages to cellulose fibers was analyzed by using diffusibility and corresponding affinity of the acids to cellulose fibers, which were estimated by their molecular sizes and Hansen solubility parameters (HSP). Both experimental results and theoretical speculations revealed consistent agreement, indicating that smaller acid molecules could diffuse into cellulose fiber more rapidly and deeply, resulting in more acid degradation. Besides, the aliphatic acid such as BTCA has higher molecular affinity than BPTCA to cellulose, causing additional more degradation of cellulose. Both factors are potential reasons of the observed more severe tensile strength loss of the BTCA treated cotton fabrics.

  6. Cutting line determination for plant propagation

    NASA Astrophysics Data System (ADS)

    Lo, Li-Yun; Hsia, Chi-Chun; Sun, Hua-Hong; Chen, Hsiang-Ju; Wu, Xin-Ting; Hu, Min-Chun

    2014-01-01

    Investigating an efficient method for plant propagation can help not only prevent extinction of plants but also facilitate the development of botanical industries. In this paper, we propose to use image processing techniques to determine the cutting-line for the propagation of two kinds of plants, i.e. Melaleuca alternifolia Cheel and Cinnamomum kanehirai Hay, which have quite different characteristics in terms of shape, structure, and propagation way (e.g. propagation by seeding and rooting, respectively). The proposed cutting line determination methods can be further applied to develop an automatic control system to reduce labor cost and increase the effectiveness of plant propagation.

  7. Analysis of biomolecular interactions using affinity microcolumns: A review

    PubMed Central

    Zheng, Xiwei; Li, Zhao; Beeram, Sandya; Podariu, Maria; Matsuda, Ryan; Pfaunmiller, Erika L.; White, Christopher J.; Carter, NaTasha; Hage, David S.

    2014-01-01

    Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and frontal analysis methods are discussed. The techniques of peak decay analysis, ultrafast affinity extraction, split-peak analysis, and band-broadening studies are also explored. The principles of these methods are examined and various applications are provided to illustrate the use of these methods with affinity microcolumns. It is shown how these techniques can be utilized to provide information on the binding strength and kinetics of an interaction, as well as on the number and types of binding sites. It is further demonstrated how information on competition or displacement effects can be obtained by these methods. PMID:24572459

  8. Photoelectron spectra of small LaOn- clusters: decreasing electron affinity upon increasing the number of oxygen atoms

    NASA Astrophysics Data System (ADS)

    Klingeler, R.; Lüttgens, G.; Pontius, N.; Rochow, R.; Bechthold, P. S.; Neeb, M.; Eberhardt, W.

    We present mass selected photoelectron spectra of small lanthanum oxide cluster anions LaOn- (n=1-5) which have been generated in a laser vaporization cluster source. The electron affinity of the lanthanum oxide clusters drops continuously with the number of chemisorbed oxygen atoms as revealed from the anion photoelectron spectra. The decreasing electron affinity behaves contrary to several other metal oxide clusters. The geometry of some of the measured clusters are discussed in comparsion with configuration interaction and density functional calculations using a Gaussian94 program package.

  9. Coherent Propagation of Elementary Excitations in Solid ^4He

    NASA Astrophysics Data System (ADS)

    Goodkind, John M.; Ho, Pei-Chun

    1998-03-01

    We have measured the interaction of heat pulses and acoustic pulses propagating along orthogonal paths in solid ^4He with small amounts of ^3He impurities. The interaction is revealed as a variation of the acoustic attenuation, alpha, and velocity, v, as a function of the delay between launching of the heat pulses and the acoustic pulses. alpha and v pass through extreema at delay times corresponding to the relative propagation velocities of the acoustic waves and the excitations created by the heat pulses. The propagation velocities of the various excitations, determined in this way, are between 50 and 150 m/sec and they increase with decreasing temperature. There are two distinct peaks and a long tail at temperatures above about 500 mK indicating that more than one mode is propagating. The peak effect occurs at a different delay time for alpha than for v at temperatures near the attenuation peak (PC HO, I. P. Bindloss, and J. M. Goodkind, J. Low Temp. Phys., November 1997), providing further evidence for more than one type of propagating mode. The sign of the effect reverses as T is decreased and the change of alpha is of opposite sign to that expected from the equilibrium T dependence of alpha. We will discuss the relation of this phenomenon to previous indications of propagating modes in solid ^4He (G.A. Lengua and J. M. Goodkind, J. Low Temp. Phys., 79), 251 (1990)and to the possible Bose-Einstein condensation (PC HO, I. P. Bindloss, and J. M. Goodkind, J. Low Temp. Phys., November 1997).

  10. Interfacial Partitioning of a Loop Hinge Residue Contributes to Diacylglycerol Affinity of Conserved Region 1 Domains*

    PubMed Central

    Stewart, Mikaela D.; Cole, Taylor R.; Igumenova, Tatyana I.

    2014-01-01

    Conventional and novel isoenzymes of PKC are activated by the membrane-embedded second messenger diacylglycerol (DAG) through its interactions with the C1 regulatory domain. The affinity of C1 domains to DAG varies considerably among PKCs. To gain insight into the origin of differential DAG affinities, we conducted high-resolution NMR studies of C1B domain from PKCδ (C1Bδ) and its W252Y variant. The W252Y mutation was previously shown to render C1Bδ less responsive to DAG (Dries, D. R., Gallegos, L. L., and Newton, A. C. (2007) A single residue in the C1 domain sensitizes novel protein kinase C isoforms to cellular diacylglycerol production. J. Biol. Chem. 282, 826–830) and thereby emulate the behavior of C1B domains from conventional PKCs that have a conserved Tyr at the equivalent position. Our data revealed that W252Y mutation did not perturb the conformation of C1Bδ in solution but significantly reduced its propensity to partition into a membrane-mimicking environment in the absence of DAG. Using detergent micelles doped with a paramagnetic lipid, we determined that both the residue identity at position 252 and complexation with diacylglycerol influence the geometry of C1Bδ-micelle interactions. In addition, we identified the C-terminal helix α1 of C1Bδ as an interaction site with the head groups of phosphatidylserine, a known activator of PKCδ. Taken together, our studies (i) reveal the identities of C1Bδ residues involved in interactions with membrane-mimicking environment, DAG, and phosphatidylserine, as well as the affinities associated with each event and (ii) suggest that the initial ligand-independent membrane recruitment of C1B domains, which is greatly facilitated by the interfacial partitioning of Trp-252, is responsible, at least in part, for the differential DAG affinities. PMID:25124034

  11. Phosphatidylserine and Phosphatidylethanolamine Bind to Protein Z Cooperatively and with Equal Affinity

    PubMed Central

    Sengupta, Tanusree; Manoj, Narayanan

    2016-01-01

    Protein Z (PZ) is an anticoagulant that binds with high affinity to Protein Z-dependent protease inhibitor (ZPI) and accelerates the rate of ZPI-mediated inhibition of factor Xa (fXa) by more than 1000-fold in the presence of Ca2+ and phospholipids. PZ promotion of the ZPI-fXa interaction results from the anchoring of the Gla domain of PZ onto phospholipid surfaces and positioning the bound ZPI in close proximity to the Gla-anchored fXa, forming a ternary complex of PZ/ZPI/fXa. Although interaction of PZ with phospholipid membrane appears to be absolutely crucial for its cofactor activity, little is known about the binding of different phospholipids to PZ. The present study was conceived to understand the interaction of different phospholipids with PZ. Experiments with both soluble lipids and model membranes revealed that PZ binds to phosphatidylserine (PS) and phosphatidylethanolamine (PE) with equal affinity (Kd~48 μM); further, PS and PE bound to PZ synergistically. Equilibrium dialysis experiments revealed two lipid-binding sites for both PS and PE. PZ binds with weaker affinity to other phospholipids, e.g., phosphatidic acid, phosphatidylglycerol, phosphatidylcholine and binding of these lipids is not synergistic with respect to PS. Both PS and PE -containing membranes supported the formation of a fXa-PZ complex. PZ protection of fXa from antithrombin inhibition were also shown to be comparable in presence of both PS: PC and PE: PC membranes. These findings are particularly important and intriguing since they suggest a special affinity of PZ, in vivo, towards activated platelets, the primary membrane involved in blood coagulation process. PMID:27584039

  12. High affinity binding of [3H]-tyramine in the central nervous system.

    PubMed Central

    Vaccari, A.

    1986-01-01

    Optimum assay conditions for the association of [3H]-para-tyramine [( 3H]-pTA) with rat brain membranes were characterized, and a saturable, reversible, drug-specific, and high affinity binding mechanism for this trace amine was revealed. The binding capacity (Bmax) for [3H]-pTA in the corpus striatum was approximately 30 times higher than that in the cerebellum, with similar dissociation constants (KD). The binding process of [3H]-pTA involved the dopamine system, inasmuch as (a) highest binding capacity was associated with dopamine-rich regions; (b) dopamine and pTA equally displaced specifically bound [3H]-pTA; (c) there was a severe loss in striatal binding capacity for [3H]-pTA and, reportedly, for [3H]-dopamine, following unilateral nigrostriatal lesion; (d) acute in vivo reserpine treatment markedly decreased the density of [3H]-pTA and, reportedly, of [3H]-dopamine binding sites. In competition experiments [3H]-pTA binding sites, though displaying nanomolar affinity for dopamine, revealed micromolar affinities for the dopamine agonists apomorphine and pergolide, and for several dopamine antagonists, while having very high affinity for reserpine, a marker for the catecholamine transporter in synaptic vesicles. The binding process of [3H]-pTA was both energy-dependent (ouabain-sensitive), and ATP-Mg2+-insensitive; furthermore, the potencies of various drugs in competing for [3H]-pTA binding to rat striatal membranes correlated well (r = 0.96) with their reported potencies in inhibiting [3H]-dopamine uptake into striatal synaptosomes. It is concluded that [3H]-pTA binds at a site located on/within synaptic vesicles where it is involved in the transport mechanism of dopamine. PMID:3801770

  13. Wave Propagation in Bimodular Geomaterials

    NASA Astrophysics Data System (ADS)

    Kuznetsova, Maria; Pasternak, Elena; Dyskin, Arcady; Pelinovsky, Efim

    2016-04-01

    Observations and laboratory experiments show that fragmented or layered geomaterials have the mechanical response dependent on the sign of the load. The most adequate model accounting for this effect is the theory of bimodular (bilinear) elasticity - a hyperelastic model with different elastic moduli for tension and compression. For most of geo- and structural materials (cohesionless soils, rocks, concrete, etc.) the difference between elastic moduli is such that their modulus in compression is considerably higher than that in tension. This feature has a profound effect on oscillations [1]; however, its effect on wave propagation has not been comprehensively investigated. It is believed that incorporation of bilinear elastic constitutive equations within theory of wave dynamics will bring a deeper insight to the study of mechanical behaviour of many geomaterials. The aim of this paper is to construct a mathematical model and develop analytical methods and numerical algorithms for analysing wave propagation in bimodular materials. Geophysical and exploration applications and applications in structural engineering are envisaged. The FEM modelling of wave propagation in a 1D semi-infinite bimodular material has been performed with the use of Marlow potential [2]. In the case of the initial load expressed by a harmonic pulse loading strong dependence on the pulse sign is observed: when tension is applied before compression, the phenomenon of disappearance of negative (compressive) strains takes place. References 1. Dyskin, A., Pasternak, E., & Pelinovsky, E. (2012). Periodic motions and resonances of impact oscillators. Journal of Sound and Vibration, 331(12), 2856-2873. 2. Marlow, R. S. (2008). A Second-Invariant Extension of the Marlow Model: Representing Tension and Compression Data Exactly. In ABAQUS Users' Conference.

  14. Affinity+: Semi-Structured Brainstorming on Large Displays

    SciTech Connect

    Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.; LaMothe, Ryan R.; Endert, Alexander

    2013-04-27

    Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

  15. Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations

    PubMed Central

    Michielssens, Servaas; de Groot, Bert L.; Grubmüller, Helmut

    2015-01-01

    Conformational selection is an established mechanism in molecular recognition. Despite its power to explain binding events, it is hardly used in protein/ligand design to modulate molecular recognition. Here, we explore the opportunities and limitations of design by conformational selection. Using appropriate thermodynamic cycles, our approach predicts the effects of a conformational shift on binding affinity and also allows one to disentangle the effects induced by a conformational shift from other effects influencing the binding affinity. The method is assessed and applied to explain the contribution of a conformational shift on the binding affinity of six ubiquitin mutants showing different conformational shifts in six different complexes. PMID:25992736

  16. Energy propagation throughout chemical networks.

    PubMed

    Le Saux, Thomas; Plasson, Raphaël; Jullien, Ludovic

    2014-06-14

    In order to maintain their metabolism from an energy source, living cells rely on chains of energy transfer involving functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has only been recently reproduced at a steady state in simple chemical systems. As observed in living cells, the spontaneous onset of energy-transfer chains notably drives local generation of singular dissipative chemical structures: continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones but in the absence of any membrane or predetermined material structure.

  17. LCMV: Propagation, quantitation, and storage

    PubMed Central

    Seedhom, Mina O.

    2011-01-01

    Lymphocytic choriomeningitis virus (LCMV) is an enveloped ambisense RNA virus and the prototypic virus of the arenavirus group. It can cause viral meningitis and other ailments in humans, but it's natural host is the mouse. The LCMV/mouse model has been useful for examining mechanisms of viral persistence and basic concepts of virus-induced immunity and immunopathology. Here we discuss strain differences and biosafety containment issues for LCMV. Recommendations are made for techniques to propagate LCMV to high titers, to quantify it by plaque assay and PCR techniques, and to preserve its infectivity by appropriate storage. PMID:18770534

  18. ACTS and OLYMPUS propagation experiments

    NASA Technical Reports Server (NTRS)

    Bostian, Charles W.; Baker, Kenneth R.

    1988-01-01

    The OLYMPUS and ACTS satellites both provide opportunities for 10 to 30 GHz propagation measurements. The spacecraft are sufficiently alike that OLYMPUS can be used to test some prototype ACTS equipment and experiments. Data are particularly needed on short term signal behavior and in support of uplink power control and adaptive forward error correction (FEC) techniques. The Virginia Tech Satellite Communications Group has proposed a set of OLYMPUS experiments including attenuation and fade rate measurements, data communications, uplink power control, rain scatter interference, and small-scale site diversity operation. A digital signal processing receiver for the OLYMPUS and ACTS beacon signals is being developed.

  19. Mode II fatigue crack propagation.

    NASA Technical Reports Server (NTRS)

    Roberts, R.; Kibler, J. J.

    1971-01-01

    Fatigue crack propagation rates were obtained for 2024-T3 bare aluminum plates subjected to in-plane, mode I, extensional loads and transverse, mode II, bending loads. These results were compared to the results of Iida and Kobayashi for in-plane mode I-mode II extensional loads. The engineering significance of mode I-mode II fatigue crack growth is considered in view of the present results. A fatigue crack growth equation for handling mode I-mode II fatigue crack growth rates from existing mode I data is also discussed.

  20. Modeling of Transionospheric Radio Propagation

    DTIC Science & Technology

    1975-08-01

    sin cpj dcp dq (17) where and VXz = Fresnel-zone radius at scattering layer 2 2 7 (0,0’) = [l + tan e cos (0 - «(*)] ß...y /nai, - 7 «T MODELING OF JRANSIONOSPHKir RADIO PROPAGATION RADI ^ja By: E. J. TREMOUW C L. RINO (£>. Augm IB?5 Prepared for: ROME A|R...following three relationships arise from Eqs. (1) and (2) 2 Ro cos (26) ( 7 ) R [ r. 2 o 0 = y ^ll + ^^cos (26) 2 L

  1. Ultrasound propagation measurements and applications

    NASA Technical Reports Server (NTRS)

    Lynnworth, L. C.; Papadakis, E. P.; Fowler, K. A.

    1977-01-01

    This paper reviews three systems designed for accurately measuring the propagation of ultrasonic pulses. The three systems are presented in order of velocity-measuring precision: + or - 100 ns, + or - 1 ns, + or - 0.2 ns. Also included is a brief discussion of phase and group velocities, with reference to dispersive, highly attenuating materials. Measurement of attenuation by pulse-echo buffer rod techniques is described briefly. These techniques and instruments have been used to measure sound velocity and attenuation in a variety of materials and shapes, over a wide temperature range.

  2. Propagation modelling in microcellular environments

    NASA Astrophysics Data System (ADS)

    Sharples, P. A.; Mehler, M. J.

    This paper describes a microcellular model, based on ray tracing techniques. Ray tracing is a stationary phase technique which relies on the quasi-optical properties of radio waves in regions where any obstacles are large in terms of a wavelength. The model described is a very versatile implementation which can be used to study both indoor and outdoor propagation phenomena for a number of different types of service. In its fullest form it requires input data of a sophistication that is not commercially available. However, this allows the model to be used to assess the implications in terms of the achievable accuracy when using commercial building databases.

  3. Light Propagation through Anisotropic Turbulence

    DTIC Science & Technology

    2011-03-01

    Kolmogorov stratospheric turbulence on star image motion,” Proc. SPIE 3126, 113–123 (1997). 5. B. E . Stribling, B. M . Welsh, and M . C. Roggemann...746407 (2009). 10. M . Chang, C. O. Font, F. Santiago, Y. Luna, E . Roura, and S. Restaino, “Marine environment optical propagation measure- ments,” Proc...Anisotropic factor as a function of alpha for several zeta values. Toselli et al. Vol. 28, No. 3 / March 2011 / J. Opt. Soc. Am. A 487 14. M . S

  4. Continuous propagation of microalgae. III.

    NASA Technical Reports Server (NTRS)

    Hanson, D. T.; Fredrickson, A. G.; Tsuchiya, H. M.

    1971-01-01

    Data are presented which give the specific photosynthetic rate and the specific utilization rates of urea and carbon dioxide as functions of specific growth rate for Chlorella. A mathematical model expresses a set of mass balance relations between biotic and environmental materials. Criteria of validity are used to test this model. Predictive procedures are complemented by a particular model of microbial growth. Methods are demonstrated for predicting substrate utilization rates, production rates of extracellular metabolites, growth limiting conditions, and photosynthetic quotients from propagator variables.

  5. High Genetic Stability of Dengue Virus Propagated in MRC-5 Cells as Compared to the Virus Propagated in Vero Cells

    PubMed Central

    Butler, Michael; Wu, Suh-Chin

    2008-01-01

    This work investigated the replication kinetics of the four dengue virus serotypes (DEN-1 to DEN-4), including dengue virus type 4 (DEN-4) recovered from an infectious cDNA clone, in Vero cells and in MRC-5 cells grown on Cytodex 1 microcarriers. DEN-1 strain Hawaii, DEN-2 strain NGC, DEN-3 strain H-87, and DEN-4 strain H-241 , and DEN-4 strain 814669 derived from cloned DNA, were used to infect Vero cells and MRC-5 cells grown in serum-free or serum-containing microcarrier cultures. Serum-free and serum-containing cultures were found to yield comparable titers of these viruses. The cloned DNA-derived DEN-4 started genetically more homogeneous was used to investigate the genetic stability of the virus propagated in Vero cells and MRC-5 cells. Sequence analysis revealed that the DEN-4 propagated in MRC-5 cells maintained a high genetic stability, compared to the virus propagated in Vero cells. Amino acid substitutions of Gly104Cys and Phe108Ile were detected at 70%, 60%, respectively, in the envelope (E) protein of DEN-4 propagated in Vero cells, whereas a single mutation of Glu345Lys was detected at 50% in E of the virus propagated in MRC-5 cells. Sequencing of multiple clones of three separate DNA fragments spanning 40% of the genome also indicated that DEN-4 propagated in Vero cells contained a higher number of mutations than the virus growing in MRC-5 cells. Although Vero cells yielded a peak virus titer approximately 1 to 17 folds higher than MRC-5 cells, cloned DEN-4 from MRC-5 cells maintained a greater stability than the virus from Vero cells. Serum-free microcarrier cultures of MRC-5 cells offer a potentially valuable system for the large-scale production of live-attenuated DEN vaccines. PMID:18350148

  6. Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities

    NASA Astrophysics Data System (ADS)

    Yao, Yuyu; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2016-03-01

    The results of an investigation into the influence of sulfolane, a commonly used supercharging agent, on electrospray ionization mass spectrometry (ESI-MS) measurements of protein-ligand affinities are described. Binding measurements carried out on four protein-carbohydrate complexes, lysozyme with β- d-GlcNAc-(1→4)-β- d-GlcNAc-(1→4)-β- d-GlcNAc-(1→4)- d-GlcNAc, a single chain variable fragment and α- d-Gal-(1→2)-[α- d-Abe-(1→3)]-α- d-Man-OCH3, cholera toxin B subunit homopentamer with β- d-Gal-(1→3)-β- d-GalNAc-(1→4)[α- d-Neu5Ac-(2→3)]-β- d-Gal-(1→4)-β- d-Glc, and a fragment of galectin 3 and α- l-Fuc-(1→2)-β- d-Gal-(1→3)-β- d-GlcNAc-(1→3)-β- d-Gal-(1→4)-β- d-Glc, revealed that sulfolane generally reduces the apparent (as measured by ESI-MS) protein-ligand affinities. To establish the origin of this effect, a detailed study was undertaken using the lysozyme-tetrasaccharide interaction as a model system. Measurements carried out using isothermal titration calorimetry (ITC), circular dichroism, and nuclear magnetic resonance spectroscopies reveal that sulfolane reduces the binding affinity in solution but does not cause any significant change in the higher order structure of lysozyme or to the intermolecular interactions. These observations confirm that changes to the structure of lysozyme in bulk solution are not responsible for the supercharging effect induced by sulfolane. Moreover, the agreement between the ESI-MS and ITC-derived affinities indicates that there is no dissociation of the complex during ESI or in the gas phase (i.e., in-source dissociation). This finding suggests that supercharging of lysozyme by sulfolane is not related to protein unfolding during the ESI process. Binding measurements performed using liquid sample desorption ESI-MS revealed that protein supercharging with sulfolane can be achieved without a reduction in affinity.

  7. Light propagation through anisotropic turbulence.

    PubMed

    Toselli, Italo; Agrawal, Brij; Restaino, Sergio

    2011-03-01

    A wealth of experimental data has shown that atmospheric turbulence can be anisotropic; in this case, a Kolmogorov spectrum does not describe well the atmospheric turbulence statistics. In this paper, we show a quantitative analysis of anisotropic turbulence by using a non-Kolmogorov power spectrum with an anisotropic coefficient. The spectrum we use does not include the inner and outer scales, it is valid only inside the inertial subrange, and it has a power-law slope that can be different from a Kolmogorov one. Using this power spectrum, in the weak turbulence condition, we analyze the impact of the power-law variations α on the long-term beam spread and scintillation index for several anisotropic coefficient values ς. We consider only horizontal propagation across the turbulence cells, assuming circular symmetry is maintained on the orthogonal plane to the propagation direction. We conclude that the anisotropic coefficient influences both the long-term beam spread and the scintillation index by the factor ς(2-α).

  8. OPEX propagation measurements and studies

    NASA Technical Reports Server (NTRS)

    Arbesser-Rastburg, Bertram

    1990-01-01

    With the launch of the telecommunications Olympus satellite a new area began for the Olympus Propagation Experiments (OPEX) group. The years of preparations are now paying off - the experiments are underway and the co-operative effort is now turning its attention to the processing and analysis of data and to the interpretation of results. The aim here is to give a short review of the accomplishments made since NAPEX 13 and the work planned for the future. When ESA's Olympus was launched in summer of 1989 it carried a payload producing three unmodulated beacons at 12.5, 19.8, and 29.7 GHz. The main purpose of these beacons is to enable scientists to carry out long term slant path propagation experiments at these frequencies. The OPEX group, which was set up under ESA auspices in 1980, had been preparing for this event very carefully. The specifications for the equipment to be used and the elaboration of standard procedures for data processing and analysis have been worked out jointly. Today the OPEX community includes approximately 30 groups of experimenters. Immediately after achieving platform stability at the orbital location at 341 degrees east, ESA performed the In-Orbit Tests. Most measurements were carried out in Belgium using terminals specially developed for this purpose. A summary of the test results is given.

  9. Simplified propagation of standard uncertainties

    SciTech Connect

    Shull, A.H.

    1997-06-09

    An essential part of any measurement control program is adequate knowledge of the uncertainties of the measurement system standards. Only with an estimate of the standards` uncertainties can one determine if the standard is adequate for its intended use or can one calculate the total uncertainty of the measurement process. Purchased standards usually have estimates of uncertainty on their certificates. However, when standards are prepared and characterized by a laboratory, variance propagation is required to estimate the uncertainty of the standard. Traditional variance propagation typically involves tedious use of partial derivatives, unfriendly software and the availability of statistical expertise. As a result, the uncertainty of prepared standards is often not determined or determined incorrectly. For situations meeting stated assumptions, easier shortcut methods of estimation are now available which eliminate the need for partial derivatives and require only a spreadsheet or calculator. A system of simplifying the calculations by dividing into subgroups of absolute and relative uncertainties is utilized. These methods also incorporate the International Standards Organization (ISO) concepts for combining systematic and random uncertainties as published in their Guide to the Expression of Measurement Uncertainty. Details of the simplified methods and examples of their use are included in the paper.

  10. Joint Acoustic Propagation Experiment (JAPE)

    NASA Technical Reports Server (NTRS)

    Carnes, Benny L.; Olsen, Robert O.; Kennedy, Bruce W.

    1993-01-01

    The Joint Acoustic Propagation Experiment (JAPE), performed under the auspices of NATO and the Acoustics Working Group, was conducted at White Sands Missile Range, New Mexico, USA, during the period 11-28 Jul. 1991. JAPE consisted of 220 trials using various acoustic sources including speakers, propane cannon, various types of military vehicles, helicopters, a 155mm howitzer, and static high explosives. Of primary importance to the performance of these tests was the intensive characterization of the atmosphere before and during the trials. Because of the wide range of interests on the part of the participants, JAPE was organized in such a manner to provide a broad cross section of test configurations. These included short and long range propagation from fixed and moving vehicles, terrain masking, and vehicle detection. A number of independent trials were also performed by individual participating agencies using the assets available during JAPE. These tests, while not documented in this report, provided substantial and important data to those groups. Perhaps the most significant feature of JAPE is the establishment of a permanent data base which can be used by not only the participants but by others interested in acoustics. A follow-on test was performed by NASA LaRC during the period 19-29 Aug. 1991 at the same location. These trials consisted of 59 overflights of supersonic aircraft in order to establish the relationship between atmospheric turbulence and the received sonic boom energy at the surface.

  11. Microwave propagation on acupuncture channels.

    PubMed

    Krevsky, Michael A; Zinina, Ekaterina S; Koshurinov, Yuri; Ovechkin, Aleck M; Tkachenko, Yuri A; Han, Wantaek; Lee, Sang-Min; Yoon, Gilwon

    2006-01-01

    Quantitative studies on functional state of acupuncture points and meridians have been done mostly by electrical measurement that requires the contact of the electrode on skin and is subject to pressure, humidity, etc. In this study, a new modality of using microwave was investigated. Microwave energy in the frequency range of 250 approximately 550MHz was irradiated on an acupuncture point. Transmitted microwave energy along the meridian was measured at the next acupuncture point of the same meridian. Diabetic and cancer patients were compared with healthy persons. Normal group consisted of 50 healthy persons. Diabetic group included 50 diabetic patients. Breast cancer group had also 50 patients. All 12 meridians on both right and left hands and feet were measured. For the diabetic group, the microwave energy propagation in this frequency range was 1.417 dB lower along Lung channel and 1.601 dB higher along Spleen channel compared with the normal group regardless of sex and diabetic types. For cancer patients, the propagation was 1.620 dB lower along Liver channel and 1.245 dB higher along Kidney channel compared with the normal group. Microwave energy proved to be a potential diagnostic method.

  12. A Field Study of Lightning Surges Propagating through Low-voltage Electric Appliances

    NASA Astrophysics Data System (ADS)

    Ishii, Tsunayoshi; Sakamoto, Yoshiki; Oguchi, Shuichi; Okabe, Shigemitsu

    In today's highly information-based society, lightning damage has a significant impact on an increasing number of electric appliances such as personal computers and facsimile machines. Lightning surge protection devices for electric appliances are on the market and concern for lightning protection has been increasing, but there are still many unknown aspects of lightning surges that propagate into residences. To provide effective lightning protection measures, clarification of surge propagation patterns is needed. The Tokyo Electric Power Company has observed the patterns of lightning surge propagation into houses using lightning surge waveform detectors installed at ordinary residences and obtained data on 30 lightning surge current waveforms between 2008 and 2009. This paper discusses various aspects of lightning surge currents propagating into low-voltage appliances, including home electric appliances, based on the lightning surge current waveform data obtained from lightning observations. The result revealed the patterns of lightning surge currents propagating into the ground and lines of low-voltage appliances.

  13. Bidirectional elastic image registration using B-spline affine transformation.

    PubMed

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C; Ma, Hongxia; Leader, Joseph; Kaminski, Naftali; Gur, David; Pu, Jiantao

    2014-06-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bidirectional instead of the traditional unidirectional objective/cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy.

  14. Bidirectional Elastic Image Registration Using B-Spline Affine Transformation

    PubMed Central

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C.; Wang, Chen; Kaminski, Naftali; Pu, Jiantao

    2014-01-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-Spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bi-directional instead of the traditional unidirectional objective / cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy. PMID:24530210

  15. A thermodynamic approach to the affinity optimization of drug candidates.

    PubMed

    Freire, Ernesto

    2009-11-01

    High throughput screening and other techniques commonly used to identify lead candidates for drug development usually yield compounds with binding affinities to their intended targets in the mid-micromolar range. The affinity of these molecules needs to be improved by several orders of magnitude before they become viable drug candidates. Traditionally, this task has been accomplished by establishing structure activity relationships to guide chemical modifications and improve the binding affinity of the compounds. As the binding affinity is a function of two quantities, the binding enthalpy and the binding entropy, it is evident that a more efficient optimization would be accomplished if both quantities were considered and improved simultaneously. Here, an optimization algorithm based upon enthalpic and entropic information generated by Isothermal Titration Calorimetry is presented.

  16. Antibody Affinity Maturation in Fishes—Our Current Understanding

    PubMed Central

    Magor, Brad G.

    2015-01-01

    It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036

  17. Microscale spatiotemporal dynamics during neocortical propagation of human focal seizures.

    PubMed

    Wagner, Fabien B; Eskandar, Emad N; Cosgrove, G Rees; Madsen, Joseph R; Blum, Andrew S; Potter, N Stevenson; Hochberg, Leigh R; Cash, Sydney S; Truccolo, Wilson

    2015-11-15

    Some of the most clinically consequential aspects of focal epilepsy, e.g. loss of consciousness, arise from the generalization or propagation of seizures through local and large-scale neocortical networks. Yet, the dynamics of such neocortical propagation remain poorly understood. Here, we studied the microdynamics of focal seizure propagation in neocortical patches (4×4 mm) recorded via high-density microelectrode arrays (MEAs) implanted in people with pharmacologically resistant epilepsy. Our main findings are threefold: (1) a newly developed stage segmentation method, applied to local field potentials (LFPs) and multiunit activity (MUA), revealed a succession of discrete seizure stages, each lasting several seconds. These different stages showed characteristic evolutions in overall activity and spatial patterns, which were relatively consistent across seizures within each of the 5 patients studied. Interestingly, segmented seizure stages based on LFPs or MUA showed a dissociation of their spatiotemporal dynamics, likely reflecting different contributions of non-local synaptic inputs and local network activity. (2) As previously reported, some of the seizures showed a peak in MUA that happened several seconds after local seizure onset and slowly propagated across the MEA. However, other seizures had a more complex structure characterized by, for example, several MUA peaks, more consistent with the succession of discrete stages than the slow propagation of a simple wavefront of increased MUA. In both cases, nevertheless, seizures characterized by spike-wave discharges (SWDs, ~2-3 Hz) eventually evolved into patterns of phase-locked MUA and LFPs. (3) Individual SWDs or gamma oscillation cycles (25-60 Hz), characteristic of two different types of recorded seizures, tended to propagate with varying degrees of directionality, directions of propagation and speeds, depending on the identified seizure stage. However, no clear relationship was observed between the MUA

  18. Microscale Spatiotemporal Dynamics during Neocortical Propagation of Human Focal Seizures

    PubMed Central

    Wagner, Fabien B.; Eskandar, Emad N.; Cosgrove, G. Rees; Madsen, Joseph R.; Blum, Andrew S.; Potter, N. Stevenson; Hochberg, Leigh R.; Cash, Sydney S.; Truccolo, Wilson

    2015-01-01

    Some of the most clinically consequential aspects of focal epilepsy, e.g. loss of consciousness, arise from the generalization or propagation of seizures through local and large-scale neocortical networks. Yet, the dynamics of such neocortical propagation remain poorly understood. Here, we studied the microdynamics of focal seizure propagation in neocortical patches (4 × 4 mm) recorded via high-density microelectrode arrays (MEAs) implanted in people with pharmacologically resistant epilepsy. Our main findings are threefold: (1) A newly developed stage segmentation method, applied to local field potentials (LFPs) and multi-unit activity (MUA), revealed a succession of discrete seizure stages, each lasting several seconds. These different stages showed characteristic evolutions in overall activity and spatial patterns, which were relatively consistent across seizures within each of the 5 patients studied. Interestingly, segmented seizure stages based on LFPs or MUA showed a dissociation of their spatiotemporal dynamics, likely reflecting different contributions of non-local synaptic inputs and local network activity. (2) As previously reported, some of the seizures showed a peak in MUA that happened several seconds after local seizure onset and slowly propagated across the MEA. However, other seizures had a more complex structure characterized by, for example, several MUA peaks, more consistent with the succession of discrete stages than the slow propagation of a simple wavefront of increased MUA. In both cases, nevertheless, seizures characterized by spike-wave discharges (SWDs, ~ 2–3Hz) eventually evolved into patterns of phase-locked MUA and LFPs. (3) Individual SWDs or gamma oscillation cycles (25–60 Hz), characteristic of two different types of recorded seizures, tended to propagate with varying degrees of directionality, directions of propagation and speeds, depending on the identified seizure stage. However, no clear relationship was observed between the

  19. Electrospun polyethersulfone affinity membrane: membrane preparation and performance evaluation.

    PubMed

    Ma, Zuwei; Lan, Zhengwei; Matsuura, Takeshi; Ramakrishna, Seeram

    2009-11-01

    Non-woven polyethersulfone (PES) membranes were prepared by electrospinning. After heat treatment and surface activation, the membranes were covalently functionalized with ligands to be used as affinity membranes. The membranes were characterized in terms of fiber diameter, porosity, specific area, pore size, ligand density and binding capacities. To evaluate the binding efficiency of the membrane, dynamic adsorption of bovine serum albumin (BSA) on the Cibacron blue F3GA (CB) functionalized PES membrane was studied. Experimental breakthrough curves were fitted with the theoretical curves based on the plate model to estimate plate height (H(p)) of the affinity membrane. The high value of H(p) (1.6-8 cm) of the affinity membrane implied a poor dynamic binding efficiency, which can be explained by the intrinsic microstructures of the material. Although the electrospun membrane might not be an ideal candidate for the preparative affinity membrane chromatography for large-scale production, it still can be used for fast small-scale protein purification in which a highly efficient binding is not required. Spin columns packed with protein A/G immobilized PES membranes were demonstrated to be capable of binding IgG specifically. SDS-PAGE results demonstrated that the PES affinity membrane had high specific binding selectivity for IgG molecules and low non-specific protein adsorption. Compared with other reported affinity membranes, the PES affinity membrane had a comparable IgG binding capacity of 4.5 mg/ml, and had a lower flow through pressure drop due to its larger pore size. In conclusion, the novel PES affinity membrane is an ideal spin column packing material for fast protein purification.

  20. Considering affinity: an ethereal conversation (part two of three).

    PubMed

    Winsor, Mary P

    2015-06-01

    In 1840 Hugh Strickland published a diagram showing the relationships of genera of birds in the kingfisher family. Three years later he applied this mapping idea to genera of birds of prey and songbirds, creating a large wall chart that he displayed to colleagues but never published. Both of his diagrams featured a scale of degrees of affinity. The meaning of taxonomic affinity was something Darwin thought about deeply. Details in the chart undermine Strickland's claim that his method was purely inductive.

  1. Proton affinity of methyl nitrate - Less than proton affinity of nitric acid

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    Several state-of-the-art ab initio quantum mechanical methods were used to investigate the equilibrium structure, dipole moments, harmonic vibrational frequencies, and IR intensities of methyl nitrate, methanol, and several structures of protonated methyl nitrate, using the same theoretical methods as in an earlier study (Lee and Rice, 1992) of nitric acid. The ab initio results for methyl nitrate and methanol were found to be in good agreement with available experimental data. The proton affinity (PA) of methyl nitrate was calculated to be 176.9 +/-5 kcal/mol, in excellent agreement with the experimental value 176 kcal/mol obtained by Attina et al. (1987) and less than the PA value of nitric acid. An explanation of the discrepancy of the present results with those of an earlier study on protonated nitric acid is proposed.

  2. Propagation characteristics of an extremely anisotropic metamaterial loaded helical guide.

    PubMed

    Sharma, Dushyant K; Pathak, Surya K

    2016-12-26

    In this study, we report slow wave propagation characteristics of an extremely anisotropic metamaterial loaded helical guide (EAMLHG). An analytical expression has been theoretically derived and numerically computed to get exact solutions of all possible guided modes of propagation. Anisotropy is defined in terms of positive longitudinal permittivity (ϵz > 0) and negatives transverse permittivity value (ϵt < 0). The waveguide supports hybrid (HE) mode propagation and possesses characteristics of backward wave (BW) mode, forward wave (FW) mode, zero-group velocity and mode-degeneracy. The large value of effective index of BW mode and mode-degeneracy mechanism leads to slowing and trapping of electromagnetic (EM) wave. Closed-form guided mode energy propagation expressions has been also derived and computed which exhibits zero power flow at mode degeneracy point. A comparative study is also carried out between extremely anisotropic metamaterial helical waveguide (EAMLHG) and conventional extremely anisotropic metamaterial cylindrical guide (EAMCG), which reveals enhanced slow wave behaviour. Engineering feasible design and analysis is also presented by combining alternate disks of silver and glass as an extremely anisotropic medium which exhibits lossy and dispersive properties. This type of waveguide can find applications as a filter, phase shifter, and delay lines in microwave to THz applications and, as an optical buffer in optoelectronics applications.

  3. MULTI-LAYER STUDY OF WAVE PROPAGATION IN SUNSPOTS

    SciTech Connect

    Felipe, T.; Khomenko, E.; Collados, M.; Beck, C.

    2010-10-10

    We analyze the propagation of waves in sunspots from the photosphere to the chromosphere using time series of co-spatial Ca II H intensity spectra (including its line blends) and polarimetric spectra of Si I {lambda}10,827 and the He I {lambda}10,830 multiplet. From the Doppler shifts of these lines we retrieve the variation of the velocity along the line of sight at several heights. Phase spectra are used to obtain the relation between the oscillatory signals. Our analysis reveals standing waves at frequencies lower than 4 mHz and a continuous propagation of waves at higher frequencies, which steepen into shocks in the chromosphere when approaching the formation height of the Ca II H core. The observed nonlinearities are weaker in Ca II H than in He I lines. Our analysis suggests that the Ca II H core forms at a lower height than the He I {lambda}10,830 line: a time delay of about 20 s is measured between the Doppler signal detected at both wavelengths. We fit a model of linear slow magnetoacoustic wave propagation in a stratified atmosphere with radiative losses according to Newton's cooling law to the phase spectra and derive the difference in the formation height of the spectral lines. We show that the linear model describes well the wave propagation up to the formation height of Ca II H, where nonlinearities start to become very important.

  4. Shock Propagation and Instability Structures in Compressed Silica Aerogels

    SciTech Connect

    Howard, W M; Molitoris, J D; DeHaven, M R; Gash, A E; Satcher, J H

    2002-05-30

    We have performed a series of experiments examining shock propagation in low density aerogels. High-pressure ({approx}100 kbar) shock waves are produced by detonating high explosives. Radiography is used to obtain a time sequence imaging of the shocks as they enter and traverse the aerogel. We compress the aerogel by impinging shocks waves on either one or both sides of an aerogel slab. The shock wave initially transmitted to the aerogel is very narrow and flat, but disperses and curves as it propagates. Optical images of the shock front reveal the initial formation of a hot dense region that cools and evolves into a well-defined microstructure. Structures observed in the shock front are examined in the framework of hydrodynamic instabilities generated as the shock traverses the low-density aerogel. The primary features of shock propagation are compared to simulations, which also include modeling the detonation of the high explosive, with a 2-D Arbitrary Lagrange Eulerian hydrodynamics code The code includes a detailed thermochemical equation of state and rate law kinetics. We will present an analysis of the data from the time resolved imaging diagnostics and form a consistent picture of the shock transmission, propagation and instability structure.

  5. PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity.

    PubMed

    Fansa, Eyad Kalawy; Kösling, Stefanie Kristine; Zent, Eldar; Wittinghofer, Alfred; Ismail, Shehab

    2016-04-11

    The phosphodiesterase 6 delta subunit (PDE6δ) shuttles several farnesylated cargos between membranes. The cargo sorting mechanism between cilia and other compartments is not understood. Here we show using the inositol polyphosphate 5'-phosphatase E (INPP5E) and the GTP-binding protein (Rheb) that cargo sorting depends on the affinity towards PDE6δ and the specificity of cargo release. High-affinity cargo is exclusively released by the ciliary transport regulator Arl3, while low-affinity cargo is released by Arl3 and its non-ciliary homologue Arl2. Structures of PDE6δ/cargo complexes reveal the molecular basis of the sorting signal which depends on the residues at the -1 and -3 positions relative to farnesylated cysteine. Structure-guided mutation allows the generation of a low-affinity INPP5E mutant which loses exclusive ciliary localization. We postulate that the affinity to PDE6δ and the release by Arl2/3 in addition to a retention signal are the determinants for cargo sorting and enrichment at its destination.

  6. Insulin and epidermal growth factor-urogastrone: Affinity crosslinking to specific binding sites in rat liver membranes

    PubMed Central

    Sahyoun, N.; Hock, R. A.; Hollenberg, M. D.

    1978-01-01

    Both insulin and human epidermal growth factor-urogastrone (EGF/URO) can be covalently linked to specific rat liver membrane binding sites by glutaraldehyde coupling followed by sodium borohydride reduction to yield affinity-labeled membrane constituents sufficiently stable for solubilization and further analysis by various techniques. Solubilization of membranes covalently labeled with 125I-labeled insulin yields a component with chromatographic properties identical to those of a soluble insulin receptor characterized in previous studies. A second soluble insulin-binding component that is not revealed by the affinity-labeling method and that has not yet been reported can also be detected. Membranes similarly labeled with 125I-labeled EGF/URO yield one major and two minor ligand-specific soluble (Triton X-100) affinity-labeled components, as detected by chromatography on Sepharose 6B. Further analysis of the EGF/URO-labeled components by affinity chromatography on concanavalin A-Sepharose, by disc gel electrophoresis, and by enzymatic digestion suggests that the major specific binding component for EGF/URO in liver membranes is a glycoprotein subunit of approximately 100,000 daltons that possesses a 20,000-dalton portion inaccessible to proteolytic cleavage when the subunit is anchored in the membrane. The affinity labeling approach described should prove of use for the study of other polypeptide receptors that, like the EGF/URO receptor, lose their ligand recognition property subsequent to membrane solubilization. PMID:205865

  7. Development and characterization of small bispecific albumin-binding domains with high affinity for ErbB3.

    PubMed

    Nilvebrant, Johan; Astrand, Mikael; Löfblom, John; Hober, Sophia

    2013-10-01

    Affinity proteins based on small scaffolds are currently emerging as alternatives to antibodies for therapy. Similarly to antibodies, they can be engineered to have high affinity for specific proteins. A potential problem with small proteins and peptides is their short in vivo circulation time, which might limit the therapeutic efficacy. To circumvent this issue, we have engineered bispecificity into an albumin-binding domain (ABD) derived from streptococcal Protein G. The inherent albumin binding was preserved while the opposite side of the molecule was randomized for selection of high-affinity binders. Here we present novel ABD variants with the ability to bind to the epidermal growth factor receptor 3 (ErbB3). Isolated candidates were shown to have an extraordinary thermal stability and affinity for ErbB3 in the nanomolar range. Importantly, they were also shown to retain their affinity to albumin, hence demonstrating that the intended strategy to engineer bispecific single-domain proteins against a tumor-associated receptor was successful. Moreover, competition assays revealed that the new binders could block the natural ligand Neuregulin-1 from binding to ErbB3, indicating a potential anti-proliferative effect. These new binders thus represent promising candidates for further development into ErbB3-signaling inhibitors, where the albumin interaction could result in prolonged in vivo half-life.

  8. Molecular cloning, expression profile, odorant affinity, and stability of two odorant-binding proteins in Macrocentrus cingulum Brischke (Hymenoptera: Braconidae).

    PubMed

    Ahmed, Tofael; Zhang, Tiantao; Wang, Zhenying; He, Kanglai; Bai, Shuxiong

    2017-02-01

    The polyembryonic endoparasitoid wasp Macrocentrus cingulum Brischke (Hymenoptera: Braconidae) is deployed successfully as a biocontrol agent for corn pest insects from the Lepidopteran genus Ostrinia in Europe and throughout Asia, including Japan, Korea, and China. The odorants are recognized, bound, and solubilized by odorant-binding protein (OBP) in the initial biochemical recognition steps in olfaction that transport them across the sensillum lymph to initiate behavioral response. In the present study, we examine the odorant-binding effects on thermal stability of McinOBP2, McinOBP3, and their mutant form that lacks the third disulfide bonds. Real-time PCR experiments indicate that these two are expressed mainly in adult antennae, with expression levels differing by sex. Odorant-binding affinities of aldehydes, terpenoids, and aliphatic alcohols were measured with circular dichroism spectroscopy based on changes in the thermal stability of the proteins upon their affinities to odorants. The obtained results reveal higher affinity of trans-caryophelle, farnesene, and cis-3-Hexen-1-ol exhibits to both wild and mutant McinOBP2 and McinOBP3. Although conformational flexibility of the mutants and shape of binding cavity make differences in odorant affinity between the wild-type and mutant, it suggested that lacking the third disulfide bond in mutant proteins may have chance to incorrect folded structures that reduced the affinity to these odorants. In addition, CD spectra clearly indicate proteins enriched with α-helical content.

  9. Direct measurement of equilibrium constants for high-affinity hemoglobins.

    PubMed

    Kundu, Suman; Premer, Scott A; Hoy, Julie A; Trent, James T; Hargrove, Mark S

    2003-06-01

    The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (K(D) < 1 micro M) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and approximately 100 micro M(-1) respectively, indicate that they are not capable of facilitating oxygen transport.

  10. Functionalized multi-walled carbon nanotubes as affinity ligands

    NASA Astrophysics Data System (ADS)

    Yu, L.; Li, C. M.; Zhou, Q.; Gan, Y.; Bao, Q. L.

    2007-03-01

    Functionalization of carbon nanotubes is very challenging for their applications. The paper here describes a new method to functionalize multi-walled carbon nanotubes (MWCNTs) as specific affinity adsorbents. MWCNTs were acid purified and pretreated with (3-aminopropyl)-triethoxysilane (APTES) in order to introduce abundant amino groups on the surface of MWCNTs. After the conversion of amino groups to carboxyl groups by succinic acid anhydride, MWCNTs were attached to protein A or aminodextran using 1-ethyl-3,3' (dimethylamion)-propylcarbodiimide as a biofunctional crosslinker. The incorporation of aminodextran as a spacer arm noticeably increased the binding capacity of the APTES-modified MWCNTs for protein A. The application of affinity MWCNTs for purification of immunoglobulin G was then evaluated. The affinity of MWCNTs with AMD spacer exhibited a high adsorption capacity of ~361 µg IgG/mg MWCNT (wet basis). About 75% of bound IgG was eluted from affinity MWCNTs (ANT-I and ANT-II) and ELISA confirmed that the biological activity of IgG was well preserved during the course of affinity separation. The functionalized MWCNTs could be potentially used in affinity chromatography.

  11. Binding Kinetics versus Affinities in BRD4 Inhibition.

    PubMed

    Kuang, Ming; Zhou, Jingwei; Wang, Laiyou; Liu, Zhihong; Guo, Jiao; Wu, Ruibo

    2015-09-28

    Bromodomains (BRDs) are protein modules that selectively recognize histones as a "reader" by binding to an acetylated lysine substrate. The human BRD4 has emerged as a promising drug target for a number of disease pathways, and several potent BRD inhibitors have been discovered experimentally recently. However, the detailed inhibition mechanism especially for the inhibitor binding kinetics is not clear. Herein, by employing classical molecular dynamics (MD) and state-of-the-art density functional QM/MM MD simulations, the dynamic characteristics of ZA-loop in BRD4 are revealed. And then the correlation between binding pocket size and ZA-loop motion is elucidated. Moreover, our simulations found that the compound (-)-JQ1 could be accommodated reasonably in thermodynamics whereas it is infeasible in binding kinetics against BRD4. Its racemate (+)-JQ1 proved to be both thermodynamically reasonable and kinetically achievable against BRD4, which could explain the previous experimental results that (+)-JQ1 shows a high inhibitory effect toward BRD4 (IC50 is 77 nM) while (-)-JQ1 is inactive (>10 μM). Furthermore, the L92/L94/Y97 in the ZA-loop and Asn140 in the BC-loop are identified to be critical residues in (+)-JQ1 binding/releasing kinetics. All these findings shed light on further selective inhibitor design toward BRD family, by exploiting the non-negligible ligand binding kinetics features and flexible ZA-loop motions of BRD, instead of only the static ligand-protein binding affinity.

  12. Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation

    PubMed Central

    Goenka, Radhika; Matthews, Andrew H.; Zhang, Bochao; O’Neill, Patrick J.; Scholz, Jean L.; Migone, Thi-Sau; Leonard, Warren J.; Stohl, William; Hershberg, Uri

    2014-01-01

    We have assessed the role of B lymphocyte stimulator (BLyS) and its receptors in the germinal center (GC) reaction and affinity maturation. Despite ample BLyS retention on B cells in follicular (FO) regions, the GC microenvironment lacks substantial BLyS. This reflects IL-21–mediated down-regulation of the BLyS receptor TACI (transmembrane activator and calcium modulator and cyclophilin ligand interactor) on GC B cells, thus limiting their capacity for BLyS binding and retention. Within the GC, FO helper T cells (TFH cells) provide a local source of BLyS. Whereas T cell–derived BLyS is dispensable for normal GC cellularity and somatic hypermutation, it is required for the efficient selection of high affinity GC B cell clones. These findings suggest that during affinity maturation, high affinity clones rely on TFH-derived BLyS for their persistence. PMID:24367004

  13. Isolation and characterisation of putative adhesins from Helicobacter pylori with affinity for heparan sulphate proteoglycan.

    PubMed

    Ruiz-Bustos, E; Ochoa, J L; Wadström, T; Ascencio, F

    2001-03-01

    A pool of heparan sulphate-binding proteins (HSBPs) from Helicobacter pylori culture supernates was obtained by sequential ammonium sulphate precipitation and affinity chromatography on heparin-Sepharose. The chromatographic procedure yielded one major fraction that contained proteins with heparan sulphate affinity as revealed by inhibition studies of heparan sulphate binding to H. pylori cells. Preparative iso-electric focusing, SDS-PAGE and blotting experiments, with peroxidase(POD)-labelled heparan sulphate as a probe, indicated the presence of two major extracellular proteins with POD-heparan sulphate affinity. One protein had a molecular mass of 66.2 kDa and a pI of 5.4, whilst the second protein had a molecular mass of 71.5 kDa and a pI of 5.0. The N-terminal amino acid sequence of the 71.5-kDa HSBP did not show homology to any other heparin-binding protein, nor to known proteins of H. pylori, whereas the 66.2-kDa HSBP showed a high homology to an Escherichia coli chaperon protein and equine haemoglobin. A third HSBP was isolated from an outer-membrane protein (OMP) fraction of H. pylori cells with a molecular mass of 47.2 kDa. The amino acid sequence of an internal peptide of the OMP-HSBP did not show homology to the extracellular HSBP of H. pylori, or to another microbial HSBP.

  14. Synthesis and characterisation of magnetised Dacron-heparin composite employed for antithrombin affinity purification.

    PubMed

    Mercês, Aurenice Arruda Dutra das; Silva, Ricardo de Souza; Silva, Karciano José Santos; Maciel, Jackeline da Costa; Oliveira, Givanildo Bezerra; Buitrago, Davian Martinez; de Aguiar, José Albino Oliveira; de Carvalho-Júnior, Luiz Bezerra

    2016-12-01

    Human antithrombin is a blood derivative widely used in the treatment of coagulation dysfunction. Affinity chromatography using heparin (HEP) derivatives is usually used for antithrombin purification. In this study, an affinity procedure based on a magnetic Dacron-HEP composite is proposed. Dacron was firstly converted to Dacron-hydrazide and magnetised by co-precipitation with of Fe(2+)/Fe(3+) (mDAC). HEP was activated by carbodiimide and N-hydroxysuccinimide and covalently linked to mDAC (mDAC-HEP). EDX and infrared spectra analyses confirmed each synthesis step of mDAC-HEP. This composite exhibited superparamagnetism behaviour. Human plasma was incubated with mDAC-HEP (fresh and stored over a long period) and washed with phosphate buffer containing increasing concentrations of NaCl. Human plasma antithrombin activity was reduced by approximately 20% in the presence of the 1.0M NaCl fraction, and this eluate was able to prolong coagulation time (aPTT) using both preparations. Electrophoresis of the eluates revealed bands corresponding to the expected size of antithrombin (58kDa). The mDAC-HEP particles are reusable. This method presents the following advantages: easy, low-cost synthesis of the composite, magnet-based affinity purification steps, and reusability.

  15. Evolution of promoter affinity for transcription factors in the human lineage.

    PubMed

    Molineris, Ivan; Grassi, Elena; Ala, Ugo; Di Cunto, Ferdinando; Provero, Paolo

    2011-08-01

    Changes in gene regulation are believed to play an important role in the evolution of animals. It has been suggested that changes in cis-regulatory regions are responsible for many or most of the anatomical and behavioral differences between humans and apes. However, the study of the evolution of cis-regulatory regions is made problematic by the degeneracy of transcription factor (TF) binding sites and the shuffling of their positions. In this work, we use the predicted total affinity of a promoter for a large collection of TFs as the basis for studying the evolution of cis-regulatory regions in mammals. We introduce the human specificity of a promoter, measuring the divergence between the affinity profile of a human promoter and its orthologous promoters in other mammals. The promoters of genes involved in functional categories such as neural processes and signal transduction, among others, have higher human specificity compared with the rest of the genome. Clustering of the human-specific affinities (HSAs) of neural genes reveals patterns of promoter evolution associated with functional categories such as synaptic transmission and brain development and to diseases such as bipolar disorder and autism.

  16. The high-affinity peptidoglycan binding domain of Pseudomonas phage endolysin KZ144

    SciTech Connect

    Briers, Yves; Schmelcher, Mathias; Loessner, Martin J.; Hendrix, Jelle; Engelborghs, Yves; Volckaert, Guido; Lavigne, Rob

    2009-05-29

    The binding affinity of the N-terminal peptidoglycan binding domain of endolysin KZ144 (PBD{sub KZ}), originating from Pseudomonas aeruginosa bacteriophage {phi}KZ, has been examined using a fusion protein of PBD{sub KZ} and green fluorescent protein (PBD{sub KZ}-GFP). A fluorescence recovery after photobleaching analysis of bound PBD{sub KZ}-GFP molecules showed less than 10% fluorescence recovery in the bleached area within 15 min. Surface plasmon resonance analysis confirmed this apparent high binding affinity revealing an equilibrium affinity constant of 2.95 x 10{sup 7} M{sup -1} for the PBD{sub KZ}-peptidoglycan interaction. This unique domain, which binds to the peptidoglycan of all tested Gram-negative species, was harnessed to improve the specific activity of the peptidoglycan hydrolase domain KMV36C. The chimeric peptidoglycan hydrolase (PBD{sub KZ}-KMV36C) exhibits a threefold higher specific activity than the native catalytic domain (KMV36C). These results demonstrate that the modular assembly of functional domains is a rational approach to improve the specific activity of endolysins from phages infecting Gram-negatives.

  17. Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions

    PubMed Central

    Zhao, Huaying; Fu, Yan; Glasser, Carla; Andrade Alba, Eric J; Mayer, Mark L; Patterson, George; Schuck, Peter

    2016-01-01

    The dynamic assembly of multi-protein complexes underlies fundamental processes in cell biology. A mechanistic understanding of assemblies requires accurate measurement of their stoichiometry, affinity and cooperativity, and frequently consideration of multiple co-existing complexes. Sedimentation velocity analytical ultracentrifugation equipped with fluorescence detection (FDS-SV) allows the characterization of protein complexes free in solution with high size resolution, at concentrations in the nanomolar and picomolar range. Here, we extend the capabilities of FDS-SV with a single excitation wavelength from single-component to multi-component detection using photoswitchable fluorescent proteins (psFPs). We exploit their characteristic quantum yield of photo-switching to imprint spatio-temporal modulations onto the sedimentation signal that reveal different psFP-tagged protein components in the mixture. This novel approach facilitates studies of heterogeneous multi-protein complexes at orders of magnitude lower concentrations and for higher-affinity systems than previously possible. Using this technique we studied high-affinity interactions between the amino-terminal domains of GluA2 and GluA3 AMPA receptors. DOI: http://dx.doi.org/10.7554/eLife.17812.001 PMID:27436096

  18. Affinity chromatography of chaperones based on denatured proteins: Analysis of cell lysates of different origin.

    PubMed

    Marchenko, N Yu; Sikorskaya, E V; Marchenkov, V V; Kashparov, I A; Semisotnov, G V

    2016-03-01

    Molecular chaperones are involved in folding, oligomerization, transport, and degradation of numerous cellular proteins. Most of chaperones are heat-shock proteins (HSPs). A number of diseases of various organisms are accompanied by changes in the structure and functional activity of chaperones, thereby revealing their vital importance. One of the fundamental properties of chaperones is their ability to bind polypeptides lacking a rigid spatial structure. Here, we demonstrate that affinity chromatography using sorbents with covalently attached denatured proteins allows effective purification and quantitative assessment of their bound protein partners. Using pure Escherichia coli chaperone GroEL (Hsp60), the capacity of denatured pepsin or lysozyme-based affinity sorbents was evaluated as 1 mg and 1.4 mg of GroEL per 1 ml of sorbent, respectively. Cell lysates of bacteria (E. coli, Thermus thermophilus, and Yersinia pseudotuberculosis), archaea (Halorubrum lacusprofundi) as well as the lysate of rat liver mitochondria were analyzed using affinity carrier with denatured lysozyme. It was found that, apart from Hsp60, other proteins with a molecular weight of about 100, 50, 40, and 20 kDa are able to interact with denatured lysozyme.

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

    PubMed

    Reinhard, André; Nürnberger, Thorsten

    2017-01-01

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

  20. Routes to improve binding capacities of affinity resins demonstrated for Protein A chromatography.

    PubMed

    Müller, Egbert; Vajda, Judith

    2016-05-15

    Protein A chromatography is a well-established platform in downstream purification of monoclonal antibodies. Dynamic binding capacities are continuously increasing with almost every newly launched Protein A resin. Nevertheless, binding capacities of affinity chromatography resins cannot compete with binding capacities obtained with modern ion exchange media. Capacities of affinity resins are roughly 50% lower. High binding capacities of ion exchange media are supported by spacer technologies. In this article, we review existing spacer technologies of affinity chromatography resins. A yet known effective approach to increase the dynamic binding capacity of Protein A resins is oligomerization of the particular Protein A motifs. This resembles the tentacle technology used in ion exchange chromatography. Dynamic binding capacities of a hexameric ligand are roughly twice as high compared to capacities obtained with a tetrameric ligand. Further capacity increases up to 130mg/ml can be realized with the hexamer ligand, if the sodium phosphate buffer concentration is increased from 20 to 100mM. Equilibrium isotherms revealed a BET shape for the hexamer ligand at monoclonal antibody liquid phase concentrations higher than 9mg/ml. The apparent multilayer formation may be due to hydrophobic forces. Other quality attributes such as recovery, aggregate content, and overall purity of the captured monoclonal antibody are not affected.

  1. Identification of proteins interacting with ammodytoxins in Vipera ammodytes ammodytes venom by immuno-affinity chromatography.

    PubMed

    Brgles, Marija; Kurtović, Tihana; Kovačič, Lidija; Križaj, Igor; Barut, Miloš; Lang Balija, Maja; Allmaier, Günter; Marchetti-Deschmann, Martina; Halassy, Beata

    2014-01-01

    In order to perform their function, proteins frequently interact with other proteins. Various methods are used to reveal protein interacting partners, and affinity chromatography is one of them. Snake venom is composed mostly of proteins, and various protein complexes in the venom have been found to exhibit higher toxicity levels than respective components separately. Complexes can modulate envenomation activity of a venom and/or potentiate its effect. Our previous data indicate that the most toxic components of the Vipera ammodytes ammodytes (Vaa) venom isolated so far-ammodytoxins (Atxs)-are contributing to the venom's toxicity only moderately; therefore, we aimed to explore whether they have some interacting partner(s) potentiating toxicity. For screening of possible interactions, immuno-affinity chromatography combined with identification by mass spectrometry was used. Various chemistries (epoxy, carbonyldiimidazole, ethylenediamine) as well as protein G functionality were used to immobilize antibodies on monolith support, a Convective Interaction Media disk. Monoliths have been demonstrated to better suit the separation of large biomolecules. Using such approach, several proteins were indicated as potential Atx-binding proteins. Among these, the interaction of Atxs with a Kunitz-type inhibitor was confirmed by far-Western dot-blot and surface plasmon resonance measurement. It can be concluded that affinity chromatography on monolithic columns combined with mass spectrometry identification is a successful approach for screening of protein interactions and it resulted with detection of the interaction of Atx with Kunitz-type inhibitor in Vaa venom for the first time.

  2. Vibration Propagation in Spider Webs

    NASA Astrophysics Data System (ADS)

    Hatton, Ross; Otto, Andrew; Elias, Damian

    Due to their poor eyesight, spiders rely on web vibrations for situational awareness. Web-borne vibrations are used to determine the location of prey, predators, and potential mates. The influence of web geometry and composition on web vibrations is important for understanding spider's behavior and ecology. Past studies on web vibrations have experimentally measured the frequency response of web geometries by removing threads from existing webs. The full influence of web structure and tension distribution on vibration transmission; however, has not been addressed in prior work. We have constructed physical artificial webs and computer models to better understand the effect of web structure on vibration transmission. These models provide insight into the propagation of vibrations through the webs, the frequency response of the bare web, and the influence of the spider's mass and stiffness on the vibration transmission patterns. Funded by NSF-1504428.

  3. Light propagation in nanorod arrays

    NASA Astrophysics Data System (ADS)

    Rahachou, A. I.; Zozoulenko, I. V.

    2007-03-01

    We study the propagation of TM- and TE-polarized light in two-dimensional arrays of silver nanorods of various diameters in a gelatin background. We calculate the transmittance, reflectance and absorption of arranged and disordered nanorod arrays and compare the exact numerical results with the predictions of the Maxwell-Garnett effective-medium theory. We show that interactions between nanorods, multipole contributions and formations of photonic gaps affect strongly the transmittance spectra that cannot be accounted for in terms of the conventional effective-medium theory. We also demonstrate and explain the degradation of the transmittance in arrays with randomly located rods as well as the weak influence of their fluctuating diameter. For TM modes we outline the importance of the skin effect, which causes the full reflection of the incoming light. We then illustrate the possibility of using periodic arrays of nanorods as high-quality polarizers.

  4. Light propagation in inhomogeneous universes

    NASA Technical Reports Server (NTRS)

    Schneider, Peter; Weiss, Achim

    1988-01-01

    Refsdal's (1970) method is generalized to study the propagation of light rays through an inhomogeneous universe. The probability distribution for the linear component of the cumulative shear (CS) along light rays is derived, and it is shown that the CS can be dominated by nonlinear components, espcially for light rays in empty cones. The amplification tail of the amplification probability distribution is compared with analytic results; these linear investigations are shown to underestimate the high-amplification probability and hence the importance of the amplification bias in source counts. The distribution of the ellipticity of images of infinitesimal circular sources is derived, and it is shown that this can be dominated by the nonlinear contributions to the CS.

  5. ETS-V propagation experiments in Japan

    NASA Technical Reports Server (NTRS)

    Ohmori, Shingo

    1988-01-01

    Propagation experiments on ship, aircraft, and land mobile earth stations were carried out using the Engineering Test Satellite-V (ETS-V), which was launched in August 1987. The propagation experiments are one of the missions of the Experimental Mobile Satellite System (EMSS). Initial experimental results of ETS-V/EMSS on propagation using ship, aircraft, and land mobiles with ETS-V are given.

  6. Multipath Propagation over Snow at Millimeter Wavelengths,

    DTIC Science & Technology

    1980-02-01

    Propagation Branch Electromagnetic Sciences Division APPROVED: ALLAN C. SCHELL , Chief Electromagnetic Sciences Division FOR THE COMANDER: JOHN P...type of snow cover. A computer program was developed in order to model the reflection as a specular process, with the underlying terrain represented...data. 2,B’ 3II Contents 1. INTRODUCTION 9 2. ANALYSIS OF MULTIPATH PROPAGATION 10 2. 1 Propagation Mechanisms 12 2.2 Model Calculations for Flat Terrain

  7. ACTS Propagation Measurements in Maryland and Virginia

    NASA Technical Reports Server (NTRS)

    Dissanayake, Asoka; Lin, Kuan-Ting

    1996-01-01

    Rapid growth in new satellite services incorporating very small aperture terminals (VSAT) and ultra small aperture terminals (USAT) is expected in the coming years. Small size terminals allow for widespread use of satellite services in small business and domestic applications. Due to congestion of lower frequency bands such as C and Ku, most of these services will use Ka-band (2/20 GHz) frequencies. Propagation impairments produced by the troposphere is a limiting factor for the effective use of the 20/30 GHz band and the use of smaller Earth terminals makes it difficult to provide sufficient link margins for propagation related outages. In this context, reliable prediction of propagation impairments for low margin systems becomes important. Due to the complexity of propagation phenomena propagation modeling is mainly attempted on an empirical basis. As such, the availability of reliable measured data that extend to probability levels well in excess of the traditional limit of 1 percent is of great importance in the development, validation, and refinement of propagation models. The beacon payload on the Advanced Communications Technology Satellite (ACTS) together with the propagation measurement terminals developed under the NASA ACTS propagation program provide an excellent opportunity to collect such data on a long-term basis. This paper presents the results of ACTS propagation measurements conducted in the Washington, DC metropolitan area by COMSAT Laboratories.

  8. A stochastic model for propagation through tissue.

    PubMed

    Lacaze, Bernard

    2009-10-01

    Attenuation of ultrasonic waves is often assumed linear with respect to frequency in biological applications whereas it is considered quadratic when the propagation occurs in the atmosphere or the water. In the latter case, other studies show that a Gaussian propagation duration can explain this attenuation behavior and provide a model for the energy loss in the stationary limit. The present paper defines an equivalent random propagation duration with Cauchy distribution, which is appropriate for the propagation of ultrasound through tissue. The model adds an unobserved noise that represents the signal deterioration. In addition, the model agrees with the mode downshift in the case of a narrowband signal.

  9. Quench propagation velocity for highly stabilized conductors

    SciTech Connect

    Mints, R.G. |; Ogitsu, T. |; Devred, A.

    1995-05-01

    Quench propagation velocity in conductors having a large amount of stabilizer outside the multifilamentary area is considered. It is shown that the current redistribution process between the multifilamentary area and the stabilizer can strongly effect the quench propagation. A criterion is derived determining the conditions under which the current redistribution process becomes significant, and a model of effective stabilizer area is suggested to describe its influence on the quench propagation velocity. As an illustration, the model is applied to calculate the adiabatic quench propagation velocity for a conductor geometry with a multifilamentary area embedded inside the stabilizer.

  10. Purification to homogeneity of an active opioid receptor from rat brain by affinity chromatography.

    PubMed

    Loukas, S; Mercouris, M; Panetsos, F; Zioudrou, C

    1994-05-10

    Active opioid binding proteins were solubilized from rat brain membranes in high yield with sodium deoxycholate in the presence of NaCl. Purification of opioid binding proteins was accomplished by opioid antagonist affinity chromatography. Chromatography using the delta-opioid antagonist N,N-diallyl-Tyr-D-Leu-Gly-Tyr-Leu attached to omega-aminododecyl-agarose (Affi-G) (procedure A) yielded a partially purified protein that binds selectively the delta-opioid agonist [3H]Tyr-D-Ser-Gly-Phe-Leu-Thr ([3H]DSLET), with a Kd of 19 +/- 3 nM and a Bmax of 5.1 +/- 0.4 nmol/mg of protein. Subsequently, Lens culinaris agglutinin-Sepharose 4B chromatography of the Affi-G eluate resulted in isolation of an electrophoretically homogeneous protein of 58 kDa that binds selectively [3H]DSLET with a Kd of 21 +/- 3 nM and a Bmax of 16.5 +/- 1.0 nmol/mg of protein. Chromatography using the nonselective antagonist 6-aminonaloxone coupled to 6-aminohexanoic acid-Sepharose 4B (Affi-NAL) (procedure B) resulted in isolation of a protein that binds selectively [3H]DSLET with a Kd of 32 +/- 2 nM and a Bmax of 12.4 +/- 0.5 nmol/mg of protein, and NaDodSO4/PAGE revealed a major band of apparent molecular mass 58 kDa. Polyclonal antibodies (Anti-R IgG) raised against the Affi-NAL protein inhibit the specific [3H]DSLET binding to the Affi-NAL eluate and to the solubilized membranes. Moreover, the Anti-R IgG inhibits the specific binding of radiolabeled Tyr-D-Ala-Gly-N-methyl-Phe-Gly-ol (DAMGO; mu-agonist), DSLET (delta-agonist), and naloxone to homogenates of rat brain membranes with equal potency. Furthermore, immunoaffinity chromatography of solubilized membranes resulted in the retention of a major protein of apparent molecular mass 58 kDa. In addition, immunoblotting of solubilized membranes and purified proteins from the Affi-G and Affi-NAL matrices revealed that the Anti-R IgG interacts with a protein of 58 kDa.

  11. The serotonin transporter: Examination of the changes in transporter affinity induced by ligand binding

    SciTech Connect

    Humphreys, C.J.

    1989-01-01

    The plasmalemmal serotonin transporter uses transmembrane gradients of Na{sup +}, Cl{sup {minus}} and K{sup +} to accumulate serotonin within blood platelets. Transport is competitively inhibited by the antidepressant imipramine. Like serotonin transport, imipramine binding requires Na{sup +}. Unlike serotonin, however, imipramine does not appear to be transported. To gain insight into the mechanism of serotonin transport the author have analyzed the influences of Na{sup +} and Cl{sup {minus}}, the two ions cotransported with serotonin, on both serotonin transport and the interaction of imipramine and other antidepressant drugs with the plasmalemmal serotonin transporter of human platelets. Additionally, the author have synthesized, purified and characterized the binding of 2-iodoimipramine to the serotonin transporter. Finally, the author have conducted a preliminary study of the inhibition of serotonin transport and imipramine binding produced by dicyclohexylcarbodiimide. My results reveal many instances of positive heterotropic cooperativity in ligand binding to the serotonin transporter. Na{sup +} binding enhances the transporters affinity for imipramine and several other antidepressant drugs, and also increases the affinity for Cl{sup {minus}}. Cl{sup {minus}} enhances the transporters affinity for imipramine, as well as for Na{sup +}. At concentrations in the range of its K{sub M} for transport serotonin is a competitive inhibitor of imipramine binding. At much higher concentrations, however, serotonin also inhibits imipramines dissociation rate constant. This latter effect which is Na{sup +}-independent and species specific, is apparently produced by serotonin binding at a second, low affinity site on, or near, the transporter complex. Iodoimipramine competitively inhibit both ({sup 3}H)imipramine binding and ({sup 3}H)serotonin transport.

  12. Innovation in chemistry courses in France in the mid-eighteenth century: experiments and affinities.

    PubMed

    Lehman, Christine

    2010-03-01

    In the middle of the eighteenth century, chemistry was the object of spectacular public infatuation. Each course was specialised, depending on its particular audience. In order to meet the range of expectations of its diverse public, chemistry taught in France during this period combined apprenticeship and growing theoretical sophistication, while at the same time remaining popular and spectacular. The analysis of manuscript notes taken by Rouelle's, Venel's and Macquer's students reveals an innovative chemistry, based on experiment, in which theory and practice went hand in hand. The experimental approach was based on the widespread use of Geoffroy's affinity table, which made it possible to both interpret and predict operations.

  13. Evidence of land plant affinity for the Devonian fossil Protosalvinia (Foerstia)

    USGS Publications Warehouse

    Romankiw, L.A.; Hatcher, P.G.; Roen, J.B.

    1988-01-01

    The Devonian plant fossil Protosalvinia (Foerstia) has been examined by solid-state 13C nuclear magnetic resonance spectroscopy (NMR) and pyrolysis-gas chromatography-mass spectrometry (PY-GC-MS). Results of these studies reveal that the chemical structure of Protosalvinia is remarkably similar to that of coalified wood. A well-defined phenolic carbon peak in the NMR spectra and the appearance of phenol and alkylated phenols in pyrolysis products are clearly indicative of lignin-like compounds. These data represent significant new information on the chemical nature of Protosalvinia and provide the first substantial organic geochemical evidence for land plant affinity. -Authors

  14. Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice.

    PubMed

    Keck, Zhen-Yong; Wang, Yong; Lau, Patrick; Lund, Garry; Rangarajan, Sneha; Fauvelle, Catherine; Liao, Grant C; Holtsberg, Frederick W; Warfield, Kelly L; Aman, M Javad; Pierce, Brian G; Fuerst, Thomas R; Bailey, Justin R; Baumert, Thomas F; Mariuzza, Roy A; Kneteman, Norman M; Foung, Steven K H

    2016-12-01

    Direct-acting antivirals (DAAs) have led to a high cure rate in treated patients with chronic hepatitis C virus (HCV) infection, but this still leaves a large number of treatment failures secondary to the emergence of resistance-associated variants (RAVs). To increase the barrier to resistance, a complementary strategy is to use neutralizing human monoclonal antibodies (HMAbs) to prevent acute infection. However, earlier efforts with the selected antibodies led to RAVs in animal and clinical studies. Therefore, we identified an HMAb that is less likely to elicit RAVs for affinity maturation to increase potency and, more important, breadth of protection. Selected matured antibodies show improved affinity and neutralization against a panel of diverse HCV isolates. Structural and modeling studies reveal that the affinity-matured HMAb mediates virus neutralization, in part, by inducing conformational change to the targeted epitope, and that the maturated light chain is responsible for the improved affinity and breadth of protection. A matured HMAb protected humanized mice when challenged with an infectious HCV human serum inoculum for a prolonged period. However, a single mouse experienced breakthrough infection after 63 days when the serum HMAb concentration dropped by several logs; sequence analysis revealed no viral escape mutation.

  15. Nanoparticle multivalency counterbalances the ligand affinity loss upon PEGylation.

    PubMed

    Hennig, Robert; Pollinger, Klaus; Veser, Anika; Breunig, Miriam; Goepferich, Achim

    2014-11-28

    The conjugation of receptor ligands to shielded nanoparticles is a widely used strategy to precisely control nanoparticle-cell interactions. However, it is often overlooked that a ligand's affinity can be severely impaired by its attachment to the polyethylene glycol (PEG) chains that are frequently used to protect colloids from serum protein adsorption. Using the model ligand EXP3174, a small-molecule antagonist for the angiotensin II receptor type 1 (AT1R), we investigated the ligand's affinity before and after its PEGylation and when attached to PEGylated nanoparticles. The PEGylated ligand displayed a 580-fold decreased receptor affinity compared to the native ligand. Due to their multivalency, the nanoparticles regained a low nanomolar receptor affinity, which is in the range of the affinity of the native ligand. Moreover, a four orders of magnitude higher concentration of free ligand was required to displace PEGylated nanoparticles carrying EXP3174 from the receptor. On average, one nanoparticle was decorated with 11.2 ligand molecules, which led to a multivalent enhancement factor of 22.5 compared to the monovalent PEGylated ligand. The targeted nanoparticles specifically bound the AT1R and showed no interaction to receptor negative cells. Our study shows that the attachment of a small-molecule ligand to a PEG chain can severely affect its receptor affinity. Concomitantly, when the ligand is tethered to nanoparticles, the immense avidity greatly increases the ligand-receptor interaction. Based on our results, we highly recommend the affinity testing of receptor ligands before and after PEGylation to identify potent molecules for active nanoparticle targeting.

  16. Protein Complex Affinity Capture from Cryomilled Mammalian Cells.

    PubMed

    LaCava, John; Jiang, Hua; Rout, Michael P

    2016-12-09

    Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.

  17. Protein Complex Affinity Capture from Cryomilled Mammalian Cells

    PubMed Central

    LaCava, John; Jiang, Hua; Rout, Michael P.

    2016-01-01

    Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets. PMID:28060343

  18. Attenuation of outdoor sound propagation levels by a snow cover

    NASA Astrophysics Data System (ADS)

    Albert, Donald G.

    1993-11-01

    The absorption of sound energy by the ground has been studied extensively because of its importance in understanding noise propagation through the atmosphere. This report investigates the attenuative effect of snow on sound propagation, and provides, quantitative measurements and an accurate model for predicting these effects. Summer and winter experiments were conducted at a site in northern Vermont to investigate the effect of a snow cover on low energy sound propagation in the 5- to 500-Hz frequency band for propagation distances between 1 and 274 m. Pistol shots were used as the source of the acoustic waves, with geophones and microphones serving as the receivers. A comparison of the summer and winter recordings revealed a number of effects caused by the introduction of a 0.25-m-thick snow cover. The peak amplitude of the air wave was more strongly attenuated in the winter, with a decay rate proportional to r(exp 1.6) versus r(exp 1.2) in the summer, corresponding to an order of magnitude difference in the signal levels after 100 m of propagation. The waveforms were also markedly changed, with broadened pulses and greatly enhanced low frequencies appearing in the winter recordings. The pulse broadening and peak amplitude decay rates of the acoustic waveforms were successfully predicted theoretically using a layered, rigid, porous model of the snow, with an assumed surface effective flow resistivity of 20 kN s/m to the 4th. Calculations of ground motion induced by the atmospheric sound waves were made using a viscoelastic model of the ground and the wavenumber integration technique.

  19. Wave propagation in axially moving periodic strings

    NASA Astrophysics Data System (ADS)

    Sorokin, Vladislav S.; Thomsen, Jon Juel

    2017-04-01

    The paper deals with analytically studying transverse waves propagation in an axially moving string with periodically modulated cross section. The structure effectively models various relevant technological systems, e.g. belts, thread lines, band saws, etc., and, in particular, roller chain drives for diesel engines by capturing both their spatial periodicity and axial motion. The Method of Varying Amplitudes is employed in the analysis. It is shown that the compound wave traveling in the axially moving periodic string comprises many components with different frequencies and wavenumbers. This is in contrast to non-moving periodic structures, for which all components of the corresponding compound wave feature the same frequency. Due to this "multi-frequency" character of the wave motion, the conventional notion of frequency band-gaps appears to be not applicable for the moving periodic strings. Thus, for such structures, by frequency band-gaps it is proposed to understand frequency ranges in which the primary component of the compound wave attenuates. Such frequency band-gaps can be present for a moving periodic string, but only if its axial velocity is lower than the transverse wave speed, and, the higher the axial velocity, the narrower the frequency band-gaps. The revealed effects could be of potential importance for applications, e.g. they indicate that due to spatial inhomogeneity, oscillations of axially moving periodic chains always involve a multitude of frequencies.

  20. Nonstructural 5A Protein of Hepatitis C Virus Interacts with Pyruvate Carboxylase and Modulates Viral Propagation

    PubMed Central

    Kim, Jong-Wook; Hwang, Soon B.

    2013-01-01

    Hepatitis C virus (HCV) is highly dependent on cellular factors for its own propagation. By employing tandem affinity purification method, we identified pyruvate carboxylase (PC) as a cellular partner for NS5A protein. NS5A interacted with PC through the N-terminal region of NS5A and the biotin carboxylase domain of PC. PC expression was decreased in cells expressing NS5A and HCV-infected cells. Promoter activity of PC was also decreased by NS5A protein. However, FAS expression was increased in cells expressing NS5A and cell culture grown HCV (HCVcc)-infected cells. Silencing of PC promoted fatty acid synthase (FAS) expression level. These data suggest HCV may modulate PC via NS5A protein for its own propagation. PMID:23861867

  1. Explosion propagation in inert porous media.

    PubMed

    Ciccarelli, G

    2012-02-13

    Porous media are often used in flame arresters because of the high surface area to volume ratio that is required for flame quenching. However, if the flame is not quenched, the flow obstruction within the porous media can promote explosion escalation, which is a well-known phenomenon in obstacle-laden channels. There are many parallels between explosion propagation through porous media and obstacle-laden channels. In both cases, the obstructions play a duel role. On the one hand, the obstruction enhances explosion propagation through an early shear-driven turbulence production mechanism and then later by shock-flame interactions that occur from lead shock reflections. On the other hand, the presence of an obstruction can suppress explosion propagation through momentum and heat losses, which both impede the unburned gas flow and extract energy from the expanding combustion products. In obstacle-laden channels, there are well-defined propagation regimes that are easily distinguished by abrupt changes in velocity. In porous media, the propagation regimes are not as distinguishable. In porous media the entire flamefront is affected, and the effects of heat loss, turbulence and compressibility are smoothly blended over most of the propagation velocity range. At low subsonic propagation speeds, heat loss to the porous media dominates, whereas at higher supersonic speeds turbulence and compressibility are important. This blending of the important phenomena results in no clear transition in propagation mechanism that is characterized by an abrupt change in propagation velocity. This is especially true for propagation velocities above the speed of sound where many experiments performed with fuel-air mixtures show a smooth increase in the propagation velocity with mixture reactivity up to the theoretical detonation wave velocity.

  2. Visualizing the Propagation of Acute Lung Injury

    PubMed Central

    Cereda, Maurizio; Xin, Yi; Meeder, Natalie; Zeng, Johnathan; Jiang, YunQing; Hamedani, Hooman; Profka, Harrilla; Kadlecek, Stephen; Clapp, Justin; Deshpande, Charuhas G.; Wu, Jue; Gee, James C.; Kavanagh, Brian P.; Rizi, Rahim R.

    2015-01-01

    Background Mechanical ventilation worsens acute respiratory distress syndrome (ARDS), but this secondary ‘ventilator-associated’ injury is variable and difficult to predict. We aimed to visualize the propagation of such ventilator-induced injury, in the presence (and absence) of a primary underlying lung injury, and to determine the predictors of propagation. Methods Anesthetized rats (n=20) received acid aspiration (HCl) followed by ventilation with moderate tidal volume (VT). In animals surviving ventilation for at least two hours, propagation of injury was quantified using serial computed tomography (CT). Baseline lung status was assessed by oxygenation, lung weight, and lung strain (VT/expiratory lung volume). Separate groups of rats without HCl aspiration were ventilated with large (n=10) or moderate (n=6) VT. Results In 15 rats surviving longer than two hours, CT opacities spread outwards from the initial site of injury. Propagation was associated with higher baseline strain (propagation vs. no propagation, mean ± SD: 1.52 ± 0.13 vs. 1.16 ± 0.20, p<0.01), but similar oxygenation and lung weight. Propagation did not occur where baseline strain <1.29. In healthy animals, large VT caused injury that was propagated inwards from the lung periphery; in the absence of preexisting injury, propagation did not occur where strain was <2.0. Conclusions Compared with healthy lungs, underlying injury causes propagation to occur at a lower strain threshold and, it originates at the site of injury; this suggests that tissue around the primary lesion is more sensitive. Understanding how injury is propagated may ultimately facilitate a more individualized monitoring or management. PMID:26536308

  3. The Structural Basis of Sirtuin Substrate Affinity

    SciTech Connect

    Cosgrove,M.; Bever, K.; Avalos, J.; Muhammad, S.; Zhang, X.; Wolberger, C.

    2006-01-01

    Sirtuins comprise a family of enzymes that catalyze the deacetylation of acetyllysine side chains in a reaction that consumes NAD+. Although several crystal structures of sirtuins bound to non-native acetyl peptides have been determined, relatively little about how sirtuins discriminate among different substrates is understood. We have carried out a systematic structural and thermodynamic analysis of several peptides bound to a single sirtuin, the Sir2 homologue from Thermatoga maritima (Sir2Tm). We report structures of five different forms of Sir2Tm: two forms bound to the p53 C-terminal tail in the acetylated and unacetylated states, two forms bound to putative acetyl peptide substrates derived from the structured domains of histones H3 and H4, and one form bound to polypropylene glycol (PPG), which resembles the apoenzyme. The structures reveal previously unobserved complementary side chain interactions between Sir2Tm and the first residue N-terminal to the acetyllysine (position -1) and the second residue C-terminal to the acetyllysine (position +2). Isothermal titration calorimetry was used to compare binding constants between wild-type and mutant forms of Sir2Tm and between additional acetyl peptide substrates with substitutions at positions -1 and +2. The results are consistent with a model in which peptide positions -1 and +2 play a significant role in sirtuin substrate binding. This model provides a framework for identifying sirtuin substrates.

  4. Gradient-based habitat affinities predict species vulnerability to drought.

    PubMed

    Debinski, Diane M; Caruthers, Jennet C; Cook, Dianne; Crowley, Jason; Wickham, Hadley

    2013-05-01

    Ecological fingerprints of climate change are becoming increasingly evident at broad geographical scales as measured by species range shifts and changes in phenology. However, finer-scale species-level responses to environmental fluctuations may also provide an important bellwether of impending future community responses. Here we examined changes in abundance of butterfly species along a hydrological gradient of six montane meadow habitat types in response to drought. Our data collection began prior to the drought, and we were able to track changes for 11 years, of which eight were considered mild to extreme drought conditions. We separated the species into those that had an affinity for hydric vs. xeric habitats. We suspected that drought would favor species with xeric habitat affinities, but that there could be variations in species-level responses along the hydrological gradient. We also suspected that mesic meadows would be most sensitive to drought conditions. Temporal trajectories were modeled for both species groups (hydric vs. xeric affinity) and individual species. Abundances of species with affinity for xeric habitats increased in virtually all meadow types. Conversely, abundances of species with affinity for hydric habitats decreased, particularly in mesic and xeric meadows. Mesic meadows showed the most striking temporal abundance trajectory: Increasing abundances of species with xeric habitat affinity were offset by decreasing or stable abundances of species with hydric habitat affinity. The one counterintuitive finding was that, in some hydric meadows, species with affinity for hydric habitats increased. In these cases, we suspect that decreasing moisture conditions in hydric meadows actually increased habitat suitability because sites near the limit of moisture extremes for some species became more acceptable. Thus, species responses were relatively predictable based upon habitat affinity and habitat location along the hydrological gradient, and

  5. The proton affinities of saturated and unsaturated heterocyclic molecules

    NASA Astrophysics Data System (ADS)

    Kabli, Samira; van Beelen, Eric S. E.; Ingemann, Steen; Henriksen, Lars; Hammerum, Steen

    2006-03-01

    The proton affinities derived from G3-calculations of 23 five-membered ring heteroaromatic molecules agree well with the experimentally determined values available in the literature. The calculated local proton affinities show that the principal site of protonation of the heteroaromatic compounds examined is an atom of the ring, carbon when there is only one heteroatom in the ring, and nitrogen where there are two or more heteroatoms. The experimental proton affinities of non-aromatic cyclic ethers, amines and thioethers are also in excellent agreement with the calculated values, with two exceptions (oxetane, N-methylazetidine). The literature proton affinities of the four simple cyclic ethers, oxetane, tetrahydrofuran, tetrahydropyran and oxepane were confirmed by Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry, in order to examine the disagreement between the values predicted by extrapolation or additivity for tetrahydrofuran and tetrahydropyran and those determined by experiment and by calculation. The proton affinity differences between the pairs tetrahydropyran/1,4-dioxane, piperidine/morpholine and related compounds show that introduction of an additional oxygen atom in the ring considerably lowers the basicity.

  6. Improving antibody binding affinity and specificity for therapeutic development.

    PubMed

    Bostrom, Jenny; Lee, Chingwei V; Haber, Lauric; Fuh, Germaine

    2009-01-01

    Affinity maturation is an important part of the therapeutic antibody development process as in vivo activity often requires high binding affinity. Here, we describe a targeted approach for affinity improvement of therapeutic antibodies. Sets of CDR residues that are solvent accessible and relatively diverse in natural antibodies are targeted for diversification. Degenerate oligonucleotides are used to generate combinatorial phage-displayed antibody libraries with varying degree of diversity at randomized positions from which high-affinity antibodies can be selected. An advantage of using antibodies for therapy is their exquisite target specificity, which enables selective antigen binding and reduces off-target effects. However, it can be useful, and often it is necessary, to generate cross-reactive antibodies binding to not only the human antigen but also the corresponding non-human primate or rodent orthologs. Such cross-reactive antibodies can be used to validate the therapeutic targeting and examine the safety profile in preclinical animal models before committing to a costly development track. We show how affinity improvement and cross-species binding can be achieved in a one-step process.

  7. High-affinity K+ uptake in pepper plants.

    PubMed

    Martínez-Cordero, M Angeles; Martínez, Vicente; Rubio, Francisco

    2005-06-01

    High-affinity K+ uptake is an essential process for plant nutrition under K+-limiting conditions. The results presented here demonstrate that pepper (Capsicum annuum) plants grown in the absence of NH4+ and starved of K+ show an NH4+-sensitive high-affinity K+ uptake that allows plant roots to deplete external K+ to values below 1 microM. When plants are grown in the presence of NH4+, high-affinity K+ uptake is not inhibited by NH4+. Although NH4+-grown plants deplete external K+ below 1 microM in the absence of NH4+, when 1 mM NH4+ is present they do not deplete external K+ below 10 microM. A K+ transporter of the HAK family, CaHAK1, is very likely mediating the NH4+-sensitive component of the high-affinity K+ uptake in pepper roots. CaHAK1 is strongly induced in the roots that show the NH4+-sensitive high-affinity K+ uptake and its induction is reduced in K+-starved plants grown in the presence of NH4+. The NH4+-insensitive K+ uptake may be mediated by an AKT1-like K+ channel.

  8. Affine kinematics in planar fibrous connective tissues: an experimental investigation.

    PubMed

    Jayyosi, C; Affagard, J-S; Ducourthial, G; Bonod-Bidaud, C; Lynch, B; Bancelin, S; Ruggiero, F; Schanne-Klein, M-C; Allain, J-M; Bruyère-Garnier, K; Coret, M

    2017-03-29

    The affine transformation hypothesis is usually adopted in order to link the tissue scale with the fibers scale in structural constitutive models of fibrous tissues. Thanks to the recent advances in imaging techniques, such as multiphoton microscopy, the microstructural behavior and kinematics of fibrous tissues can now be monitored at different stretching within the same sample. Therefore, the validity of the affine hypothesis can be investigated. In this paper, the fiber reorientation predicted by the affine assumption is compared to experimental data obtained during mechanical tests on skin and liver capsule coupled with microstructural imaging using multiphoton microscopy. The values of local strains and the collagen fibers orientation measured at increasing loading levels are used to compute a theoretical estimation of the affine reorientation of collagen fibers. The experimentally measured reorientation of collagen fibers during loading could not be successfully reproduced with this simple affine model. It suggests that other phenomena occur in the stretching process of planar fibrous connective tissues, which should be included in structural constitutive modeling approaches.

  9. Biphasic Affinity Chromatographic Approach for Deep Tyrosine Phosphoproteome Analysis.

    PubMed

    Deng, Zhenzhen; Dong, Mingming; Wang, Yan; Dong, Jing; Li, Shawn S-C; Zou, Hanfa; Ye, Mingliang

    2017-02-21

    Tyrosine phosphorylation (pTyr) is important for normal physiology and implicated in many human diseases, particularly cancer. Identification of pTyr sites is critical to dissecting signaling pathways and understanding disease pathologies. However, compared with serine/threonine phosphorylation (pSer/pThr), the analysis of pTyr at the proteome level is more challenging due to its low abundance. Here, we developed a biphasic affinity chromatographic approach where Src SH2 superbinder was coupled with NeutrAvidin affinity chromatography, for tyrosine phosphoproteome analysis. With the use of competitive elution agent biotin-pYEEI, this strategy can distinguish high-affinity phosphotyrosyl peptides from low-affinity ones, while the excess competitive agent is readily removed by using NeutrAvidin agarose resin in an integrated tip system. The excellent performance of this system was demonstrated by analyzing tyrosine phosphoproteome of Jurkat cells from which 3,480 unique pTyr sites were identified. The biphasic affinity chromatography method for deep Tyr phosphoproteome analysis is rapid, sensitive, robust, and cost-effective. It is widely applicable to the global analysis of the tyrosine phosphoproteome associated with tyrosine kinase signal transduction.

  10. Protein purification by aminosquarylium cyanine dye-affinity chromatography.

    PubMed

    Silva, M S; Graça, V C; Reis, L V; Santos, P F; Almeida, P; Queiroz, J A; Sousa, F

    2013-12-01

    The most selective purification method for proteins and other biomolecules is affinity chromatography. This method is based on the unique biological-based specificity of the biomolecule-ligand interaction and commonly uses biological ligands. However, these ligands may present some drawbacks, mainly because of their cost and lability. Dye-affinity chromatography overcomes the limitations of biological ligands and is widely used owing to the low cost of synthetic dyes and to their resistance to biological and chemical degradation. In this work, immobilized aminosquarylium cyanine dyes are used in order to exploit affinity interactions with standard proteins such as lysozyme, α-chymotrypsin and trypsin. These studies evaluate the affinity interactions occurring between the immobilized ligand and the different proteins, as a reflection of the sum of several molecular interactions, namely ionic, hydrophobic and van der Waals, spread throughout the structure, in a defined spatial manner. The results show the possibility of using an aminosquarylium cyanine dye bearing a N-hexyl pendant chain, with a ligand density of 1.8 × 10(-2) mmol of dye/g of chromatographic support, to isolate lysozyme, α-chymotrypsin and trypsin from a mixture. The application of a decreasing ammonium sulfate gradient resulted in the recovery of lysozyme in the flowthrough. On the other hand, α-chymotrypsin and trypsin were retained, involving different interactions with the ligand. In conclusion, this study demonstrates the potential applicability of ligands such as aminosquarylium cyanine dyes for the separation and purification of proteins by affinity chromatography.

  11. Affinity labelling and identification of the high-affinity choline carrier from synaptic membranes of Torpedo electromotor nerve terminals with [3H]choline mustard.

    PubMed

    Rylett, R J

    1988-12-01

    The physiological mechanisms regulating activity of the sodium-dependent, high-affinity choline transporter and the molecular events in the translocation process remain unclear; the protein has not been purified or characterized biochemically. In the present study, [3H]choline mustard aziridinium ion [( 3H]ChM Az), a nitrogen mustard analogue of choline, bound irreversibly to presynaptic plasma membranes from Torpedo electric organ in a hemicholinium-sensitive, and sodium-, time-, and temperature-dependent manner. Specific binding of this ligand was greatest when it was incubated with membranes in the presence of sodium at 30 degrees C. Separation of the 3H-labelled membrane proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that most of the radiolabel was associated with a polypeptide of apparent molecular mass of approximately 42,000 daltons; labelling of this species was abolished in membranes incubated with ligand in the presence of HC-3. Two other 3H-labelled polypeptides were detected, with apparent molecular masses of approximately 58,000 and 90,000 daltons; radiolabelling of the former was also HC-3 sensitive. [3H]ChM Az may be a useful affinity ligand in the purification of the choline carrier from cholinergic neurons.

  12. Rapid vegetative propagation method for carob

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many fruit species are propagated by vegetative methods such as budding, grafting, cutting, suckering, layering etc. to avoid heterozygosity. Carob trees (Ceratonia siliqua L.) are of highly economical value and it is among the most difficult-to-propagate fruit species. In this study, air-layering p...

  13. Propagation of major plant-virus hosts.

    PubMed

    Hull, Roger

    2009-08-01

    Plant viruses are propagated in host plants, which are usually grown in glasshouses, screen houses, or growth cabinets. In most cases, the plants are grown from seed; in some cases, they are propagated as cuttings. This unit describes the basic techniques of growing suitable plants from seed and cuttings.

  14. Nondestructive evaluation of pyroshock propagation using hydrocodes

    NASA Astrophysics Data System (ADS)

    Lee, Juho; Hwang, Dae-Hyeon; Jang, Jae-Kyeong; Lee, Jung-Ryul; Han, Jae-Hung

    2016-04-01

    Pyroshock or pyrotechnic shock generated by explosive events of pyrotechnic devices can induce fatal failures in electronic payloads. Therefore, understanding and estimation of pyroshock propagation through complex structures are necessary. However, an experimental approach using real pyrotechnic devices is quite burdensome because pyrotechnic devices can damage test structures and newly manufactured test structures are necessary for each experiment. Besides, pyrotechnic experiments are quite expensive, time-consuming, and dangerous. Consequently, nondestructive evaluation (NDE) of pyroshock propagation without using real pyrotechnic devices is necessary. In this study, nondestructive evaluation technique for pyroshock propagation estimation using hydrocodes is proposed. First, pyroshock propagation is numerically analyzed using AUTODYN, a commercial hydrocodes. Hydrocodes can handle stress wave propagation including elastic, plastic, and shock wave in the time domain. Test structures are modeled and pyroshock time history is applied to where the pyroshock propagation originates. Numerical NDE results of pyroshock propagation on test structures are analyzed in terms of acceleration time histories and acceleration shock response spectra (SRS) results. To verify the proposed numerical methodology, impact tests using airsoft gun are performed. The numerical analysis results for the impact tests are compared with experimental results and they show good agreements. The proposed numerical techniques enable us to nondestructively characterize pyroshock propagation.

  15. Vehicular sources in acoustic propagation experiments

    NASA Technical Reports Server (NTRS)

    Prado, Gervasio; Fitzgerald, James; Arruda, Anthony; Parides, George

    1990-01-01

    One of the most important uses of acoustic propagation models lies in the area of detection and tracking of vehicles. Propagation models are used to compute transmission losses in performance prediction models and to analyze the results of past experiments. Vehicles can also provide the means for cost effective experiments to measure acoustic propagation conditions over significant ranges. In order to properly correlate the information provided by the experimental data and the propagation models, the following issues must be taken into consideration: the phenomenology of the vehicle noise sources must be understood and characterized; the vehicle's location or 'ground truth' must be accurately reproduced and synchronized with the acoustic data; and sufficient meteorological data must be collected to support the requirements of the propagation models. The experimental procedures and instrumentation needed to carry out propagation experiments are discussed. Illustrative results are presented for two cases. First, a helicopter was used to measure propagation losses at a range of 1 to 10 Km. Second, a heavy diesel-powered vehicle was used to measure propagation losses in the 300 to 2200 m range.

  16. Propagation testing multi-cell batteries.

    SciTech Connect

    Orendorff, Christopher J.; Lamb, Joshua; Steele, Leigh Anna Marie; Spangler, Scott Wilmer

    2014-10-01

    Propagation of single point or single cell failures in multi-cell batteries is a significant concern as batteries increase in scale for a variety of civilian and military applications. This report describes the procedure for testing failure propagation along with some representative test results to highlight the potential outcomes for different battery types and designs.

  17. PROPHET: An applicaton of propagation forecasting principles

    NASA Technical Reports Server (NTRS)

    Argo, P. E.; Rothmuller, I. J.

    1979-01-01

    A propagation assessment and forecasting terminal, PROPHET, is described. The terminal is a key element of the environmental prediction and assessment system which uses real time solar/geophysical data to provide real time knowledge of propagation conditions. The terminal uses models to translate data from satellite and ground based sources into performance predictions for specific systems.

  18. Uncertainty Propagation in an Ecosystem Nutrient Budget.

    EPA Science Inventory

    New aspects and advancements in classical uncertainty propagation methods were used to develop a nutrient budget with associated error for a northern Gulf of Mexico coastal embayment. Uncertainty was calculated for budget terms by propagating the standard error and degrees of fr...

  19. Propagation of almond rootstocks and trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Millions of almond trees in production in California and elsewhere were propagated by nurseries using the grafting technique called budding. This gives a uniform orchard and allows the grower to select nut cultivar (scion) and rootstock combinations. Grafting is a form of clonal propagation and resu...

  20. Ethanol-Induced ADH Activity in Zebrafish: Differential Concentration-Dependent Effects on High- Versus Low-Affinity ADH Enzymes.

    PubMed

    Tran, Steven; Nowicki, Magda; Facciol, Amanda; Chatterjee, Diptendu; Gerlai, Robert

    2016-04-01

    Zebrafish express enzymes that metabolize ethanol in a manner comparable to that of mammals, including humans. We previously demonstrated that acute ethanol exposure increases alcohol dehydrogenase (ADH) activity in an inverted U-shaped dose-dependent manner. It was hypothesized that the biphasic dose-response was due to the increased activity of a high-affinity ADH isoform following exposure to low concentrations of ethanol and increased activity of a low-affinity ADH isoform following exposure to higher concentrations of ethanol. To test this hypothesis, we exposed zebrafish to different concentrations of ethanol (0%, 0.25%, 0.5%, and 1.0% v/v) for 30 min and measured the total ADH activity in the zebrafish liver. However, we also repeated this enzyme activity assay using a low concentration of the substrate (ethanol) to determine the activity of high-affinity ADH isoforms. We found that total ADH activity in response to ethanol induces an inverted U-shaped dose-response similar to our previous study. Using a lower substrate level in our enzyme assay targeting high-affinity isozymes, we found a similar dose-response. However, the difference in activity between the high and low substrate assays (high substrate activity - low substrate activity), which provide an index of activity for low-affinity ADH isoforms, revealed no significant effect of ethanol exposure. Our results suggest that the inverted U-shaped dose-response for total ADH activity in response to ethanol is driven primarily by high-affinity isoforms of ADH.

  1. Understanding the differential nitrogen sensing mechanism in rice genotypes through expression analysis of high and low affinity ammonium transporter genes.

    PubMed

    Gaur, Vikram Singh; Singh, U S; Gupta, Atul K; Kumar, Anil

    2012-03-01

    Two rice genotypes, Kalanamak 3119 (KN3119) and Pusa Basmati 1(PB1) differing in their optimum nitrogen requirements (30 and 120 kg/ha, respectively) were undertaken to study the expression of both high and low affinity ammonium transporter genes responsible for ammonium uptake. Exposing the roots of the seedlings of both the genotypes to increasing (NH(4))(2)SO(4) concentrations revealed that all the three families of rice AMT genes are expressed, some of which get altered in a genotype and concentration specific manner. This indicates that individual ammonium transporter genes have defined contributions for ammonium uptake and plant growth. Interestingly, in response to increasing nitrogen concentrations, a root specific high affinity gene, AMT1;3, was repressed in the roots of KN3119 but not in PB1 indicating the existence of a differential ammonium sensing mechanism. This also indicates that not only AMT1;3 is involved not only in ammonium uptake but may also in ammonium sensing. Further, if it can differentiate and could be used as a biomarker for nitrogen responsiveness. Expression analysis of low affinity AMT genes showed that, both AMT2;1 and AMT2;2 have high levels of expression in both roots and shoots and in KN3119 are induced at low ammonium concentrations. Expressions of AMT3 family genes were higher shoots than in the roots indicating that these genes are probably involved in the translocation and distribution of ammonium ions in leaves. The expression of the only high affinity AMT gene, AMT1;1, along with six low affinity AMT genes in the shoots suggests that low affinity AMTs in the shoots leaves are involved in supporting AMT1;1 to carry out its activities/function efficiently.

  2. Two high-affinity ligand binding states of uterine estrogen receptor distinguished by modulation of hydrophobic environment

    SciTech Connect

    Hutchens, T.W.; Li, C.M.; Zamah, N.M.; Besch, P.K.

    1987-02-10

    The steroid binding function of soluble (cytosolic) estrogen receptors from calf uteri was evaluated under conditions known to modify the extent of hydrophobic interaction with receptor-associated proteins. Receptor preparations were equilibrated into 6 M urea buffers and control buffers by chromatography through small columns of Sephadex G-25 or by dialysis at 0.6 /sup 0/C. Equilibrium dissociation constants (K/sub d/) and binding capacities (n) of experimental and control receptor preparations were determined by 13-point Scatchard analyses using concentrations of 17..beta..-(/sup 3/H)estradiol from 0.05 to 10 nM. Nonspecific binding was determined at each concentration by parallel incubations with a 200-fold molar excess of the receptor-specific competitor diethylstilbestrol. The control receptor population was consistently found to be a single class of binding sites with a high affinity for estradiol which was unaffected by G-25 chromatography, by dialysis, by dilution, or by the presence of 0.4 M KCl. However, equilibration into 6 M urea induced a discrete (10-fold) reduction in receptor affinity to reveal a second, thermodynamically stable, high-affinity binding state. The presence of 0.4 M KCl did not significantly influence the discrete change in receptor affinity induced by urea. The effects of urea on both receptor affinity and binding capacity were reversible, suggesting a lack of covalent modification. These results demonstrate nonenzymatic means by which not only the binding capacity but also the affinity of receptor for estradiol can be reversibly controlled, suggesting that high concentrations of urea might be more effectively utilized during the physicochemical characterization and purification of steroid receptor proteins.

  3. Crack propagation driven by crystal growth

    SciTech Connect

    A. Royne; Paul Meaking; A. Malthe-Sorenssen; B. Jamtveit; D. K. Dysthe

    2011-10-01

    Crystals that grow in confinement may exert a force on their surroundings and thereby drive crack propagation in rocks and other materials. We describe a model of crystal growth in an idealized crack geometry in which the crystal growth and crack propagation are coupled through the stress in the surrounding bulk solid. Subcritical crack propagation takes place during a transient period, which may be very long, during which the crack velocity is limited by the kinetics of crack propagation. When the crack is sufficiently large, the crack velocity becomes limited by the kinetics of crystal growth. The duration of the subcritical regime is determined by two non-dimensional parameters, which relate the kinetics of crack propagation and crystal growth to the supersaturation of the fluid and the elastic properties of the surrounding material.

  4. The affine structure of gravitational theories: Symplectic groups and geometry

    NASA Astrophysics Data System (ADS)

    Capozziello, Salvatore; Cirilo-Lombardo, D. J.; de Laurentis, Mariafelicia

    2014-09-01

    We give a geometrical description of gravitational theories from the viewpoint of symmetries and affine structure. We show how gravity, considered as a gauge theory, can be consistently achieved by the nonlinear realization of the conformal-affine group in an indirect manner: due to the partial isomorphism between CA(3, 1) and the centrally extended Sp( 8), we perform a nonlinear realization of the centrally extended (CE)Sp( 8) in its semi-simple version. In particular, starting from the bundle structure of gravity, we derive the conformal-affine Lie algebra and then, by the nonlinear realization, we define the coset field transformations, the Cartan forms and the inverse Higgs constraints. Finally, we discuss the geometrical Lagrangians where all the information on matter fields and their interactions can be contained.

  5. Affinity maturation of antibodies requires integrity of the adult thymus.

    PubMed

    AbuAttieh, Mouhammed; Bender, Diane; Liu, Esther; Wettstein, Peter; Platt, Jeffrey L; Cascalho, Marilia

    2012-02-01

    The generation of B-cell responses to proteins requires a functional thymus to produce CD4(+) T cells which helps in the activation and differentiation of B cells. Because the mature T-cell repertoire has abundant cells with the helper phenotype, one might predict that in mature individuals, the generation of B-cell memory would proceed independently of the thymus. Contrary to that prediction, we show here that the removal of the thymus after the establishment of the T-cell compartment or sham surgery without removal of the thymus impairs the affinity maturation of antibodies. Because removal or manipulation of the thymus did not decrease the frequency of mutation of the Ig variable heavy chain exons encoding antigen-specific antibodies, we conclude that the thymus controls affinity maturation of antibodies in the mature individual by facilitating the selection of B cells with high-affinity antibodies.

  6. A fast quantum algorithm for the affine Boolean function identification

    NASA Astrophysics Data System (ADS)

    Younes, Ahmed

    2015-02-01

    Bernstein-Vazirani algorithm (the one-query algorithm) can identify a completely specified linear Boolean function using a single query to the oracle with certainty. The first aim of the paper is to show that if the provided Boolean function is affine, then one more query to the oracle (the two-query algorithm) is required to identify the affinity of the function with certainty. The second aim of the paper is to show that if the provided Boolean function is incompletely defined, then the one-query and the two-query algorithms can be used as bounded-error quantum polynomial algorithms to identify certain classes of incompletely defined linear and affine Boolean functions respectively with probability of success at least 2/3.

  7. Enhancing Community Detection By Affinity-based Edge Weighting Scheme

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.

  8. On the electron affinity of the oxygen atom

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Langhoff, S. R.; Partridge, H.; Taylor, P. R.

    1986-01-01

    The electron affinity (EA) of oxygen is computed to be 1.287 eV, using 2p electron full configuration-interaction (CI) wave functions expanded in a 6s5p3d2f Slater-type orbital basis. The best complete active space self-consistent field - multireference CI (CASSCF-MRCI) result including only 2p correlation is 1.263 eV. However, inclusion of 2s intrashell and 2s2p intershell correlation increases the computed EA to 1.290 at the CASSCF-MRCI level. At the full CI basis set limit, the 2s contribution to the electron affinity is estimated to be as large as 0.1 eV. This study clearly establishes the synergistic effect between the higher excitations and basis set completeness on the electron affinity when the 2s electrons are correlated.

  9. On the electron affinity of the oxygen atom

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Langhoff, S. R.; Partridge, H.; Taylor, P. R.

    1986-01-01

    The electron affinity of oxygen is computed to be 1.287 eV, at the full CI level using a 6s5p3d 2f Slater-type orbital basis and correlating only the 2p electrons. The best CASSCF-MRCI result including only 2p correlation is 1.263 eV. However, inclusion of 2s intrashell and 2s2p intershell coorelation increases the computed EA to 1.290 eV at the CASSCF-MRCI level. At the full CI basis set limit, the 2s contribution to the electron affinity is estimated to be as large as 0.1 eV. The higher excitation contribution to the electron affinity is found to increase substantially with basis set completeness, especially when the 2s electrons are correlated. Relativistic effects are shown to make a small (less than 0.01 eV) change in the EA.

  10. AMPK beta subunits display isoform specific affinities for carbohydrates.

    PubMed

    Koay, Ann; Woodcroft, Ben; Petrie, Emma J; Yue, Helen; Emanuelle, Shane; Bieri, Michael; Bailey, Michael F; Hargreaves, Mark; Park, Jong-Tae; Park, Kwan-Hwa; Ralph, Stuart; Neumann, Dietbert; Stapleton, David; Gooley, Paul R

    2010-08-04

    AMP-activated protein kinase (AMPK) is a heterotrimer of catalytic (alpha) and regulatory (beta and gamma) subunits with at least two isoforms for each subunit. AMPK beta1 is widely expressed whilst AMPK beta2 is highly expressed in muscle and both beta isoforms contain a mid-molecule carbohydrate-binding module (beta-CBM). Here we show that beta2-CBM has evolved to contain a Thr insertion and increased affinity for glycogen mimetics with a preference for oligosaccharides containing a single alpha-1,6 branched residue. Deletion of Thr-101 reduces affinity for single alpha-1,6 branched oligosaccharides by 3-fold, while insertion of this residue into the equivalent position in the beta1-CBM sequence increases affinity by 3-fold, confirming the functional importance of this residue.

  11. Uncertainty propagation in nuclear forensics.

    PubMed

    Pommé, S; Jerome, S M; Venchiarutti, C

    2014-07-01

    Uncertainty propagation formulae are presented for age dating in support of nuclear forensics. The age of radioactive material in this context refers to the time elapsed since a particular radionuclide was chemically separated from its decay product(s). The decay of the parent radionuclide and ingrowth of the daughter nuclide are governed by statistical decay laws. Mathematical equations allow calculation of the age of specific nuclear material through the atom ratio between parent and daughter nuclides, or through the activity ratio provided that the daughter nuclide is also unstable. The derivation of the uncertainty formulae of the age may present some difficulty to the user community and so the exact solutions, some approximations, a graphical representation and their interpretation are presented in this work. Typical nuclides of interest are actinides in the context of non-proliferation commitments. The uncertainty analysis is applied to a set of important parent-daughter pairs and the need for more precise half-life data is examined.

  12. S-Band propagation measurements

    NASA Technical Reports Server (NTRS)

    Briskman, Robert D.

    1994-01-01

    A geosynchronous satellite system capable of providing many channels of digital audio radio service (DARS) to mobile platforms within the contiguous United States using S-band radio frequencies is being implemented. The system is designed uniquely to mitigate both multipath fading and outages from physical blockage in the transmission path by use of satellite spatial diversity in combination with radio frequency and time diversity. The system also employs a satellite orbital geometry wherein all mobile platforms in the contiguous United States have elevation angles greater than 20 deg to both of the diversity satellites. Since implementation of the satellite system will require three years, an emulation has been performed using terrestrial facilities in order to allow evaluation of DARS capabilities in advance of satellite system operations. The major objective of the emulation was to prove the feasibility of broadcasting from satellites 30 channels of CD quality programming using S-band frequencies to an automobile equipped with a small disk antenna and to obtain quantitative performance data on S-band propagation in a satellite spatial diversity system.

  13. VPSim: Variance propagation by simulation

    SciTech Connect

    Burr, T.; Coulter, C.A.; Prommel, J.

    1997-12-01

    One of the fundamental concepts in a materials control and accountability system for nuclear safeguards is the materials balance (MB). All transfers into and out of a material balance area are measured, as are the beginning and ending inventories. The resulting MB measures the material loss, MB = T{sub in} + I{sub B} {minus} T{sub out} {minus} I{sub E}. To interpret the MB, the authors must estimate its measurement error standard deviation, {sigma}{sub MB}. When feasible, they use a method usually known as propagation of variance (POV) to estimate {sigma}{sub MB}. The application of POV for estimating the measurement error variance of an MB is straightforward but tedious. By applying POV to individual measurement error standard deviations they can estimate {sigma}{sub MB} (or more generally, they can estimate the variance-covariance matrix, {Sigma}, of a sequence of MBs). This report describes a new computer program (VPSim) that uses simulation to estimate the {Sigma} matrix of a sequence of MBs. Given the proper input data, VPSim calculates the MB and {sigma}{sub MB}, or calculates a sequence of n MBs and the associated n-by-n covariance matrix, {Sigma}. The covariance matrix, {Sigma}, contains the variance of each MB in the diagonal entries and the covariance between pairs of MBs in the off-diagonal entries.

  14. Mesozooplankton affinities in a recovering freshwater estuary

    NASA Astrophysics Data System (ADS)

    Chambord, Sophie; Maris, Tom; Colas, Fanny; Van Engeland, Tom; Sossou, Akoko-C.; Azémar, Frédéric; Le Coz, Maïwen; Cox, Tom; Buisson, Laetitia; Souissi, Sami; Meire, Patrick; Tackx, Michèle

    2016-08-01

    Water quality of the Scheldt estuary (Belgium/The Netherlands) has considerably improved in recent years, especially in the upstream, freshwater reaches. Within the zooplankton community, the copepod Eurytemora affinis, typically abundant in brackish water and quasi-absent from freshwater before 2007, has since substantially developed in the latter, where it now represents 90% of the crustacean mesozooplankton community. Simultaneously, cyclopoid copepod abundance has greatly decreased, while cladoceran abundance did not change. The study aim was: 1) to verify if the zooplankton community described for the period 2007-2009 by Mialet et al. (2011) has stabilized until present, and 2) to look for the environmental conditions favouring E. affinis development and causing changes in the upstream freshwater zooplankton community. The 2002-2012 temporal evolution of the zooplankton distribution at three stations in the upstream freshwater Scheldt estuary was analyzed. Water quality remained better after 2007 than before, and some factors revealed continuous improvement in annual mean concentrations (e.g. increase in O2, decrease in BOD5 and NH4sbnd N concentration). The increase in oxygen and the decrease in NH4sbnd N concentration, together with low discharge during summer were the main environmental factors explaining the development and timing of E. affinis in the upstream freshwater reach. In this reach, E. affinis maximal abundance is shifted to higher temperatures (summer) compared to its typical maximum spring abundance peak in the brackish zone of the Scheldt estuary and in most temperate estuaries. The changes in zooplankton community followed a temporal and spatial gradient induced by the spatio-temporal evolution of water quality improvement. The most downstream station (3) allowed E. affinis development (oxygen concentration > 4 mg L-1; NH4sbnd N concentration < 2 mg L-1, discharge (Q) < 50 m3 s-1) from 2007 onwards, and this station showed the highest E

  15. An Earth with affinities to Enstatite Chondrites

    NASA Astrophysics Data System (ADS)

    McDonough, W. F.

    2015-12-01

    The Enstatite chondrite model for the Earth, as envisaged by Marc Javoy and colleagues, has strengths and weaknesses. The overwhelming evidence against layered mantle scenarios makes the existing enstatite Earth models unacceptable. Increasingly, stable and radiogenic isotope data for the Earth and the range of chondrites find that many (but not all) isotopic ratios are shared between the Earth and enstatite chondrites. This significant amount of overlap in isotope space compels one to reconsider the enstatite chondrite model for the Earth. During early solar system formation (circa +1 Ma) radial inward migration of the Jupiter and Saturn in the disk (e.g., Grand Tack model) would fully disrupted an asteroid belt, resulting in mixing and redistribution of preexisting components, while much later after the disk is gone (e.g., +100 Ma) gravitational scattering by these planets may have transported small bodies from the outer reaches of the solar system inward towards the rocky planets (Nice model). Astromineralogy reveals variations in the proportion of olivine to pyroxene in accretion disks, some with inner disk regions being richer in olivine relative to the disk wide composition, while other disks show the abundance of olivine is greater in the outer (vs the inner) part of the circumstellar disk, with differences in disk mineralogy being relating to type of star (e.g., T Tauri vs Herbig Ae/Be stars). The inner disk regions (a few AU) show higher abundances of large grains and generally higher crystallinity as compared to outer disk regions, suggesting grain growth occurs more rapidly in the inner disk regions. Recent results from geoneutrino measurements are most consistent with geochemical models that predict 20 TW of radiogenic power, less so with existing enstatite Earth models predicting less power in the planet. At 1 AU the Earth accreted a greater proportion of olivine to pyroxene (i.e., Mg/Si of pyrolite) than that available to the known enstatite chondrite

  16. Solid support resins and affinity purification mass spectrometry.

    PubMed

    Havis, Spencer; Moree, Wilna J; Mali, Sujina; Bark, Steven J

    2017-02-28

    Co-affinity purification-mass spectrometry (CoAP-MS) is a primary technology for elucidating the protein-protein interactions that form the basis of all biological processes. A critical component of CoAP-MS is the affinity purification (AP) of the bait protein, usually by immobilization of an antibody to a solid-phase resin. This Minireview discusses common resins, reagents, tagging methods, and their consideration for successful AP of tagged proteins. We discuss our experiences with different solid supports, their impact in AP experiments, and propose areas where chemistry can advance this important technology.

  17. Affine generalization of the Komar complex of general relativity

    NASA Astrophysics Data System (ADS)

    Mielke, Eckehard W.

    2001-02-01

    On the basis of the ``on shell'' Noether identities of the metric-affine gauge approach of gravity, an affine superpotential is derived which comprises the energy- and angular-momentum content of exact solutions. In the special case of general relativity (GR) or its teleparallel equivalent, the Komar or Freud complex, respectively, are recovered. Applying this to the spontaneously broken anti-de Sitter gauge model of McDowell and Mansouri with an induced Euler term automatically yields the correct mass and spin of the Kerr-AdS solution of GR with a (induced) cosmological constant without the factor two discrepancy of the Komar formula.

  18. A quantum affine algebra for the deformed Hubbard chain

    NASA Astrophysics Data System (ADS)

    Beisert, Niklas; Galleas, Wellington; Matsumoto, Takuya

    2012-09-01

    The integrable structure of the one-dimensional Hubbard model is based on Shastry's R-matrix and the Yangian of a centrally extended \\mathfrak {sl}(2|2) superalgebra. Alcaraz and Bariev have shown that the model admits an integrable deformation whose R-matrix has recently been found. This R-matrix is of trigonometric type and here we derive its underlying exceptional quantum affine algebra. We also show how the algebra reduces to the above-mentioned Yangian and to the conventional quantum affine \\mathfrak {sl}(2|2) algebra in two special limits.

  19. Fast left ventricle tracking in CMR images using localized anatomical affine optical flow

    NASA Astrophysics Data System (ADS)

    Queirós, Sandro; Vilaça, João. L.; Morais, Pedro; Fonseca, Jaime C.; D'hooge, Jan; Barbosa, Daniel

    2015-03-01

    In daily cardiology practice, assessment of left ventricular (LV) global function using non-invasive imaging remains central for the diagnosis and follow-up of patients with cardiovascular diseases. Despite the different methodologies currently accessible for LV segmentation in cardiac magnetic resonance (CMR) images, a fast and complete LV delineation is still limitedly available for routine use. In this study, a localized anatomically constrained affine optical flow method is proposed for fast and automatic LV tracking throughout the full cardiac cycle in short-axis CMR images. Starting from an automatically delineated LV in the end-diastolic frame, the endocardial and epicardial boundaries are propagated by estimating the motion between adjacent cardiac phases using optical flow. In order to reduce the computational burden, the motion is only estimated in an anatomical region of interest around the tracked boundaries and subsequently integrated into a local affine motion model. Such localized estimation enables to capture complex motion patterns, while still being spatially consistent. The method was validated on 45 CMR datasets taken from the 2009 MICCAI LV segmentation challenge. The proposed approach proved to be robust and efficient, with an average distance error of 2.1 mm and a correlation with reference ejection fraction of 0.98 (1.9 +/- 4.5%). Moreover, it showed to be fast, taking 5 seconds for the tracking of a full 4D dataset (30 ms per image). Overall, a novel fast, robust and accurate LV tracking methodology was proposed, enabling accurate assessment of relevant global function cardiac indices, such as volumes and ejection fraction

  20. Relative binding affinity does not predict biological response to xenoestrogens in rat endometrial adenocarcinoma cells.

    PubMed

    Strunck, E; Stemmann, N; Hopert, A; Wünsche, W; Frank, K; Vollmer, G

    2000-10-01

    The possible adverse effects of the so-called environmental estrogens have raised considerable concern. Developmental, endocrine and reproductive disorders in wildlife animals have been linked to high exposure to persistent environmental chemicals with estrogen-like activity (xenoestrogens); yet, the potential impact of environmental estrogens on human health is currently under debate also due to lack of data. A battery of in vitro assays exist for identifying compounds with estrogenic activity, but only a few models are available to assess estrogenic potency in a multiparametric analysis. We have recently established the endometrial adenocarcinoma cell line RUCA-I; it enables us to compare estrogenic effects both in vitro and in vivo as these cells are estrogen responsive in vitro and grow estrogen sensitive tumors if inoculated in syngeneic animals in vivo. Here we report in vitro data concerning (a) the relative binding affinity of the selected synthetic chemicals Bisphenol A, nonylphenol, p-tert-octylphenol, and o,p-DDT to the estrogen receptor of RUCA-I cells and (b) the relative potency of these compounds in inducing increased production of complement C3, an endogenous estrogen-responsive gene. Competitive Scatchard analysis revealed that xenoestrogens bound with an at least 1000-fold lower affinity to the estrogen receptor of RUCA-I cells than estradiol itself, thereby exhibiting the following affinity ranking, estradiol>nonylphenol>bisphenol A approximately p-tert-octylphenol>o,p-DDT. Despite these low binding affinities, bisphenol A, nonylphenol and p-tert-octylphenol increased production of complement C3 in a dose dependent manner. Compared with estradiol, only 100-fold higher concentrations were needed for all the compounds to achieve similar levels of induction, except o,p-DDT which was by far less potent. Northern blot analyses demonstrated that the increased production of complement C3 was mediated by an increased transcription. In summary, cultured

  1. Relative affinity of angiotensin peptides and novel ligands at AT1 and AT2 receptors.

    PubMed

    Bosnyak, Sanja; Jones, Emma S; Christopoulos, Arthur; Aguilar, Marie-Isabel; Thomas, Walter G; Widdop, Robert E

    2011-10-01

    AT1R (angiotensin type 1 receptor) and AT2R (angiotensin type 2 receptor) are well known to be involved in the complex cardiovascular actions of AngII (angiotensin II). However, shorter peptide fragments of AngII are thought to have biological activity in their own right and elicit effects that oppose those mediated by AngII. In the present study, we have used HEK (human embryonic kidney)-293 cells stably transfected with either AT1R or AT2R to perform a systematic analysis of binding affinities of all the major angiotensin peptides. Additionally, we tested the novel AT2R agonist Compound 21, as well as the MasR (Mas receptor) agonist and antagonist AVE0991 and A-779 respectively, for their ability to bind to AT1R or AT2R. Candesartan, CGP42214 and PD123319 were used as reference compounds. Binding studies using 125I-[Sar1Ile8]AngII on the AT1R-transfected HEK-293 cells revealed only AngII, AngIII [angiotensin III; angiotensin-(2-8)] and candesartan to have high affinity for AT1R. In the AT2R-transfected HEK-293 cells, competition for 125I-[Sar1Ile8]AngII binding was observed for all ligands except candesartan, AVE0991 and A-779, the latter two compounds having negligible affinity at either AT1R or AT2R. The rank order of affinity of ligands at AT2R was CGP42112>AngII≥AngIII>Compound 21≥PD123319≫AngIV [angiotensin IV; angiotensin-(3-8)]>Ang-(1-7) [angiotensin-(1-7)]. Of note, although AngIV and Ang-(1-7) exhibited only modest affinity at AT2R compared with AngII, these two angiotensin peptides, together with AngIII, had substantial AT2R selectivity over AT1R. Collectively, our results suggest that shorter angiotensin peptides can act as endogenous ligands at AT2R.

  2. Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel.

    PubMed

    Henry, Pauline C; Kanelis, Voula; O'Brien, M Christine; Kim, Brian; Gautschi, Ivan; Forman-Kay, Julie; Schild, Laurent; Rotin, Daniela

    2003-05-30

    The epithelial Na+ channel (alphabetagammaENaC) regulates salt and fluid homeostasis and blood pressure. Each ENaC subunit contains a PY motif (PPXY) that binds to the WW domains of Nedd4, a Hect family ubiquitin ligase containing 3-4 WW domains and usually a C2 domain. It has been proposed that Nedd4-2, but not Nedd4-1, isoforms can bind to and suppress ENaC activity. Here we challenge this notion and show that, instead, the presence of a unique WW domain (WW3*) in either Nedd4-2 or Nedd4-1 determines high affinity interactions and the ability to suppress ENaC. WW3* from either Nedd4-2 or Nedd4-1 binds ENaC-PY motifs equally well (e.g. Kd approximately 10 microm for alpha- or betaENaC, 3-6-fold higher affinity than WW4), as determined by intrinsic tryptophan fluorescence. Moreover, dNedd4-1, which naturally contains a WW3* instead of WW2, is able to suppress ENaC function equally well as Nedd4-2. Homology models of the WW3*.betaENaC-PY complex revealed that a Pro and Ala conserved in all WW3*, but not other Nedd4-WW domains, help form the binding pocket for PY motif prolines. Extensive contacts are formed between the betaENaC-PY motif and the Pro in WW3*, and the small Ala creates a large pocket to accommodate the peptide. Indeed, mutating the conserved Pro and Ala in WW3* reduces binding affinity 2-3-fold. Additionally, we demonstrate that mutations in PY motif residues that form contacts with the WW domain based on our previously solved structure either abolish or severely reduce binding affinity to the WW domain and that the extent of binding correlates with the level of ENaC suppression. Independently, we show that a peptide encompassing the PY motif of sgk1, previously proposed to bind to Nedd4-2 and alter its ability to regulate ENaC, does not bind (or binds poorly) the WW domains of Nedd4-2. Collectively, these results suggest that high affinity of WW domain-PY-motif interactions rather than affiliation with Nedd4-1/Nedd-2 is critical for ENaC suppression

  3. Fluctuation-controlled front propagation

    NASA Astrophysics Data System (ADS)

    Ridgway, Douglas Thacher

    1997-09-01

    the symmetry of the absorbing state, but which is unsuccessful at capturing the behavior of diffusion-limited growth. In an effort to find a simpler model system, we turned to modelling fitness increases in evolution. The work was motivated by an experiment on vesicular stomatitis virus, a short (˜9600bp) single-stranded RNA virus. A highly bottlenecked viral population increases in fitness rapidly until a certain point, after which the fitness increases at a slower rate. This is well modeled by a constant population reproducing and mutating on a smooth fitness landscape. Mean field theory of this system displays the same infinite propagation velocity blowup as mean field diffusion-limited aggregation. However, we have been able to make progress on a number of fronts. One is solving systems of moment equations, where a hierarchy of moments is truncated arbitrarily at some level. Good results for front propagation velocity are found with just two moments, corresponding to inclusion of the basic finite population clustering effect ignored by mean field theory. In addition, for small mutation rates, most of the population will be entirely on a single site or two adjacent sites, and the density of these cases can be described and solved. (Abstract shortened by UMI.)

  4. Intrinsic excitability state of local neuronal population modulates signal propagation in feed-forward neural networks

    NASA Astrophysics Data System (ADS)

    Han, Ruixue; Wang, Jiang; Yu, Haitao; Deng, Bin; Wei, Xilei; Qin, Yingmei; Wang, Haixu

    2015-04-01

    Reliable signal propagation across distributed brain areas is an essential requirement for cognitive function, and it has been investigated extensively in computational studies where feed-forward network (FFN) is taken as a generic model. But it is still unclear how distinct local network states, which are intrinsically generated by synaptic interactions within each layer, would affect the ability of FFN to transmit information. Here we investigate the impact of such network states on propagating transient synchrony (synfire) and firing rate by a combination of numerical simulations and analytical approach. Specifically, local network dynamics is attributed to the competition between excitatory and inhibitory neurons within each layer. Our results show that concomitant with different local network states, the performance of signal propagation differs dramatically. For both synfire propagation and firing rate propagation, there exists an optimal local excitability state, respectively, that optimizes the performance of signal propagation. Furthermore, we find that long-range connections strongly change the dependence of spiking activity propagation on local network state and propose that these two factors work jointly to determine information transmission across distributed networks. Finally, a simple mean field approach that bridges response properties of long-range connectivity and local subnetworks is utilized to reveal the underlying mechanism.

  5. The propagation from meteorological to hydrological drought and its potential influence factors

    NASA Astrophysics Data System (ADS)

    Huang, Shengzhi; Li, Pei; Huang, Qiang; Leng, Guoyong; Hou, Beibei; Ma, Lan

    2017-04-01

    It is important to investigate the propagation from meteorological to hydrological drought and its potential influence factors, which helps to reveal drought propagation process, thereby being helpful for drought mitigation. In this study, Standardized Precipitation Index (SPI) and Standardized Streamflow Index (SSI) were adopted to characterize meteorological and hydrological droughts, respectively. The propagation time from meteorological to hydrological drought was investigated. The cross wavelet analysis was utilized to examine the correlations between hydrological and meteorological droughts in the Wei River Basin (WRB), a typical arid and semi-arid region in China. Moreover, the potential influence factors on the propagation were explored from the perspectives of large-scale atmospheric circulation anomaly and underlying surface characteristics. Results indicated: (1) the propagation time from meteorological to hydrological drought has noticeably seasonal characteristics, that in spring and summer is short, whilst that in autumn and winter is long; (2) hydrological and meteorological droughts are primarily characterized by statistically positive linkages on both long and short time scales; (3) El Niño Southern Oscillation (ENSO) and Arctic Oscillation (AO) are strongly correlated with actual evaporation, thus strongly impacting the propagation time from meteorological to hydrological drought. Additionally, the propagation time has roughly positive associations with the parameter w of the Fu's equation from the Budyko framework.

  6. Glutamine is required for snakehead fish vesiculovirus propagation via replenishing the tricarboxylic acid cycle.

    PubMed

    Sun, Lindan; Yi, Lizhu; Zhang, Chi; Liu, Xiaodan; Feng, Shuangshuang; Chen, Wenjie; Lan, Jiangfeng; Zhao, Lijuan; Tu, Jiagang; Lin, Li

    2016-11-01

    Snakehead fish vesiculovirus (SHVV), a member of the family Rhabdoviridae, has caused mass mortality in snakehead fish culture in China. Previous transcriptomic sequencing of SHVV-infected and non-infected striped snakehead fish cells (SSN-1) showed that glutaminase (GLS), the critical enzyme of glutamine metabolism, was upregulated upon SHVV infection. It therefore drew our attention to investigating the role of glutamine in SHVV propagation. Glutamine deprivation significantly reduced the expression of the mRNAs and proteins of SHVV, and the production of virus particles, indicating that glutamine was required for SHVV propagation. Glutamine can be converted to glutamate by GLS, and then be converted to α-ketoglutarate, to join in the tricarboxylic acid (TCA) cycle. Addition of the TCA cycle intermediate α-ketoglutarate, oxaloacetic acid or pyruvate significantly restored SHVV propagation, indicating that the requirement of glutamine for SHVV propagation was due to its replenishment of the TCA cycle. Inhibiting the activity of GLS in SSN-1 cells by an inhibitor, bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide, decreased SHVV propagation, while overexpression of GLS increased SHVV propagation. Taken together, our data have revealed the relationship between glutamine metabolism and SHVV propagation.

  7. Intrinsic excitability state of local neuronal population modulates signal propagation in feed-forward neural networks.

    PubMed

    Han, Ruixue; Wang, Jiang; Yu, Haitao; Deng, Bin; Wei, Xilei; Qin, Yingmei; Wang, Haixu

    2015-04-01

    Reliable signal propagation across distributed brain areas is an essential requirement for cognitive function, and it has been investigated extensively in computational studies where feed-forward network (FFN) is taken as a generic model. But it is still unclear how distinct local network states, which are intrinsically generated by synaptic interactions within each layer, would affect the ability of FFN to transmit information. Here we investigate the impact of such network states on propagating transient synchrony (synfire) and firing rate by a combination of numerical simulations and analytical approach. Specifically, local network dynamics is attributed to the competition between excitatory and inhibitory neurons within each layer. Our results show that concomitant with different local network states, the performance of signal propagation differs dramatically. For both synfire propagation and firing rate propagation, there exists an optimal local excitability state, respectively, that optimizes the performance of signal propagation. Furthermore, we find that long-range connections strongly change the dependence of spiking activity propagation on local network state and propose that these two factors work jointly to determine information transmission across distributed networks. Finally, a simple mean field approach that bridges response properties of long-range connectivity and local subnetworks is utilized to reveal the underlying mechanism.

  8. Propagated infra-slow intrinsic brain activity reorganizes across wake and slow wave sleep.

    PubMed

    Mitra, Anish; Snyder, Abraham Z; Tagliazucchi, Enzo; Laufs, Helmut; Raichle, Marcus E

    2015-11-09

    Propagation of slow intrinsic brain activity has been widely observed in electrophysiogical studies of slow wave sleep (SWS). However, in human resting state fMRI (rs-fMRI), intrinsic activity has been understood predominantly in terms of zero-lag temporal synchrony (functional connectivity) within systems known as resting state networks (RSNs). Prior rs-fMRI studies have found that RSNs are generally preserved across wake and sleep. Here, we use a recently developed analysis technique to study propagation of infra-slow intrinsic blood oxygen level dependent (BOLD) signals in normal adults during wake and SWS. This analysis reveals marked changes in propagation patterns in SWS vs. wake. Broadly, ordered propagation is preserved within traditionally defined RSNs but lost between RSNs. Additionally, propagation between cerebral cortex and subcortical structures reverses directions, and intra-cortical propagation becomes reorganized, especially in visual and sensorimotor cortices. These findings show that propagated rs-fMRI activity informs theoretical accounts of the neural functions of sleep.

  9. MPPE (Multiple Pulse Propagation Experiment) results

    SciTech Connect

    Chambers, F.W.; Caporaso, G.J.; Chong, Y.P.; Deadrick, F.J.; Guethlein, G.; Fawley, W.M.; Orzechowski, T.J.; Renbarger, V.L.; Rogers, D. Jr.; Weir, J.T. ); Lee, P. ); Struve, K.W. ); Hubbard, R. ); Feinstein, L.; Keeley, D. (Science Applicatio

    1990-10-01

    The Multiple Pulse Propagation Experiment (MPPE) was conducted by the Beam Research Group of the Lawrence Livermore National Laboratory from September 1989, through January 1990, using the Advanced Test Accelerator (ATA). This experiment represents the culmination of the three previous beam propagation experiments conducted at the ATA over the past half decade. Highlights of this experiment were the multiple pulse operation of ATA, and the diagnosis of the beam propagation, and channel production at the higher repetition rates. A large database was collected on beam propagation in uniform gas and channels including m = 0 beam size and net current measurements; and m = 1 hose measurements. The generation and evolution of the electron beam driven channels was well documented. A key result of this experiment was that the beam was dominated by hose instability which limited propagation ranges. This report is organized into five sections. The experimental layout and beam parameters have been detailed in previous reports. First the beam initial conditions will be discussed in detail. Since beam injection parameters are ultimately the only variables one can specify in an atmospheric application, the control and documentation of the beam at the entrance to the gas is crucial. Next the beam lead pulse propagation in gas will be reported. Lead pulse results will be compared with past experiments. The density channel production and evolution will be briefly reported; an additional reference is available. Beam propagation in the channel will then be examined. Finally, conclusions will be presented.

  10. The accuracy of dynamic attitude propagation

    NASA Technical Reports Server (NTRS)

    Harvie, E.; Chu, D.; Woodard, M.

    1990-01-01

    Propagating attitude by integrating Euler's equation for rigid body motion has long been suggested for the Earth Radiation Budget Satellite (ERBS) but until now has not been implemented. Because of limited Sun visibility, propagation is necessary for yaw determination. With the deterioration of the gyros, dynamic propagation has become more attractive. Angular rates are derived from integrating Euler's equation with a stepsize of 1 second, using torques computed from telemetered control system data. The environmental torque model was quite basic. It included gravity gradient and unshadowed aerodynamic torques. Knowledge of control torques is critical to the accuracy of dynamic modeling. Due to their coarseness and sparsity, control actuator telemetry were smoothed before integration. The dynamic model was incorporated into existing ERBS attitude determination software. Modeled rates were then used for attitude propagation in the standard ERBS fine-attitude algorithm. In spite of the simplicity of the approach, the dynamically propagated attitude matched the attitude propagated with good gyros well for roll and yaw but diverged up to 3 degrees for pitch because of the very low resolution in pitch momentum wheel telemetry. When control anomalies significantly perturb the nominal attitude, the effect of telemetry granularity is reduced and the dynamically propagated attitudes are accurate on all three axes.

  11. A propagation model of computer virus with nonlinear vaccination probability

    NASA Astrophysics Data System (ADS)

    Gan, Chenquan; Yang, Xiaofan; Liu, Wanping; Zhu, Qingyi

    2014-01-01

    This paper is intended to examine the effect of vaccination on the spread of computer viruses. For that purpose, a novel computer virus propagation model, which incorporates a nonlinear vaccination probability, is proposed. A qualitative analysis of this model reveals that, depending on the value of the basic reproduction number, either the virus-free equilibrium or the viral equilibrium is globally asymptotically stable. The results of simulation experiments not only demonstrate the validity of our model, but also show the effectiveness of nonlinear vaccination strategies. Through parameter analysis, some effective strategies for eradicating viruses are suggested.

  12. Excitation and Propagation of Electromagnetic Waves: RBSP Observation and Modeling

    NASA Astrophysics Data System (ADS)

    Zhou, Q.; Xiao, F.; Yang, C.; Liu, S.; Spence, H. E.; Geoffrey, R.; Funsten, H. O.; Blake, J. B.; Baker, D. N.; Wygant, J. R.

    2015-12-01

    During the recovery phase of the geomagnetic storm on 30-31 March 2013, Van Allen Probe A detected enhanced magnetosonic (MS) waves in a broad range of L = 1.8-4.7 and magnetic local time (MLT) = 17-22 h, with a frequency range ˜10-100 Hz. In the meanwhile, distinct proton ring distributions with peaks at energies of ˜10 keV, were also observed in L = 3.2-4.6 and L = 5.0-5.6. Using a subtracted bi-Maxwellian distribution to model the observed proton ring distribution, we perform three-dimensional ray tracing to investigate the instability, propagation, and spatial distribution of MS waves. Numerical results show that nightside MS waves are produced by proton ring distribution and grow rapidly from the source location L = 5.6 to the location L = 5.0 but remain nearly stable at locations L < 5.0. Moreover, waves launched toward lower L shells with different initial azimuthal angles propagate across different MLT regions with divergent paths at first, then gradually turn back toward higher L shells and propagate across different MLT regions with convergent paths. The current results further reveal that MS waves are generated by a ring distribution of ˜10 keV proton and proton ring in one region can contribute to the MS wave power in another region.

  13. Do blood-borne calcifying nanoparticles self-propagate?

    PubMed

    Mathew, Grace; Mckay, David S; Ciftçioglu, Neva

    2008-01-01

    The nanotechnology industry is currently in the process of producing new nanoparticles. The biological activity of nanoparticles including adverse as well as beneficial effects tends to increase as their size decreases. The smaller the particles are, the greater their bioactivity and toxicity. Thus, one can easily conjecture the impact ofa nanoparticle if it could also self-replicate. This in vitro study reveals the self-propagating ability of unique calcifying nanoparticles (CNP) that can be as small as 50 nm in size and found in blood, blood products, and calcified soft tissues. Although specific detection techniques, morphological characteristics and biomineralizing properties of CNP are well established, their genomic information and self-propagating capability have always been challenged. The objective of this study is to document the propagation of CNP under physiological conditions, using inverted light microscopy (LM) and the Biostation IM time-lapse imaging system. Their detailed morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, validates CNP as self-replicators. Therefore these sterile-filterable, blood-borne nanoparticles should be of concern to the nanomedicine industry.

  14. Do blood-borne calcifying nanoparticles self-propagate?

    PubMed Central

    Mathew, Grace; McKay, David S; Çiftçioglu, Neva

    2008-01-01

    The nanotechnology industry is currently in the process of producing new nanoparticles. The biological activity of nanoparticles including adverse as well as beneficial effects tends to increase as their size decreases. The smaller the particles are, the greater their bioactivity and toxicity. Thus, one can easily conjecture the impact of a nanoparticle if it could also self-replicate. This in vitro study reveals the self-propagating ability of unique calcifying nanoparticles (CNP) that can be as small as 50 nm in size and found in blood, blood products, and calcified soft tissues. Although specific detection techniques, morphological characteristics and biomineralizing properties of CNP are well established, their genomic information and self-propagating capability have always been challenged. The objective of this study is to document the propagation of CNP under physiological conditions, using inverted light microscopy (LM) and the Biostation IM time-lapse imaging system. Their detailed morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, validates CNP as self-replicators. Therefore these sterile-filterable, blood-borne nanoparticles should be of concern to the nanomedicine industry. PMID:18686786

  15. Propagation of natural toad calls in a Mediterranean terrestrial environment.

    PubMed

    Penna, Mario; Llusia, Diego; Márquez, R

    2012-12-01

    Propagation patterns of animal acoustic signals provide insights into the evolution of signal design to convey signaler's information to potential recipients. However, propagation properties of vertebrate calls have been rarely studied using natural calls from individuals; instead playback calls broadcast through loudspeakers have been used extensively, a procedure that may involve acoustical and physical features differing from natural sounds. Measurements of the transmission characteristics of natural advertisement calls, which are simple tonal sounds, of the Iberian midwife toad, Alytes cisternasii, were carried out, and the results were compared with previously published results broadcasting recorded calls of the same species. Measurements of sound pressure level (SPL) of calls from individual male A. cisternasii revealed that the call amplitude decreases at distances of 1-8 m from the source at rates averaging 1-5 dB above spherical transmission loss in an omni-directional pattern. A comparison between SPLs of natural calls in the current study and of playback calls from a previous study showed that patterns of propagation did not differ in average values, but variance was significantly higher for natural calls. Results suggest that using broadcast signals for transmission experiments may result in a simplification of the conditions in which actual animals communicate in nature.

  16. In Vitro Propagation and Conservation of Bacopa monnieri L.

    PubMed

    Sharma, Neelam; Singh, Rakesh; Pandey, Ruchira

    2016-01-01

    Bacopa monnieri L. (common name brahmi) is a traditional and renowned Indian medicinal plant with high commercial value for its memory revitalizer potential. Demand for this herb has further escalated due to popularization of various brahmi-based drugs coupled with reported anticancer property. Insufficient seed availability and problems associated with seed propagation including short seed viability are the major constraints of seed conservation in the gene banks. In vitro clonal propagation, a prerequisite for in vitro conservation by enhanced axillary branching was standardized. We have developed a simple, single step protocol for in vitro establishment, propagation and medium-term conservation of B. monnieri. Single node explants, cultured on Murashige and Skoog's medium supplemented with BA (0.2 mg/L), exhibited shoot proliferation without callus formation. Rooting was achieved on the same medium. The in vitro raised plants were successfully transferred to soil with ~80 % survival. On the same medium, shoots could also be conserved for 12 months with high survival and genetic stability was maintained as revealed by molecular markers. The protocol optimized in the present study has been applied for culture establishment, shoot multiplication and medium-term conservation of several Bacopa germplasm, procured from different agro-ecological regions of India.

  17. Type I interferon controls propagation of long interspersed element-1.

    PubMed

    Yu, Qiujing; Carbone, Christopher J; Katlinskaya, Yuliya V; Zheng, Hui; Zheng, Ke; Luo, Mengcheng; Wang, P Jeremy; Greenberg, Roger A; Fuchs, Serge Y

    2015-04-17

    Type I interferons (IFN) including IFNα and IFNβ are critical for the cellular defense against viruses. Here we report that increased levels of IFNβ were found in testes from mice deficient in MOV10L1, a germ cell-specific RNA helicase that plays a key role in limiting the propagation of retrotransposons including Long Interspersed Element-1 (LINE-1). Additional experiments revealed that activation of LINE-1 retrotransposons increases the expression of IFNβ and of IFN-stimulated genes. Conversely, pretreatment of cells with IFN suppressed the replication of LINE-1. Furthermore, the efficacy of LINE-1 replication was increased in isogenic cell lines harboring inactivating mutations in diverse elements of the IFN signaling pathway. Knockdown of the IFN receptor chain IFNAR1 also stimulated LINE-1 propagation in vitro. Finally, a greater accumulation of LINE-1 was found in mice that lack IFNAR1 compared with wild type mice. We propose that LINE-1-induced IFN plays an important role in restricting LINE-1 propagation and discuss the putative role of IFN in preserving the genome stability.

  18. Detecting and preventing error propagation via competitive learning.

    PubMed

    Silva, Thiago Christiano; Zhao, Liang

    2013-05-01

    Semisupervised learning is a machine learning approach which is able to employ both labeled and unlabeled samples in the training process. It is an important mechanism for autonomous systems due to the ability of exploiting the already acquired information and for exploring the new knowledge in the learning space at the same time. In these cases, the reliability of the labels is a crucial factor, because mislabeled samples may propagate wrong labels to a portion of or even the entire data set. This paper has the objective of addressing the error propagation problem originated by these mislabeled samples by presenting a mechanism embedded in a network-based (graph-based) semisupervised learning method. Such a procedure is based on a combined random-preferential walk of particles in a network constructed from the input data set. The particles of the same class cooperate among them, while the particles of different classes compete with each other to propagate class labels to the whole network. Computer simulations conducted on synthetic and real-world data sets reveal the effectiveness of the model.

  19. Electromagnetic Propagation Prediction Inside Aircraft Cabins

    NASA Technical Reports Server (NTRS)

    Hankins, Genevieve; Vahala, Linda; Beggs, John H.

    2004-01-01

    Electromagnetic propagation models for signal strength prediction within aircraft cabins are essential for evaluating and designing a wireless communication system to be implemented onboard aircraft. A model was developed using Wireless Valley's SitePlanner; which is commercial grade software intended for predictions within office buildings. The performance of the model was evaluated through a comparison with test data measurements taken on several aircraft. The comparison concluded that the model can accurately predict power propagation within the cabin. This model can enhance researchers understanding of power propagation within aircraft cabins and will aid in future research.

  20. Propagation considerations in land mobile satellite transmission

    NASA Technical Reports Server (NTRS)

    Vogel, W. J.; Smith, E. K.

    1985-01-01

    It appears likely that the Land Mobile Satellite Services (LMSS) will be authorized by the FCC for operation in the 800 to 900 MHz (UHF) and possibly near 1500 MHz (L-band). Propagation problems are clearly an important factor in the effectiveness of this service, but useful measurements are few, and produced contradictory interpretations. A first order overview of existing measurements is presented with particular attention to the first two NASA balloon to mobile vehicle propagation experiments. Some physical insight into the interpretation of propagation effects in LMSS transmissions is provided.

  1. Asymmetric counter propagation of domain walls

    NASA Astrophysics Data System (ADS)

    Andrade-Silva, I.; Clerc, M. G.; Odent, V.

    2016-07-01

    Far from equilibrium systems show different states and domain walls between them. These walls, depending on the type of connected equilibria, exhibit a rich spatiotemporal dynamics. Here, we investigate the asymmetrical counter propagation of domain walls in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the shape and speed of the domain walls. Based on the molecular orientation, we infer that the counter propagative walls have different elastic deformations. These deformations are responsible of the asymmetric counter propagating fronts. Theoretically, based on symmetry arguments, we propose a simple bistable model under the influence of a nonlinear gradient, which qualitatively describes the observed dynamics.

  2. Photon propagator in light-shell gauge

    NASA Astrophysics Data System (ADS)

    Georgi, Howard; Kestin, Greg; Sajjad, Aqil

    2016-05-01

    We derive the photon propagator in light-shell gauge (LSG) vμAμ=0 , where vμ=(1,r ^ ) μ . This gauge is an important ingredient of the light-shell effective theory—an effective theory for describing high energy jet processes on a 2-dimensional spherical shell expanding at the speed of light around the point of the initial collision producing the jets. Since LSG is a noncovariant gauge, we cannot calculate the LSG propagator by using the standard procedure for covariant gauges. We therefore employ a new technique for computing the propagator, which we hope may be of relevance in other gauges as well.

  3. Propagation of Light Elements in the Galaxy

    NASA Technical Reports Server (NTRS)

    Moskalenko, I. V.; Strong, A. W.; Mashnik, S. G.; Jones, F. C.

    2003-01-01

    The origin and evolution of isotopes of the lightest elements d, He-3, Li, Be, and B in the universe is a key problem in such fields as astrophysics of CR, Galactic evolution, non-thermal nucleosynthesis, and cosmological studies. One of the major sources of these species is spallation by CR nuclei in the interstellar medium. On the other hand, it is the Boron/Carbon ratio in CR and Be-10 abundance which are used to fix the propagation parameters and thus spallation rate. We study production and Galactic propagation of these species using the numerical propagation code GALPROP and updated production cross sections.

  4. Propagation of sound through a sheared flow

    NASA Technical Reports Server (NTRS)

    Woolley, J. P.; Smith, C. A.; Karamcheti, K.

    1978-01-01

    Sound generated in a moving fluid must propagate through a shear layer in order to be measured by a fixed instrument. These propagation effects were evaluated for noise sources typically associated with single and co-flowing subsonic jets and for subcritical flow over airfoils in such jets. The techniques for describing acoustic propagation fall into two categories: geometric acoustics and wave acoustics. Geometric acoustics is most convenient and accurate for high frequency sound. In the frequency range of interest to the present study (greater than 150 Hz), the geometric acoustics approach was determined to be most useful and practical.

  5. Inward propagating chemical waves in Taylor vortices

    NASA Astrophysics Data System (ADS)

    Thompson, Barnaby W.; Novak, Jan; Wilson, Mark C. T.; Britton, Melanie M.; Taylor, Annette F.

    2010-04-01

    Advection-reaction-diffusion (ARD) waves in the Belousov-Zhabotinsky reaction in steady Taylor-Couette vortices have been visualized using magnetic-resonance imaging and simulated using an adapted Oregonator model. We show how propagating wave behavior depends on the ratio of advective, chemical and diffusive time scales. In simulations, inward propagating spiral flamelets are observed at high Damköhler number (Da). At low Da, the reaction distributes itself over several vortices and then propagates inwards as contracting ring pulses—also observed experimentally.

  6. Propagating confined states in phase dynamics

    NASA Technical Reports Server (NTRS)

    Brand, Helmut R.; Deissler, Robert J.

    1992-01-01

    Theoretical treatment is given to the possibility of the existence of propagating confined states in the nonlinear phase equation by generalizing stationary confined states. The nonlinear phase equation is set forth for the case of propagating patterns with long wavelengths and low-frequency modulation. A large range of parameter values is shown to exist for propagating confined states which have spatially localized regions which travel on a background with unique wavelengths. The theoretical phenomena are shown to correspond to such physical systems as spirals in Taylor instabilities, traveling waves in convective systems, and slot-convection phenomena for binary fluid mixtures.

  7. Surface acoustic wave propagation in graphene

    NASA Astrophysics Data System (ADS)

    Thalmeier, Peter; Dóra, Balázs; Ziegler, Klaus

    2010-01-01

    Surface acoustic wave (SAW) propagation is a powerful method to investigate two-dimensional (2D) electron systems. We show how SAW observables are influenced by coupling to the 2D massless Dirac electrons of graphene and argue that Landau oscillations in SAW propagation can be observed as function of gate voltage for constant field. Contrary to other transport measurements, the zero-field SAW propagation gives the wave-vector dependence of graphene conductivity for small wave numbers. We predict a crossover from Schrödinger to Dirac-like behavior as a function of gate voltage, with no attenuation in the latter for clean samples.

  8. Inward propagating chemical waves in Taylor vortices.

    PubMed

    Thompson, Barnaby W; Novak, Jan; Wilson, Mark C T; Britton, Melanie M; Taylor, Annette F

    2010-04-01

    Advection-reaction-diffusion (ARD) waves in the Belousov-Zhabotinsky reaction in steady Taylor-Couette vortices have been visualized using magnetic-resonance imaging and simulated using an adapted Oregonator model. We show how propagating wave behavior depends on the ratio of advective, chemical and diffusive time scales. In simulations, inward propagating spiral flamelets are observed at high Damköhler number (Da). At low Da, the reaction distributes itself over several vortices and then propagates inwards as contracting ring pulses--also observed experimentally.

  9. Computing Propagation Of Sound In Engine Ducts

    NASA Technical Reports Server (NTRS)

    Saylor, Silvia

    1995-01-01

    Frequency Domain Propagation Model (FREDOM) computer program accounts for acoustic loads applied to components of engines. Models propagation of noise through fluids in ducts between components and through passages within components. Used not only to analyze hardware problems, but also for design purposes. Updated version of FREQPL program easier to use. Devised specifically for use in analyzing acoustic loads in rocket engines. Underlying physical and mathematical concepts implemented also applicable to acoustic propagation in other enclosed spaces; analyzing process plumbing and ducts in industrial buildings with view toward reducing noise in work areas.

  10. A circuit mechanism for the propagation of waves of muscle contraction in Drosophila.

    PubMed

    Fushiki, Akira; Zwart, Maarten F; Kohsaka, Hiroshi; Fetter, Richard D; Cardona, Albert; Nose, Akinao

    2016-02-15

    Animals move by adaptively coordinating the sequential activation of muscles. The circuit mechanisms underlying coordinated locomotion are poorly understood. Here, we report on a novel circuit for the propagation of waves of muscle contraction, using the peristaltic locomotion of Drosophila larvae as a model system. We found an intersegmental chain of synaptically connected neurons, alternating excitatory and inhibitory, necessary for wave propagation and active in phase with the wave. The excitatory neurons (A27h) are premotor and necessary only for forward locomotion, and are modulated by stretch receptors and descending inputs. The inhibitory neurons (GDL) are necessary for both forward and backward locomotion, suggestive of different yet coupled central pattern generators, and its inhibition is necessary for wave propagation. The circuit structure and functional imaging indicated that the commands to contract one segment promote the relaxation of the next segment, revealing a mechanism for wave propagation in peristaltic locomotion.

  11. Student Engagement and Neoliberalism: Mapping an Elective Affinity

    ERIC Educational Resources Information Center

    Zepke, Nick

    2015-01-01

    The purpose of this article is to argue that student engagement, an important area for research about learning and teaching in formal higher education, has an elective affinity with neoliberalism, a hegemonic ideology in many countries of the developed world. The paper first surveys an extensive research literature examining student engagement and…

  12. "The Hunger Games": Literature, Literacy, and Online Affinity Spaces

    ERIC Educational Resources Information Center

    Curwood, Jen Scott

    2013-01-01

    This article examines adolescent literacy practices related to "The Hunger Games," a young adult novel and the first of a trilogy. By focusing on the interaction of social identities, discourses, and media paratexts within an online affinity space, this ethnographic study offers insight into how young adults engage with contemporary…

  13. Affinities and beyond! Developing Ways of Seeing in Online Spaces

    ERIC Educational Resources Information Center

    Davies, Julia

    2006-01-01

    This article presents an insider view of an online community of adults involved in sharing digital photography through a host website, Flickr. It describes how reciprocal teaching and learning partnerships in a dynamic multimodal environment are achieved through the creation of a "Third Space" or "Affinity Space", where "Funds of Knowledge" are…

  14. Electrochemical affinity biosensors for detection of mycotoxins: A review.

    PubMed

    Vidal, Juan C; Bonel, Laura; Ezquerra, Alba; Hernández, Susana; Bertolín, Juan R; Cubel, Carlota; Castillo, Juan R

    2013-11-15

    This review discusses the current state of electrochemical biosensors in the determination of mycotoxins in foods. Mycotoxins are highly toxic secondary metabolites produced by molds. The acute toxicity of these results in serious human and animal health problems, although it has been only since early 1960s when the first studied aflatoxins were found to be carcinogenic. Mycotoxins affect a broad range of agricultural products, most important cereals and cereal-based foods. A majority of countries, mentioning especially the European Union, have established preventive programs to control contamination and strict laws of the permitted levels in foods. Official methods of analysis of mycotoxins normally requires sophisticated instrumentation, e.g. liquid chromatography with fluorescence or mass detectors, combined with extraction procedures for sample preparation. For about sixteen years, the use of simpler and faster analytical procedures based on affinity biosensors has emerged in scientific literature as a very promising alternative, particularly electrochemical (i.e., amperometric, impedance, potentiometric or conductimetric) affinity biosensors due to their simplicity and sensitivity. Typically, electrochemical biosensors for mycotoxins use specific antibodies or aptamers as affinity ligands, although recombinant antibodies, artificial receptors and molecular imprinted polymers show potential utility. This article deals with recent advances in electrochemical affinity biosensors for mycotoxins and covers complete literature from the first reports about sixteen years ago.

  15. Toward an Affinity Space Methodology: Considerations for Literacy Research

    ERIC Educational Resources Information Center

    Lammers, Jayne C.; Curwood, Jen Scott; Magnifico, Alecia Marie

    2012-01-01

    As researchers seek to make sense of young people's online literacy practices and participation, questions of methodology are important to consider. In our work to understand the culture of physical, virtual and blended spheres that adolescents inhabit, we find it necessary to expand Gee's (2004) notion of affinity spaces. In this article, we draw…

  16. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    PubMed Central

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-01-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6. PMID:27291418

  17. Kinetic Studies of Biological Interactions By Affinity Chromatography

    PubMed Central

    Schiel, John E.; Hage, David S.

    2009-01-01

    The rates at which biological interactions occur can provide important information on the mechanism and behavior of such processes in living systems. This review will discuss how affinity chromatography can be used as a tool to examine the kinetics of biological interactions. This approach, referred to here as biointeraction chromatography, uses a column with an immobilized binding agent to examine the association or dissociation of this agent with other compounds. The use of HPLC-based affinity columns in kinetic studies has received particular attention in recent years. Advantages of using HPLC with affinity chromatography for this purpose include the ability to reuse the same ligand within a column for a large number of experiments, and the good precision and accuracy of this approach. A number of techniques are available for kinetic studies through the use of affinity columns and biointeraction chromatography. These approaches include plate height measurements, peak profiling, peak fitting, split-peak measurements, and peak decay analysis. The general principles for each of these methods are discussed in this review and some recent applications of these techniques are presented. The advantages and potential limitations of each approach are also considered. PMID:19391173

  18. Affinity of cefoperazone for penicillin-binding proteins.

    PubMed Central

    Matsubara, N; Minami, S; Matsuhashi, M; Takaoka, M; Mitsuhashi, S

    1980-01-01

    Cefoperazone (T-1551, CFP) a new semisynthetic cephalosporin, has a broad spectrum of antibacterial activity. We investigated the affinity of CFP to penicillin-binding proteins (PBPs) and the inhibition of peptidoglycan synthesis by CFP. CFP had high affinities for Escherichia coli PBP-3, -1Bs, -2, and -1A, in descending order, and low affinities for PBP-4, -5, and -6. Similarly, CFP showed high affinity for Pseudomonas aeruginosa PBP-3, -1A, -1B, -2, and -4, in descending order. It is known that E. coli PBP-3 and P. aeruginosa PBP-3 participate in cell division. These results are in good agreement with the formation of filamentous cells of E. coli and P. aeruginosa treated with CFP. CFP had lower inhibitory activities on D-alanine carboxypeptidase IA and IB of E. coli than that of penicillin G, but its inhibitory activities on the cross-link formation in peptidoglycan synthesis were the same as those of penicillin G and higher than those of ampicillin. Images PMID:6448021

  19. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    NASA Astrophysics Data System (ADS)

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-06-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6.

  20. Limit measures for affine cellular automata on topological Markov subgroups

    NASA Astrophysics Data System (ADS)

    Maass, Alejandro; Martínez, Servet; Sobottka, Marcelo

    2006-09-01

    Consider a topological Markov subgroup which is ps-torsion (with p prime) and an affine cellular automaton defined on it. We show that the Cesàro mean of the iterates, by the automaton of a probability measure with complete connections and summable memory decay that is compatible with the topological Markov subgroup, converges to the Haar measure.

  1. Affinity through Mathematical Activity: Cultivating Democratic Learning Communities

    ERIC Educational Resources Information Center

    Sengupta-Irving, Tesha

    2014-01-01

    In this article, the author demonstrates how a broader view of what shapes affinity is ideologically and practically linked to creating democratic learning communities. Specifically, the author explores how a teacher employed complex instruction (an equity pedagogy) with her ethnically and racially diverse students in the "lowest track"…

  2. Phosphorylation of CREB affects its binding to high and low affinity sites: implications for cAMP induced gene transcription.

    PubMed Central

    Nichols, M; Weih, F; Schmid, W; DeVack, C; Kowenz-Leutz, E; Luckow, B; Boshart, M; Schütz, G

    1992-01-01

    Cyclic AMP treatment of hepatoma cells leads to increased protein binding at the cyclic AMP response element (CRE) of the tyrosine aminotransferase (TAT) gene in vivo, as revealed by genomic footprinting, whereas no increase is observed at the CRE of the phosphoenolpyruvate carboxykinase (PEPCK) gene. Several criteria establish that the 43 kDa CREB protein is interacting with both of these sites. Two classes of CRE with different affinity for CREB are described. One class, including the TATCRE, is characterized by asymmetric and weak binding sites (CGTCA), whereas the second class containing symmetrical TGACGTCA sites shows a much higher binding affinity for CREB. Both classes show an increase in binding after phosphorylation of CREB by protein kinase A (PKA). An in vivo phosphorylation-dependent change in binding of CREB increases the occupancy of weak binding sites used for transactivation, such as the TATCRE, while high affinity sites may have constitutive binding of transcriptionally active and inactive CREB dimers, as demonstrated by in vivo footprinting at the PEPCK CRE. Thus, lower basal level and higher relative stimulation of transcription by cyclic AMP through low affinity CREs should result, allowing finely tuned control of gene activation. Images PMID:1354612

  3. Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode.

    PubMed

    Cole, David K; Sami, Malkit; Scott, Daniel R; Rizkallah, Pierre J; Borbulevych, Oleg Y; Todorov, Penio T; Moysey, Ruth K; Jakobsen, Bent K; Boulter, Jonathan M; Baker, Brian M; Yi Li

    2013-01-01

    Natural T cell receptors (TCRs) generally bind to their cognate pMHC molecules with weak affinity and fast kinetics, limiting their use as therapeutic agents. Using phage display, we have engineered a high affinity version of the A6 wild-type TCR (A6wt), specific for the human leukocyte antigen (HLA-A(∗)0201) complexed with human T cell lymphotropic virus type 111-19 peptide (A2-Tax). Mutations in just 4 residues in the CDR3β loop region of the A6wt TCR were selected that improved binding to A2-Tax by nearly 1000-fold. Biophysical measurements of this mutant TCR (A6c134) demonstrated that the enhanced binding was derived through favorable enthalpy and a slower off-rate. The structure of the free A6c134 TCR and the A6c134/A2-Tax complex revealed a native binding mode, similar to the A6wt/A2-Tax complex. However, concordant with the more favorable binding enthalpy, the A6c134 TCR made increased contacts with the Tax peptide compared with the A6wt/A2-Tax complex, demonstrating a peptide-focused mechanism for the enhanced affinity that directly involved the mutated residues in the A6c134 TCR CDR3β loop. This peptide-focused enhanced TCR binding may represent an important approach for developing antigen specific high affinity TCR reagents for use in T cell based therapies.

  4. Partial purification of the 5-hydroxytryptophan-reuptake system from human blood platelets using a citalopram-derived affinity resin

    SciTech Connect

    Biessen, E.A.L; Horn, A.S.; Robillard, G.T. )

    1990-04-03

    This paper describes a procedure for the synthesis and application of a citalopram-derived affinity resin in purifying the 5HT-reuptake system from human blood platelets. A two-step scheme has been developed for partial purification, based on wheat germ agglutinin-lectin (WGA) affinity and citalopram affinity chromatographies. Upon solubilization of the carrier with 1% digitonin, a 50-70-fold increase in specific ({sup 3}H) imipramine binding activity with a 70% recovery could be accomplished through WGA-lectin chromatography. The WGA pool was then subjected to affinity chromatography on citalopram-agarose. At least 90% of the binding capacity adsorbed to the column. Specific elution using 10 {mu}M citalopram resulted in a 22% recovery of binding activity. A 10,000-fold overall purification was obtained by using this two-step procedure. Analysis of the fractions on SDS-PAGE after {sup 125}I labeling revealed specific elution of 78- and 55-kDa proteins concomitant with the appearance of ({sup 3}H) imipramine binding activity. The pharmacological profile of the partially purified reuptake system correlated well with that derived from the crude membrane-bound reuptake system, suggesting a copurification of the 5HT binding activity and ({sup 3}H)imipramine binding activity.

  5. Determination of the minimal essential nucleotide sequence for diphtheria tox repressor binding by in vitro affinity selection.

    PubMed

    Tao, X; Murphy, J R

    1994-09-27

    The expression of diphtheria toxin in lysogenic toxigenic strains of Corynebacterium diphtheriae is controlled by the heavy metal ion-activated regulatory protein DtxR. In the presence of divalent heavy metal ions, DtxR specifically binds to the diphtheria tox operator and protects a 27-bp interrupted palindromic sequence from DNase I digestion. To determine the consensus DNA sequence for DtxR binding, we have used gel electrophoresis mobility-shift assay and polymerase chain reaction (PCR) amplification for in vitro affinity selection of DNA binding sequences from a universe of 6.9 x 10(10) variants. After 10 rounds of in vitro affinity selection, each round coupled with 30 cycles of PCR amplification, we isolated and characterized a family of DNA sequences that function as DtxR-responsive genetic elements both in vitro and in vivo. Moreover, these DNA sequences were found to bind activated DtxR with an affinity similar to that of the wild-type tox operator. The DNA sequence analysis of 21 unique in vitro affinity-selected binding sites has revealed the minimal essential nucleotide sequence for DtxR binding to be a 9-bp palindrome separated by a single base pair.

  6. Structural Basis of Species-Dependent Differential Affinity of 6-Alkoxy-5-Aryl-3-Pyridinecarboxamide Cannabinoid-1 Receptor Antagonists.

    PubMed

    Iyer, Malliga R; Cinar, Resat; Liu, Jie; Godlewski, Grzegorz; Szanda, Gergö; Puhl, Henry; Ikeda, Stephen R; Deschamps, Jeffrey; Lee, Yong-Sok; Steinbach, Peter J; Kunos, George

    2015-08-01

    6-Alkoxy-5-aryl-3-pyridincarboxamides, including the brain-penetrant compound 14G: [5-(4-chlorophenyl)-6-(cyclopropylmethoxy)-N-[(1R,2R)-2-hydroxy-cyclohexyl]-3-pyridinecarboxamide] and its peripherally restricted analog 14H: [5-(4-chlorophenyl)-N-[(1R,2R)-2-hydroxycyclohexyl]-6-(2-methoxyethoxy)-3-pyridinecarboxamide], have been recently introduced as selective, high-affinity antagonists of the human cannabinoid-1 receptor (hCB1R). Binding analyses revealed two orders of magnitude lower affinity of these compounds for mouse and rat versus human CB1R, whereas the affinity of rimonabant is comparable for all three CB1Rs. Modeling of ligand binding to CB1R and binding assays with native and mutant (Ile105Met) hCB1Rs indicate that the Ile105 to Met mutation in rodent CB1Rs accounts for the species-dependent affinity of 14G: and 14H: . Our work identifies Ile105 as a new pharmacophore component for developing better hCB1R antagonists and invalidates rodent models for assessing the antiobesity efficacy of 14G: and 14H: .

  7. Novel trends in affinity biosensors: current challenges and perspectives

    NASA Astrophysics Data System (ADS)

    Arugula, Mary A.; Simonian, Aleksandr

    2014-03-01

    Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ‘aptamers’ and ‘phages’ which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives.

  8. Semiempirical Theories of the Affinities of Negative Atomic Ions

    NASA Technical Reports Server (NTRS)

    Edie, John W.

    1961-01-01

    The determination of the electron affinities of negative atomic ions by means of direct experimental investigation is limited. To supplement the meager experimental results, several semiempirical theories have been advanced. One commonly used technique involves extrapolating the electron affinities along the isoelectronic sequences, The most recent of these extrapolations Is studied by extending the method to Include one more member of the isoelectronic sequence, When the results show that this extension does not increase the accuracy of the calculations, several possible explanations for this situation are explored. A different approach to the problem is suggested by the regularities appearing in the electron affinities. Noting that the regular linear pattern that exists for the ionization potentials of the p electrons as a function of Z, repeats itself for different degrees of ionization q, the slopes and intercepts of these curves are extrapolated to the case of the negative Ion. The method is placed on a theoretical basis by calculating the Slater parameters as functions of q and n, the number of equivalent p-electrons. These functions are no more than quadratic in q and n. The electron affinities are calculated by extending the linear relations that exist for the neutral atoms and positive ions to the negative ions. The extrapolated. slopes are apparently correct, but the intercepts must be slightly altered to agree with experiment. For this purpose one or two experimental affinities (depending on the extrapolation method) are used in each of the two short periods. The two extrapolation methods used are: (A) an isoelectronic sequence extrapolation of the linear pattern as such; (B) the same extrapolation of a linearization of this pattern (configuration centers) combined with an extrapolation of the other terms of the ground configurations. The latter method Is preferable, since it requires only experimental point for each period. The results agree within

  9. Affine Covariant Features for Fisheye Distortion Local Modelling.

    PubMed

    Furnari, Antonino; Farinella, Giovanni; Bruna, Arcangelo; Battiato, Sebastiano

    2016-11-10

    Perspective cameras are the most popular imaging sensors used in Computer Vision. However, many application fields including automotive, surveillance and robotics, require the use of wide angle cameras (e.g., fisheye), which allow to acquire a larger portion of the scene using a single device at the cost of the introduction of noticeable radial distortion in the images. Affine covariant feature detectors have proven successful in a variety of Computer Vision applications including object recognition, image registration and visual search. Moreover, their robustness to a series of variabilities related to both the scene and the image acquisition process has been thoroughly studied in the literature. In this paper, we investigate their effectiveness on fisheye images providing both theoretical and experimental analyses. As theoretical outcome, we show that the inherently non-linear radial distortion can be locally approximated by linear functions with a reasonably small error. The experimental analysis builds on Mikolajczyk's benchmark to assess the robustness of three popular affine region detectors (i.e., Maximally Stable Extremal Regions (MSER), Harris and Hessian affine region detectors), with respect to different variabilities as well as to radial distortion. To support the evaluations, we rely on the Oxford dataset and introduce a novel benchmark dataset comprising 50 images depicting different scene categories. Experiments are carried out on rectilinear images to which radial distortion is artificially added, and on real-world images acquired using fisheye lenses. Our analysis points out that affine region detectors can be effectively employed directly on fisheye images and that the radial distortion is locally modelled as an additional affine variability.

  10. Debris Flow Distributed Propagation Model

    NASA Astrophysics Data System (ADS)

    Gregoretti, C.

    The debris flow distributed propagation model is a DEM-based model. The fan is dis- cretized by square cells and each cell is assigned an altitude on the sea level. The cells of the catchment are distinguished in two categories: the source cells and the stripe cells. The source cells receive the input hydograph: the cells close to the torrent which are flooded by the debris flow overflowing the torrent embankment are source cells. The stripes cells are the cells flooded by debris flow coming from the surrounding cells. At the first time step only the source cells are flooded by debris flow coming from the torrent. At the second time step a certain number of cells are flooded by de- bris flow coming from the source cells. These cells constitute a stripe of cells and are assigned order two. At the third time step another group of cells are flooded by the debris flow coming from the cells whose order is two. These cells constitute another stripe and are assigned order three. The cell order of a stripe is the time step number corresponding to the transition from dry to flooded state. The mass transfer or mo- mentum exchange between cells is governed by two different mechanisms. The mass transfer is allowed only by a positive or equal to zero flow level difference between the drained cell and the receiving cell. The mass transfer is limited by a not negative final flow level difference between the drained cell and the receiving cells. This limitation excludes the case of possible oscillations in the mass transfer. Another limitation is that the mass drained by a cell should be less than the available mass in that cell. This last condition provides the respect of mass conservation. The first mechanism of mass transfer is the gravity. The mass in a cell is transferred to the neighbouring cells with lower altitude and flow level according to an uniform flow law: The second mecha- nism of mass transfer is the broad crested weir. The mass in a cell is transferred to the

  11. In vitro propagation of Paphiopedilum orchids.

    PubMed

    Zeng, Songjun; Huang, Weichang; Wu, Kunlin; Zhang, Jianxia; da Silva, Jaime A Teixeira; Duan, Jun

    2016-01-01

    Paphiopedilum is one of the most popular and rare orchid genera. Members of the genus are sold and exhibited as pot plants and cut flowers. Wild populations of Paphiopedilum are under the threat of extinction due to over-collection and loss of suitable habitats. A reduction in their commercial value through large-scale propagation in vitro is an option to reduce pressure from illegal collection, to attempt to meet commercial needs and to re-establish threatened species back into the wild. Although they are commercially propagated via asymbiotic seed germination, Paphiopedilum are considered to be difficult to propagate in vitro, especially by plant regeneration from tissue culture. This review aims to cover the most important aspects and to provide an up-to-date research progress on in vitro propagation of Paphiopedilum and to emphasize the importance of further improving tissue culture protocols for ex vitro-derived explants.

  12. Noise propagation in urban and industrial areas

    NASA Technical Reports Server (NTRS)

    Davies, H. G.

    1976-01-01

    Noise propagation in streets and the discrepancies between theoretical analyses and field measurements are discussed. A cell-model is used to estimate the general background level of noise due to vehicular sources distributed over the urban area.

  13. The ghost propagator in Coulomb gauge

    NASA Astrophysics Data System (ADS)

    Watson, P.; Reinhardt, H.

    2011-05-01

    We present results for a numerical study of the ghost propagator in Coulomb gauge whereby lattice results for the spatial gluon propagator are used as input to solving the ghost Dyson-Schwinger equation. We show that in order to solve completely, the ghost equation must be supplemented by a boundary condition (the value of the inverse ghost propagator dressing function at zero momentum) which determines if the solution is critical (zero value for the boundary condition) or subcritical (finite value). The various solutions exhibit a characteristic behavior where all curves follow the same (critical) solution when going from high to low momenta until `forced' to freeze out in the infrared to the value of the boundary condition. The boundary condition can be interpreted in terms of the Gribov gauge-fixing ambiguity; we also demonstrate that this is not connected to the renormalization. Further, the connection to the temporal gluon propagator and the infrared slavery picture of confinement is discussed.

  14. The ghost propagator in Coulomb gauge

    SciTech Connect

    Watson, P.; Reinhardt, H.

    2011-05-23

    We present results for a numerical study of the ghost propagator in Coulomb gauge whereby lattice results for the spatial gluon propagator are used as input to solving the ghost Dyson-Schwinger equation. We show that in order to solve completely, the ghost equation must be supplemented by a boundary condition (the value of the inverse ghost propagator dressing function at zero momentum) which determines if the solution is critical (zero value for the boundary condition) or subcritical (finite value). The various solutions exhibit a characteristic behavior where all curves follow the same (critical) solution when going from high to low momenta until 'forced' to freeze out in the infrared to the value of the boundary condition. The boundary condition can be interpreted in terms of the Gribov gauge-fixing ambiguity; we also demonstrate that this is not connected to the renormalization. Further, the connection to the temporal gluon propagator and the infrared slavery picture of confinement is discussed.

  15. Promoted Combustion Test Propagation Rate Data

    NASA Technical Reports Server (NTRS)

    Borstorff, J.; Jones, P.; Lowery, F.

    2002-01-01

    Combustion propagation rate data were examined for potential use in benchmarking a thermal model of the Promoted Combustion Test (PCT), and also for potential use in measuring the repeatability of PCT results.

  16. Radio wave propagation and acoustic sounding

    NASA Astrophysics Data System (ADS)

    Singal, S. P.

    Radio wave propagation of the decimetric and centimetric waves depends to a large extent on the boundary layer meteorological conditions which give rise to severe fadings, very often due to multipath propagation. Sodar is one of the inexpensive remote sensing techniques which can be employed to probe the boundary layer structure. In the paper a historical perspective has been given of the simultaneously conducted studies on radio waves and sodar at various places. The radio meteorological information needed for propagation studies has been clearly spelt out and conditions of a ray path especially in the presence of a ducting layer have been defined as giving rise to fading or signal enhancement conditions. Finally the potential of the sodar studies to obtain information about the boundary layer phenomena has been stressed, clearly spelling out the use of acoustic sounding in radio wave propagation studies.

  17. Propagation Regime of Iron Dust Flames

    NASA Technical Reports Server (NTRS)

    Tang, Francois-David; Goroshin, Samuel; Higgins, Andrew J.

    2012-01-01

    A flame propagating through an iron-dust mixture can propagate in two asymptotic regimes. When the characteristic time of heat transfer between particles is much smaller than the characteristic time of particle combustion, the flame propagates in the continuum regime where the heat released by reacting particles can be modelled as a space-averaged function. In contrast, when the characteristic time of heat transfer is much larger than the particle reaction time, the flame can no longer be treated as a continuum due to dominating effects associated with the discrete nature of the particle reaction. The discrete regime is characterized by weak dependence of the flame speed on the oxygen concentration compared to the continuum regime. The discrete regime is observed in flames propagating through an iron dust cloud within a gas mixture containing xenon, while the continuum regime is obtained when xenon is substituted with helium.

  18. A solid state lightning propagation speed sensor

    NASA Technical Reports Server (NTRS)

    Mach, Douglas M.; Rust, W. David

    1989-01-01

    A device to measure the propagation speeds of cloud-to-ground lightning has been developed. The lightning propagation speed (LPS) device consists of eight solid state silicon photodetectors mounted behind precision horizontal slits in the focal plane of a 50-mm lens on a 35-mm camera. Although the LPS device produces results similar to those obtained from a streaking camera, the LPS device has the advantages of smaller size, lower cost, mobile use, and easier data collection and analysis. The maximum accuracy for the LPS is 0.2 microsec, compared with about 0.8 microsecs for the streaking camera. It is found that the return stroke propagation speed for triggered lightning is different than that for natural lightning if measurements are taken over channel segments less than 500 m. It is suggested that there are no significant differences between the propagation speeds of positive and negative flashes. Also, differences between natural and triggered dart leaders are discussed.

  19. Propagation effects on attosecond pulse generation

    NASA Astrophysics Data System (ADS)

    Lorin, E.; Chelkowski, S.; Bandrauk, A.

    2007-06-01

    This paper is devoted to the dynamics of attosecond pulses created during the high order harmonic generation process. In this goal we study Ti:sapphir laser pulses propagating in a H II + gas. The dynamics and propagation of the incident pulse is obtained by solving the macroscopic Maxwell equations. The molecular gas reaction on the electric field, the polarization, is derived from TDSE's following the model presented in [9], [10]. We are especially interested in this work, in the attosecond pulse dynamics and the intensity of the first harmonics dependently of the propagation length inside the gas, on the attosecond pulse generation and propagation and the energy of return graphs in function of the driver phase.

  20. Functional comparison of engineered T cells carrying a native TCR versus TCR-like antibody-based chimeric antigen receptors indicates affinity/avidity thresholds.

    PubMed

    Oren, Ravit; Hod-Marco, Moran; Haus-Cohen, Maya; Thomas, Sharyn; Blat, Dan; Duvshani, Nerri; Denkberg, Galit; Elbaz, Yael; Benchetrit, Fabrice; Eshhar, Zelig; Stauss, Hans; Reiter, Yoram

    2014-12-01

    Adoptive transfer of Ag-specific T lymphocytes is an attractive form of immunotherapy for cancers. However, acquiring sufficient numbers of host-derived tumor-specific T lymphocytes by selection and expansion is challenging, as these cells may be rare or anergic. Using engineered T cells can overcome this difficulty. Such engineered cells can be generated using a chimeric Ag receptor based on common formats composed from Ag-recognition elements such as αβ-TCR genes with the desired specificity, or Ab variable domain fragments fused with T cell-signaling moieties. Combining these recognition elements are Abs that recognize peptide-MHC. Such TCR-like Abs mimic the fine specificity of TCRs and exhibit both the binding properties and kinetics of high-affinity Abs. In this study, we compared the functional properties of engineered T cells expressing a native low affinity αβ-TCR chains or high affinity TCR-like Ab-based CAR targeting the same specificity. We isolated high-affinity TCR-like Abs recognizing HLA-A2-WT1Db126 complexes and constructed CAR that was transduced into T cells. Comparative analysis revealed major differences in function and specificity of such CAR-T cells or native TCR toward the same antigenic complex. Whereas the native low-affinity αβ-TCR maintained potent cytotoxic activity and specificity, the high-affinity TCR-like Ab CAR exhibited reduced activity and loss of specificity. These results suggest an upper affinity threshold for TCR-based recognition to mediate effective functional outcomes of engineered T cells. The rational design of TCRs and TCR-based constructs may need to be optimized up to a given affinity threshold to achieve optimal T cell function.