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Sample records for affinity capture reveals

  1. Affine transformations capture beak shape variation in Darwin's Finches

    Science.gov (United States)

    Brenner, Michael; Campas, Otger; Mallarino, Riccardo; Abzhanov, Arhat

    2009-11-01

    Evolution by natural selection has resulted in extraordinary morphological complexity of living organisms, whose description has thus far defied any precise mathematical characterization linked to the underlying developmental genetics. Here we demonstrate that the morphological diversity of the beaks of Darwin's finches, the classical example of adaptive morphological radiation, is quantitatively accounted for through the mathematical group of affine transformations. Specifically, we show that all beak shapes of Ground Finches (genus Geospiza) are related by scaling transformations (a subgroup of the affine group), and the same scheme occurs for all the beak shapes of Tree and Warbler finches. This analysis shows that the beak shapes within each of these groups differ only by their scales, such as length and depth, each of which is knownto be under genetic control.The complete morphological variability within the beaks of Darwin's finches can be explained by extending the scaling transformations to the entire affine group, by including shear transformations. Altogether our results suggest that the mathematical theory of groups can help decode morphological variability, and points to a potentially hierarchical structure of morphological diversity and the underlying developmental processes.

  2. Twin-column CaptureSMB: a novel cyclic process for protein A affinity chromatography.

    Science.gov (United States)

    Angarita, Monica; Müller-Späth, Thomas; Baur, Daniel; Lievrouw, Roel; Lissens, Geert; Morbidelli, Massimo

    2015-04-10

    A twin-column counter-current chromatography processes, CaptureSMB, was used for the protein A affinity capture of a monoclonal antibody (mAb). By means of sequential loading, the process improves the utilization of the stationary phase by achieving loadings much closer to the static binding capacity of the resin in comparison to batch chromatography. Using a mAb capture case study with protein A affinity chromatography, the performance and product quality obtained from CaptureSMB and batch processes were compared. The effect of the flow rate, column length and titer concentration on the process performance and product quality were evaluated. CaptureSMB showed superior performance compared to batch chromatography with respect to productivity, capacity utilization, product concentration and buffer consumption. A simplified economic evaluation showed that CaptureSMB could decrease resin costs of 10-30% depending on the manufacturing scenario.

  3. Rapid purification of circular DNA by triplex-mediated affinity capture

    Science.gov (United States)

    Ji, H.; Smith, L.M.

    1997-01-07

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support. 3 figs.

  4. Radio frequency plasma polymer coatings for affinity capture MALDI mass spectrometry.

    Science.gov (United States)

    Li, Meiling; Timmons, Richard B; Kinsel, Gary R

    2005-01-01

    Surface modification of MALDI probes is an attractive approach for combining bioaffinity isolation of targeted biomolecules with mass spectrometric analysis of the captured species. In this work, we demonstrate that a polymer thin film, produced by pulsed rf plasma polymerization of allylamine and deposited directly on a MALDI probe, can be subsequently biotinylated to develop a bioaffinity capture MALDI probe. The synthesis and characterization of the probe by XPS, FT-IR, and AFM is described, and the selective isolation of avidin from a three-component mixture of avidin, lysozyme, and cytochrome c is presented. These initial results offer encouragement for the further exploration of rf plasma polymer deposition as a novel approach for the development of on-probe affinity capture MALDI probes.

  5. Density Gradient Ultracentrifugation to Isolate Endogenous Protein Complexes after Affinity Capture.

    Science.gov (United States)

    Fernandez-Martinez, Javier; LaCava, John; Rout, Michael P

    2016-07-01

    This protocol describes the isolation of native protein complexes by density gradient ultracentrifugation. The outcome of an affinity capture and native elution experiment is generally a mixture of (1) the complex(es) associated with the protein of interest under the specific conditions of capture, (2) fragments of the complex generated by degradation or disassembly during the purification procedure, and (3) the protease or reagent used to natively elute the sample. To separate these components and isolate a homogeneous complex, an additional step of purification is required. Rate-zonal density gradient ultracentrifugation is a reliable and powerful technique for separating particles based on their hydrodynamic volume. The density gradient is generated by mixing low- and high-density solutions of a suitable low-molecular-weight inert solute (e.g., sucrose or glycerol). The gradient is formed in a solvent that could be any of the solvents used for the affinity capture and native elution and should help to preserve the structure and activity of the assembly.

  6. Development of an epoxy-based monolith used for the affinity capturing of Escherichia coli bacteria.

    Science.gov (United States)

    Peskoller, Caroline; Niessner, Reinhard; Seidel, Michael

    2009-05-01

    An epoxy-based monolith has been developed for use as hydrophilic support in bioseparation. This monolith is produced by self-polymerization of polyglycerol-3-glycidyl ether in organic solvents as porogens at room temperature within 1 h. One receives a highly cross-linked structure that provides useful mechanical properties. The porosity and pore diameter can be controlled by varying the composition of the porogen. In this work, an epoxy-based monolith with a high porosity (79%) and large pore size (22 microm) is prepared and used in affinity capturing of bacterial cells. These features allow the passage of bacterial cells through the column. As affinity ligand polymyxin B is used, which allows the binding of gram-negative bacteria. The efficiency of the monolithic affinity column is studied with Escherichia coli spiked in water. Bacterial cells are concentrated on the column at pH 4 and eluted with a recovery of 97+/-3% in 200 microL by changing the pH value without impairing viability of bacteria. The dynamic capacity for the monolithic column is nearly independent of the flow rate (4x10(9)cells/column). Thereby, it is possible to separate and enrich gram-negative bacterial cells, such as E. coli, with high flow rates (10 mL/min) and low back pressure (<1 bar) in a volume as low as 200 microL compatible for real-time polymerase chain reaction, microarray formats, and biosensors.

  7. Application of a novel affinity adsorbent for the capture and purification of recombinant factor VIII compounds.

    Science.gov (United States)

    McCue, Justin T; Selvitelli, Keith; Walker, Joshua

    2009-11-06

    Recombinant Factor VIII (FVIII) therapies have been created to provide treatment for Hemophilia A, an inherited bleeding disorder caused by mutation in the FVIII gene. A major challenge in the purification of recombinant FVIII molecules is the development of an affinity chromatography step. Such a step must be highly specific and selective for the FVIII molecule, but also must be designed appropriately to ensure the FVIII molecule can be effectively recovered without resorting to harsh elution conditions which may be harmful to the product. Additionally, it is desirable to have affinity adsorbents designed to be reusable over a large number of column cycles while maintaining consistent purification performance. In this work, we describe the use of VIIISelect, a commercially available affinity adsorbent designed specifically for the purification of FVIII compounds. The VIIISelect adsorbent consists of a 13kDa recombinant protein ligand attached to a cross-linked agarose base matrix. The structure of the recombinant ligand is based upon Camelid-derived single domain antibody fragments. The VIIISelect adsorbent is produced using a process free of animal-derived raw materials, which is a highly desirable attribute for adsorbents used in the purification processes of recombinant protein therapeutics. The VIIISelect adsorbent was used as the initial capture column to purify a FVIII compound directly from clarified cell culture fluid prior to further downstream purification. The purification performance of the VIIISelect was evaluated, which included measurement of the static binding capacity, dynamic binding capacity, product recovery, impurity clearance, and adsorbent reuse. Following laboratory-scale process development, the VIIISelect adsorbent was scaled up and used in the large scale manufacturing of a FVIII compound.

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

    Science.gov (United States)

    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

  9. DNA capture reveals transoceanic gene flow in endangered river sharks.

    Science.gov (United States)

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T; Naylor, Gavin J P

    2015-10-27

    For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

  10. Advance chromatin extraction improves capture performance of protein A affinity chromatography.

    Science.gov (United States)

    Nian, Rui; Zhang, Wei; Tan, Lihan; Lee, Jeremy; Bi, Xeuzhi; Yang, Yuansheng; Gan, Hui Theng; Gagnon, Pete

    2016-01-29

    Practical effects of advance chromatin removal on performance of protein A affinity chromatography were evaluated using a caprylic acid-allantoin-based extraction method. Lacking this treatment, the practice of increasing loading residence time to increase capacity was shown to increase host protein contamination of the eluted IgG. Advance chromatin extraction suspended that compromise. Protein A ligand leakage from columns loaded with chromatin-extracted harvest was half the level observed on protein A columns loaded with non-extracted harvest. Columns loaded with chromatin-extracted harvest were cleaned more effectively by 50-100mM NaOH than columns loaded with non-extracted harvest that were cleaned with 250-500mM NaOH. Two protein A media with IgG capacities in excess of 50g/L were loaded with chromatin-extracted harvest, washed with 2.0M NaCl before elution, and the eluted IgG fraction titrated to pH 5.5 before microfiltration. Host protein contamination in the filtrate was reduced to protein A leakage to 0.5ppm, and aggregates to 1.0%. Caprylic acid and allantoin were both reduced below 5ppm. Step recovery of IgG was 99.4%. Addition of a single polishing step reduced residual protein A beneath the level of detection and aggregates to <0.1%. Overall process recovery including chromatin extraction was 90%.

  11. Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.

    Science.gov (United States)

    Hjelm, Barbara; Forsström, Björn; Igel, Ulrika; Johannesson, Henrik; Stadler, Charlotte; Lundberg, Emma; Ponten, Fredrik; Sjöberg, Anna; Rockberg, Johan; Schwenk, Jochen M; Nilsson, Peter; Johansson, Christine; Uhlén, Mathias

    2011-11-01

    A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.

  12. Affinity capture using peptide-functionalized magnetic nanoparticles to target Staphylococcus aureus

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    Kuo, Fang-Yin; Lin, Wei-Lien; Chen, Yu-Chie

    2016-04-01

    Staphylococcus aureus, a commonly found pathogen, can cause food poisoning and infections. Thus, it is necessary to develop analytical methods for the rapid screening of S. aureus in suspicious samples. Magnetic nanoparticles (MNPs) are widely used as affinity probes to selectively enrich target species from complex samples because of their high specific surface area and magnetic properties. The MNP surface should be functionalized to have the capability to target specific species. We herein propose a straightforward method to functionalize aluminum oxide-coated iron oxide (Fe3O4@Al2O3) MNPs with the peptide HHHHHHDEEGLFVD (D). The peptide D was comprised of three domains: polyhistidine (H6) used as the linker, DEE added as the spacer, and GLFVD used for targeting S. aureus. D was immobilized on the surface of Fe3O4@Al2O3 MNPs through H6-Al chelation. Our results showed that the D-functionalized Fe3O4@Al2O3 MNPs (D-Fe3O4 MNPs) possess the capability to target S. aureus. The selective trapping experiments were conducted under microwave-heating for only 60 s, and sufficient bacterial cells were trapped by the MNPs to be identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We demonstrated that the D-Fe3O4@Al2O3 MNPs combined with MALDI-MS can be used to rapidly characterize trace amounts of S. aureus in complex juice and egg samples.Staphylococcus aureus, a commonly found pathogen, can cause food poisoning and infections. Thus, it is necessary to develop analytical methods for the rapid screening of S. aureus in suspicious samples. Magnetic nanoparticles (MNPs) are widely used as affinity probes to selectively enrich target species from complex samples because of their high specific surface area and magnetic properties. The MNP surface should be functionalized to have the capability to target specific species. We herein propose a straightforward method to functionalize aluminum oxide-coated iron oxide (Fe3O4@Al2O3) MNPs with the

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

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    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.

  14. Prey-capture success revealed by echolocation signals in pipistrelle bats (Pipistrellus pygmaeus)

    DEFF Research Database (Denmark)

    Surlykke, Annemarie; Futtrup, Vibeke; Tougaard, Jakob

    2003-01-01

    Three Pipistrellus pygmaeus bats were trained to capture prey on the wing while flying in the laboratory. The bats' capture behaviour and capture success were determined and correlated with acoustic analyses of post-buzz echolocation signals. Three acoustic parameters revealed capture success: in...

  15. Ancient DNA from European early neolithic farmers reveals their near eastern affinities.

    Directory of Open Access Journals (Sweden)

    Wolfgang Haak

    Full Text Available In Europe, the Neolithic transition (8,000-4,000 B.C. from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500-4,900 calibrated B.C. and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42 and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500-4,900 calibrated B.C.. We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394 and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting

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

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    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

  17. Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides.

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    Cheng, Gong; Zhang, Ji-Lin; Liu, Yan-Lin; Sun, De-Hui; Ni, Jia-Zuan

    2012-02-13

    Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides.

  18. Surface plasmon resonance reveals a different pattern of proinsulin autoantibodies concentration and affinity in diabetic patients.

    Directory of Open Access Journals (Sweden)

    Aldana Trabucchi

    Full Text Available Type 1 diabetes mellitus (DM is characterized by autoimmune aggression against pancreatic beta cells resulting in absolute deficiency of insulin secretion. The first detectable sign of emerging autoimmunity during the preclinical asymptomatic period is the appearance of diabetes-related autoantibodies. In children at risk for type 1 DM, high-affinity Insulin autoantibodies reactive to proinsulin, are associated with diabetes risk. Autoantibodies are usually measured by radioligand binding assay (RBA that provides quasi-quantitative values reflecting potency (product between concentration and affinity of specific autoantibodies. Aiming to improve the characterization of the specific humoral immune response, we selected surface plasmon resonance (SPR as an alternative method to measure proinsulin autoantibodies (PAA. This novel technology has allowed real time detection of antibodies interaction and kinetic analysis. Herein, we have employed SPR to characterize the PAA present in sera from 28 childhood-onset (mean age 8.31±4.20 and 23 adult-onset diabetic patients (≥65 years old, BMI<30 in terms of concentration and affinity. When evaluating comparatively samples from both groups, childhood-onset diabetic patients presented lower PAA concentrations and higher affinities (median 67.12×10(-9 M and 3.50×10(7 M(-1, respectively than the adults (median 167.4×10(-9 M and 0.84×10(7 M(-1, respectively. These results are consistent with those from the reference method RBA (Standard Deviation score median 9.49 for childhood-onset group and 5.04 for adult-onset group where the binding can be directly related to the intrinsic affinity of the antibody, suggesting that there is a different etiopathogenic pathway between both types of clinical presentation of the disease. This technology has shown to be a useful tool for the characterization of PAAs parameters as an alternative to radioimmunoassay, with high versatility and reproducibility associated to

  19. Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Jørgensen, Thomas J. D.; Koefoed, Klaus;

    2013-01-01

    prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture...... of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein...... complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor...

  20. Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

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    Manoharan, Lokeshwaran; Kushwaha, Sandeep K; Hedlund, Katarina; Ahrén, Dag

    2015-12-01

    Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.

  1. Synthesis of Biotinylated Inositol Hexakisphosphate To Study DNA Double-Strand Break Repair and Affinity Capture of IP6-Binding Proteins.

    Science.gov (United States)

    Jiao, Chensong; Summerlin, Matthew; Bruzik, Karol S; Hanakahi, Leslyn

    2015-10-20

    Inositol hexakisphosphate (IP6) is a soluble inositol polyphosphate, which is abundant in mammalian cells. Despite the participation of IP6 in critical cellular functions, few IP6-binding proteins have been characterized. We report on the synthesis, characterization, and application of biotin-labeled IP6 (IP6-biotin), which has biotin attached at position 2 of the myo-inositol ring via an aminohexyl linker. Like natural IP6, IP6-biotin stimulated DNA ligation by nonhomologous end joining (NHEJ) in vitro. The Ku protein is a required NHEJ factor that has been shown to bind IP6. We found that IP6-biotin could affinity capture Ku and other required NHEJ factors from human cell extracts, including the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4, and XLF. Direct binding studies with recombinant proteins show that Ku is the only NHEJ factor with affinity for IP6-biotin. DNA-PKcs, XLF, and the XRCC4:ligase IV complex interact with Ku in cell extracts and likely interact indirectly with IP6-biotin. IP6-biotin was used to tether streptavidin to Ku, which inhibited NHEJ in vitro. These proof-of-concept experiments suggest that molecules like IP6-biotin might be used to molecularly target biologically important proteins that bind IP6. IP6-biotin affinity capture experiments show that numerous proteins specifically bind IP6-biotin, including casein kinase 2, which is known to bind IP6, and nucleolin. Protein binding to IP6-biotin is selective, as IP3, IP4, and IP5 did not compete for binding of proteins to IP6-biotin. Our results document IP6-biotin as a useful tool for investigating the role of IP6 in biological systems.

  2. Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

    Science.gov (United States)

    Carrascosa, Laura G.; Gómez-Montes, S.; Aviñó, A.; Nadal, A.; Pla, M.; Eritja, R.; Lechuga, L. M.

    2012-01-01

    A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50 fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field. PMID:22241768

  3. SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture.

    Science.gov (United States)

    Rees, Johanna S; Lilley, Kathryn S; Jackson, Antony P

    2015-02-06

    Pull-down assays can identify members of protein complexes but suffer from co-isolation of contaminants. The problem is particularly acute when the specifically interacting partners are of low-abundance and/or bind transiently with low affinity. To differentiate true interacting partners from contaminants, we have combined SILAC labelling with a proteomic method called "Interactomes by Parallel Affinity Capture" (iPAC). In our method, a cell-line stably expressing a doubly tagged target endogenous protein and its tag-less control cell-line are differentially SILAC labelled. Lysates from the two cell-lines are mixed and the tagged protein is independently purified for MS analysis using multiple affinity resins in parallel. This allows the quantitative identification of tagged proteins and their binding partners. SILAC-iPAC provides a rigorous and sensitive approach that can discriminate between genuine binding partners and contaminants, even when the contaminants in the pull-down are in large excess. We employed our method to examine the interacting partners of phosphatidyl inositol 5-phosphate 4-kinase 2β subunit (PI5P4K2β) and the Fanconi anaemia core complex in the chicken pre-B cell-line DT40. We confirmed known components of these two complexes, and we have identified new potential binding partners. Combining the iPAC approach with SILAC labelling provides a sensitive and fully quantitative method for the discrimination of specific interactions under conditions where low signal to noise ratios are unavoidable. In addition, our work provides the first characterisation of the most abundant proteins within the DT40 proteome and the non-specific DT40 'beadomes' (non-specific proteins binding to beads) for common epitope tags. Given the importance and widespread use of the DT40 cell-line, these will be important resources for the cell biology and immunology communities. Biological significance SILAC-iPAC provides an improved method for the analysis of low-affinity

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

    Science.gov (United States)

    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. Capturing Arabidopsis root architecture dynamics with ROOT-FIT reveals diversity in responses to salinity.

    Science.gov (United States)

    Julkowska, Magdalena M; Hoefsloot, Huub C J; Mol, Selena; Feron, Richard; de Boer, Gert-Jan; Haring, Michel A; Testerink, Christa

    2014-11-01

    The plant root is the first organ to encounter salinity stress, but the effect of salinity on root system architecture (RSA) remains elusive. Both the reduction in main root (MR) elongation and the redistribution of the root mass between MRs and lateral roots (LRs) are likely to play crucial roles in water extraction efficiency and ion exclusion. To establish which RSA parameters are responsive to salt stress, we performed a detailed time course experiment in which Arabidopsis (Arabidopsis thaliana) seedlings were grown on agar plates under different salt stress conditions. We captured RSA dynamics with quadratic growth functions (root-fit) and summarized the salt-induced differences in RSA dynamics in three growth parameters: MR elongation, average LR elongation, and increase in number of LRs. In the ecotype Columbia-0 accession of Arabidopsis, salt stress affected MR elongation more severely than LR elongation and an increase in LRs, leading to a significantly altered RSA. By quantifying RSA dynamics of 31 different Arabidopsis accessions in control and mild salt stress conditions, different strategies for regulation of MR and LR meristems and root branching were revealed. Different RSA strategies partially correlated with natural variation in abscisic acid sensitivity and different Na(+)/K(+) ratios in shoots of seedlings grown under mild salt stress. Applying root-fit to describe the dynamics of RSA allowed us to uncover the natural diversity in root morphology and cluster it into four response types that otherwise would have been overlooked.

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

    Science.gov (United States)

    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.

  7. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps.

    Science.gov (United States)

    Tennessen, Jacob A; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

    2014-12-04

    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.

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

    Science.gov (United States)

    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.'

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

    Energy Technology Data Exchange (ETDEWEB)

    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. EGL-1 BH3 mutants reveal the importance of protein levels and target affinity for cell-killing potency.

    Science.gov (United States)

    Lee, E F; Chen, L; Yang, H; Colman, P M; Huang, D C S; Fairlie, W D

    2008-10-01

    Studies of the cell death pathway in the nematode Caenorhabditis elegans provided the first evidence of the evolutionary conservation of apoptosis signalling. Here we show that the worm Bcl-2 homology domain-3 (BH3)-only protein EGL-1 binds mammalian pro-survival proteins very poorly, but can be converted into a high-affinity ligand for Bcl-2 and Bcl-x(L) by subtle mutation of the cysteine residue at position 62 within the BH3 domain. A 100-fold increase in affinity was observed following a single atom change (cysteine to serine substitution), and a further 10-fold increase by replacement with glycine. The low affinity of wild-type EGL-1 for mammalian pro-survival proteins and its poor expression correlates with its weak killing activity in mammalian cells whereas the high-affinity C62G mutant is a very potent killer of cells lacking Mcl-1. Cell killing by the C62S mutant with intermediate affinity only occurs when this EGL-1 BH3 domain is placed in a more stable context, namely that of Bim(S), which allows higher expression, though the kinetics of cell death now vary depending on whether Mcl-1 is neutralized by Noxa or genetically deleted. These results demonstrate how levels of BH3-only proteins, target affinity and the spectrum of neutralization of pro-survival proteins all contribute to killing activity.

  11. Timing of human protein evolution as revealed by massively parallel capture of Neandertal nuclear DNA sequences

    Science.gov (United States)

    Burbano, Hernán A.; Hodges, Emily; Green, Richard E.; Briggs, Adrian W.; Krause, Johannes; Meyer, Matthias; Good, Jeffrey M.; Maricic, Tomislav; Johnson, Philipp L.F.; Xuan, Zhenyu; Rooks, Michelle; Bhattacharjee, Arindam; Brizuela, Leonardo; Albert, Frank W.; de la Rasilla, Marco; Fortea, Javier; Rosas, Antonio; Lachmann, Michael; Hannon, Gregory J.; Pääbo, Svante

    2010-01-01

    Whole genome shotgun sequencing is now possible for extinct organisms, as well as the targeted capture of specific regions. However, targeted resequencing of megabase sized parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can be used to generate large scale targeted data from Neandertal DNA even in the presence of ~99.8% microbial DNA. It is thus now possible to generate high quality data from large regions of the nuclear genome from Neandertals and other extinct organisms. Using this approach we have sequenced ~14,000 protein coding positions that have been inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. We identify 88 amino acid substitutions that have become fixed in all humans since the divergence from the Neandertals. PMID:20448179

  12. Antibody Stabilization of Peptide–MHC Multimers Reveals Functional T Cells Bearing Extremely Low-Affinity TCRs

    DEFF Research Database (Denmark)

    Tungatt, Katie; Bianchi, Valentina; Crowther, Michael D;

    2015-01-01

    Fluorochrome-conjugated peptide-MHC (pMHC) multimers are commonly used in combination with flow cytometry for direct ex vivo visualization and characterization of Ag-specific T cells, but these reagents can fail to stain cells when TCR affinity and/or TCR cell-surface density are low. pMHC multim...

  13. Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.

    Directory of Open Access Journals (Sweden)

    Kyriakos Tsangaras

    Full Text Available The koala retrovirus (KoRV is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.

  14. A novel immuno-competitive capture mass spectrometry strategy for protein-protein interaction profiling reveals that LATS kinases regulate HCV replication through NS5A phosphorylation.

    Science.gov (United States)

    Meistermann, Hélène; Gao, Junjun; Golling, Sabrina; Lamerz, Jens; Le Pogam, Sophie; Tzouros, Manuel; Sankabathula, Sailaja; Gruenbaum, Lore; Nájera, Isabel; Langen, Hanno; Klumpp, Klaus; Augustin, Angélique

    2014-11-01

    Mapping protein-protein interactions is essential to fully characterize the biological function of a protein and improve our understanding of diseases. Affinity purification coupled to mass spectrometry (AP-MS) using selective antibodies against a target protein has been commonly applied to study protein complexes. However, one major limitation is a lack of specificity as a substantial part of the proposed binders is due to nonspecific interactions. Here, we describe an innovative immuno-competitive capture mass spectrometry (ICC-MS) method to allow systematic investigation of protein-protein interactions. ICC-MS markedly increases the specificity of classical immunoprecipitation (IP) by introducing a competition step between free and capturing antibody prior to IP. Instead of comparing only one experimental sample with a control, the methodology generates a 12-concentration antibody competition profile. Label-free quantitation followed by a robust statistical analysis of the data is then used to extract the cellular interactome of a protein of interest and to filter out background proteins. We applied this new approach to specifically map the interactome of hepatitis C virus (HCV) nonstructural protein 5A (NS5A) in a cellular HCV replication system and uncovered eight new NS5A-interacting protein candidates along with two previously validated binding partners. Follow-up biological validation experiments revealed that large tumor suppressor homolog 1 and 2 (LATS1 and LATS2, respectively), two closely related human protein kinases, are novel host kinases responsible for NS5A phosphorylation at a highly conserved position required for optimal HCV genome replication. These results are the first illustration of the value of ICC-MS for the analysis of endogenous protein complexes to identify biologically relevant protein-protein interactions with high specificity.

  15. Capture of micrococcin biosynthetic intermediates reveals C-terminal processing as an obligatory step for in vivo maturation

    Science.gov (United States)

    Bewley, Kathryn D.; Bennallack, Philip R.; Burlingame, Mark A.; Robison, Richard A.; Griffitts, Joel S.

    2016-01-01

    Thiopeptides, including micrococcins, are a growing family of bioactive natural products that are ribosomally synthesized and heavily modified. Here we use a refactored, modular in vivo system containing the micrococcin P1 (MP1) biosynthetic genes (TclIJKLMNPS) from Macrococcus caseolyticus str 115 in a genetically tractable Bacillus subtilis strain to parse the processing steps of this pathway. By fusing the micrococcin precursor peptide to an affinity tag and coupling it with catalytically defective enzymes, biosynthetic intermediates were easily captured for analysis. We found that two major phases of molecular maturation are separated by a key C-terminal processing step. Phase-I conversion of six Cys residues to thiazoles (TclIJN) is followed by C-terminal oxidative decarboxylation (TclP). This TclP-mediated oxidative decarboxylation is a required step for the peptide to progress to phase II. In phase II, Ser/Thr dehydration (TclKL) and peptide macrocycle formation (TclM) occurs. A C-terminal reductase, TclS, can optionally act on the substrate peptide, yielding MP1, and is shown to act late in the pathway. This comprehensive characterization of the MP1 pathway prepares the way for future engineering efforts. PMID:27791142

  16. New early Eocene vertebrate assemblage from western India reveals a mixed fauna of European and Gondwana affinities

    Institute of Scientific and Technical Information of China (English)

    Thierry Smith; Kishor Kumar; Rajendra S. Rana; Annelise Folie; Floréal Solé; Corentin Noiret; Thomas Steeman; Ashok Sahni; Kenneth D. Rose

    2016-01-01

    The Ypresian Cambay Shale Formation at Vastan and Mangrol lignite mines in Gujarat, western India, has yielded a rich vertebrate fauna with numerous taxa of European affinities. Here we report a new, approximately contemporary vertebrate assemblage from two fossiliferous layers in the nearby mine of Tadkeshwar. These layers have yielded a similar mammal fauna with the co-occurrence of the perissodactyl-like cambaytheriid Cambaytherium thewissi, the adapoid primates Marcgodinotius indicus and cf. Asiadapis cambayensis, and the hyaenodontid Indohyaenodon raoi. The presence of these species in both Vastan and Tadkeshwar mines and at different levels suggests that the deposits between the two major lignite seams represent a single land mammal age. Apart from the aforementioned species there is a new, smaller species of Cambaytherium, and a new genus and species of esthonychid tillodont. This fauna also contains the first large early Eocene vertebrates from India, including an unidentified Cor-yphodon-like pantodont, a dyrosaurid crocodyliform and a new giant madtsoiid snake. Among the Tadkeshwar vertebrates several taxa are of Gondwana affinities, such as Pelomedusoides turtles, dyr-osaurids, and large madtsoiids, attesting that the early Eocene was a crucial period in India during which Laurasian taxa of European affinities co-existed with relict taxa from Gondwana before the India-Asia collision. Our results suggest that terrestrial faunas could have dispersed to or from Europe during ep-isodes of contact between the Indian subcontinent and different island blocks along the northern margin of the Neotethys, such as the KohistaneLadakh island-arc system. Gondwana taxa might represent remnants of ghost lineages shared with Madagascar, which reached the Indian subcontinent during the late Cretaceous; alternatively they might have come from North Africa and passed along the southern margin of the Neotethys to reach the Indian subcontinent. These dispersals would have

  17. New early Eocene vertebrate assemblage from western India reveals a mixed fauna of European and Gondwana affinities

    Directory of Open Access Journals (Sweden)

    Thierry Smith

    2016-11-01

    Full Text Available The Ypresian Cambay Shale Formation at Vastan and Mangrol lignite mines in Gujarat, western India, has yielded a rich vertebrate fauna with numerous taxa of European affinities. Here we report a new, approximately contemporary vertebrate assemblage from two fossiliferous layers in the nearby mine of Tadkeshwar. These layers have yielded a similar mammal fauna with the co-occurrence of the perissodactyl-like cambaytheriid Cambaytherium thewissi, the adapoid primates Marcgodinotius indicus and cf. Asiadapis cambayensis, and the hyaenodontid Indohyaenodon raoi. The presence of these species in both Vastan and Tadkeshwar mines and at different levels suggests that the deposits between the two major lignite seams represent a single land mammal age. Apart from the aforementioned species there is a new, smaller species of Cambaytherium, and a new genus and species of esthonychid tillodont. This fauna also contains the first large early Eocene vertebrates from India, including an unidentified Coryphodon-like pantodont, a dyrosaurid crocodyliform and a new giant madtsoiid snake. Among the Tadkeshwar vertebrates several taxa are of Gondwana affinities, such as Pelomedusoides turtles, dyrosaurids, and large madtsoiids, attesting that the early Eocene was a crucial period in India during which Laurasian taxa of European affinities co-existed with relict taxa from Gondwana before the India-Asia collision. Our results suggest that terrestrial faunas could have dispersed to or from Europe during episodes of contact between the Indian subcontinent and different island blocks along the northern margin of the Neotethys, such as the Kohistan–Ladakh island-arc system. Gondwana taxa might represent remnants of ghost lineages shared with Madagascar, which reached the Indian subcontinent during the late Cretaceous; alternatively they might have come from North Africa and passed along the southern margin of the Neotethys to reach the Indian subcontinent. These

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

    DEFF Research Database (Denmark)

    Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida;

    2015-01-01

    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 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...

  19. Interaction structure of the complex between neuroprotective factor humanin and Alzheimer's β-amyloid peptide revealed by affinity mass spectrometry and molecular modeling.

    Science.gov (United States)

    Maftei, Madalina; Tian, Xiaodan; Manea, Marilena; Exner, Thomas E; Schwanzar, Daniel; von Arnim, Christine A F; Przybylski, Michael

    2012-06-01

    Humanin (HN) is a linear 24-aa peptide recently detected in human Alzheimer's disease (AD) brain. HN specifically inhibits neuronal cell death in vitro induced by ß-amyloid (Aß) peptides and by amyloid precursor protein and its gene mutations in familial AD, thereby representing a potential therapeutic lead structure for AD; however, its molecular mechanism of action is not well understood. We report here the identification of the binding epitopes between HN and Aß(1-40) and characterization of the interaction structure through a molecular modeling study. Wild-type HN and HN-sequence mutations were synthesized by SPPS and the HPLC-purified peptides characterized by MALDI-MS. The interaction epitopes between HN and Aß(1-40) were identified by affinity-MS using proteolytic epitope excision and extraction, followed by elution and mass spectrometric characterization of the affinity-bound peptides. The affinity-MS analyses revealed HN(5-15) as the epitope sequence of HN, whereas Aß(17-28) was identified as the Aß interaction epitope. The epitopes and binding sites were ascertained by ELISA of the complex of HN peptides with immobilized Aß(1-40) and by ELISA with Aß(1-40) and Aß-partial sequences as ligands to immobilized HN. The specificity and affinity of the HN-Aß interaction were characterized by direct ESI-MS of the HN-Aß(1-40) complex and by bioaffinity analysis using a surface acoustic wave biosensor, providing a K(D) of the complex of 610 nm. A molecular dynamics simulation of the HN-Aß(1-40) complex was consistent with the binding specificity and shielding effects of the HN and Aß interaction epitopes. These results indicate a specific strong association of HN and Aß(1-40) polypeptide and provide a molecular basis for understanding the neuroprotective function of HN.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Daniel J Cole

    2011-07-01

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

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

    DEFF Research Database (Denmark)

    Kandra, L.; Abou Hachem, Maher; Gyemant, G.;

    2006-01-01

    as binding barriers. Barley a-amylase I 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...

  3. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.

    Science.gov (United States)

    Chen, Ko-Hsuan; Miadlikowska, Jolanta; Molnár, Katalin; Arnold, A Elizabeth; U'Ren, Jana M; Gaya, Ester; Gueidan, Cécile; Lutzoni, François

    2015-04-01

    Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our

  4. High affinity capture and concentration of quinacrine in polymorphonuclear neutrophils via vacuolar ATPase-mediated ion trapping: Comparison with other peripheral blood leukocytes and implications for the distribution of cationic drugs

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Caroline; Gagné, Valérie; Fernandes, Maria J.G.; Marceau, François, E-mail: francois.marceau@crchul.ulaval.ca

    2013-07-15

    Many cationic drugs are concentrated in acidic cell compartments due to low retro-diffusion of the protonated molecule (ion trapping), with an ensuing vacuolar and autophagic cytopathology. In solid tissues, there is evidence that phagocytic cells, e.g., histiocytes, preferentially concentrate cationic drugs. We hypothesized that peripheral blood leukocytes could differentially take up a fluorescent model cation, quinacrine, depending on their phagocytic competence. Quinacrine transport parameters were determined in purified or total leukocyte suspensions at 37 °C. Purified polymorphonuclear leukocytes (PMNLs, essentially neutrophils) exhibited a quinacrine uptake velocity inferior to that of lymphocytes, but a consistently higher affinity (apparent K{sub M} 1.1 vs. 6.3 μM, respectively). However, the vacuolar (V)-ATPase inhibitor bafilomycin A1 prevented quinacrine transport or initiated its release in either cell type. PMNLs capture most of the quinacrine added at low concentrations to fresh peripheral blood leukocytes compared with lymphocytes and monocytes (cytofluorometry). Accumulation of the autophagy marker LC3-II occurred rapidly and at low drug concentrations in quinacrine-treated PMNLs (significant at ≥ 2.5 μM, ≥ 2 h). Lymphocytes contained more LAMP1 than PMNLs, suggesting that the mass of lysosomes and late endosomes is a determinant of quinacrine uptake V{sub max}. PMNLs, however, exhibited the highest capacity for pinocytosis (uptake of fluorescent dextran into endosomes). The selectivity of quinacrine distribution in peripheral blood leukocytes may be determined by the collaboration of a non-concentrating plasma membrane transport mechanism, tentatively identified as pinocytosis in PMNLs, with V-ATPase-mediated concentration. Intracellular reservoirs of cationic drugs are a potential source of toxicity (e.g., loss of lysosomal function in phagocytes). - Highlights: • Quinacrine is concentrated in acidic organelles via V-ATPase-mediated ion

  5. Specific human astrocyte subtype revealed by affinity purified GFAP antibody; unpurified serum cross-reacts with neurofilament-L in Alzheimer.

    Directory of Open Access Journals (Sweden)

    Jinte Middeldorp

    Full Text Available The human GFAP splice variants GFAPDelta164 and GFAPDeltaexon6 both result in a GFAP protein isoform with a unique out-of-frame carboxy-terminus that can be detected by the GFAP+1 antibody. We previously reported that GFAP+1 was expressed in astrocytes and in degenerating neurons in Alzheimer's disease brains. In this study we aimed at further investigating the neuronal GFAP+1 expression and we started by affinity purifying the GFAP+1 antibody. The purified antibody resulted in a loss of neuronal GFAP+1 signal, although other antibodies directed against the amino- and carboxy-terminus of GFAPalpha still revealed GFAP-immunopositive neurons, as described before. With an in-depth analysis of a western blot, followed by mass spectrometry we discovered that the previously detected neuronal GFAP+1 expression was due to cross-reactivity of the antibody with neurofilament-L (NF-L. This was confirmed by double-label fluorescent immunohistochemistry and western blotting with the unpurified GFAP+1 antibody and an antibody against NF-L. Our data imply that NF-L can accumulate in some tangle-like structures in Alzheimer brains. More importantly, the purified GFAP+1 antibody clearly revealed a specific subtype of astrocytes in the adult human brain. These large astrocytes are present throughout the brain, e.g., along the subventricular zone, in the hippocampus, in the striatum and in the spinal cord of controls, Alzheimer, and Parkinson patients. The presence of a specific GFAP-isoform suggests a specialized function of these astrocytes.

  6. Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites.

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    Anoop Narayanan

    Full Text Available Expression of KdpFABC, a K(+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS via the winged helix-turn-helix type DNA binding domain (KdpE(DBD. Exploration of E. coli KdpE(DBD and kdpFABC(BS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE(DBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE(DBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE(DBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.

  7. A capture method based on the VC1 domain reveals new binding properties of the human receptor for advanced glycation end products (RAGE

    Directory of Open Access Journals (Sweden)

    Genny Degani

    2017-04-01

    Full Text Available The Advanced Glycation and Lipoxidation End products (AGEs and ALEs are a heterogeneous class of compounds derived from the non-enzymatic glycation or protein adduction by lipoxidation break-down products. The receptor for AGEs (RAGE is involved in the progression of chronic diseases based on persistent inflammatory state and oxidative stress. RAGE is a pattern recognition receptor (PRR and the inhibition of the interaction with its ligands or of the ligand accumulation have a potential therapeutic effect. The N-terminal domain of RAGE, the V domain, is the major site of AGEs binding and is stabilized by the adjacent C1 domain. In this study, we set up an affinity assay relying on the extremely specific biological interaction AGEs ligands have for the VC1 domain. A glycosylated form of VC1, produced in the yeast Pichia pastoris, was attached to magnetic beads and used as insoluble affinity matrix (VC1-resin. The VC1 interaction assay was employed to isolate specific VC1 binding partners from in vitro generated AGE-albumins and modifications were identified/localized by mass spectrometry analysis. Interestingly, this method also led to the isolation of ALEs produced by malondialdehyde treatment of albumins. Computational studies provided a rational-based interpretation of the contacts established by specific modified residues and amino acids of the V domain. The validation of VC1-resin in capturing AGE-albumins from complex biological mixtures such as plasma and milk, may lead to the identification of new RAGE ligands potentially involved in pro-inflammatory and pro-fibrotic responses, independently of their structures or physical properties, and without the use of any covalent derivatization process. In addition, the method can be applied to the identification of antagonists of RAGE-ligand interaction.

  8. Affinity Purification of Insulin by Peptide-Ligand Affinity Chromatography

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The affinity heptapeptide (HWWWPAS) for insulin, selected from phage display library,was coupled to EAH Sepharose 4B gel and packed to a 1-mL column. The column was used for the affinity purification of insulin from protein mixture and commercial insulin preparation. It was observed that the minor impurity in the commercial insulin was removed by the affinity chromatography. Nearly 40 mg of insulin could be purified with the 1-mL affinity column. The results revealed the high specificity and capacity of the affinity column for insulin purification. Moreover, based on the analysis of the amino acids in the peptide sequence, shorter peptides were designed and synthesized for insulin chromatography. As a result, HWWPS was found to be a good alternative to HWWWPAS, while the other two peptides with three or four amino acids showed weak affinity for insulin. The results indicated that the peptide sequence of HWWWPAS was quite conservative for specific binding of insulin.

  9. Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2

    DEFF Research Database (Denmark)

    Broutin, Isabelle; Jomain, Jean-Baptiste; Tallet, Estelle;

    2010-01-01

    We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely relate...

  10. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

    Science.gov (United States)

    Martin, Paul; McGovern, Amanda; Orozco, Gisela; Duffus, Kate; Yarwood, Annie; Schoenfelder, Stefan; Cooper, Nicholas J.; Barton, Anne; Wallace, Chris; Fraser, Peter; Worthington, Jane; Eyre, Steve

    2015-01-01

    Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions. We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1). PMID:26616563

  11. Laser capture microdissection of uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation.

    Science.gov (United States)

    Hacquard, Stéphane; Delaruelle, Christine; Legué, Valérie; Tisserant, Emilie; Kohler, Annegret; Frey, Pascal; Martin, Francis; Duplessis, Sébastien

    2010-10-01

    The foliar rust caused by the basidiomycete Melampsora larici-populina is the main disease affecting poplar plantations in Europe. The biotrophic status of rust fungi is a major limitation to study gene expression of cell or tissue types during host infection. At the uredinial stage, infected poplar leaves contain distinct rust tissues such as haustoria, infection hyphae, and uredinia with sporogenous hyphae and newly formed asexual urediniospores. Laser capture microdissection (LCM) was used to isolate three areas corresponding to uredinia and subjacent zones in the host mesophyll for expression analysis with M. larici-populina whole-genome exon oligoarrays. Optimization of tissue preparation prior to LCM allowed isolation of RNA of good integrity for genome-wide expression profiling. Our results indicate that the poplar rust uredinial stage is marked by distinct genetic programs related to biotrophy in the host palisade mesophyll and to sporulation in the uredinium. A strong induction of transcripts encoding small secreted proteins, likely containing rust effectors, is observed in the mesophyll, suggesting a late maintenance of suppression of host defense in the tissue containing haustoria and infection hyphae. On the other hand, cell cycle and cell defense rescue transcripts are strongly accumulated in the sporulation area. This combined LCM-transcriptomic approach brings new insights on the molecular mechanisms underlying urediniospore formation in rust fungi.

  12. Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus*♦

    Science.gov (United States)

    Dickson, Claire F.; Kumar, Kaavya Krishna; Jacques, David A.; Malmirchegini, G. Reza; Spirig, Thomas; Mackay, Joel P.; Clubb, Robert T.; Guss, J. Mitchell; Gell, David A.

    2014-01-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins. PMID:24425866

  13. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus.

    Science.gov (United States)

    Dickson, Claire F; Kumar, Kaavya Krishna; Jacques, David A; Malmirchegini, G Reza; Spirig, Thomas; Mackay, Joel P; Clubb, Robert T; Guss, J Mitchell; Gell, David A

    2014-03-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins.

  14. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations.

    Directory of Open Access Journals (Sweden)

    Danielle A Badro

    Full Text Available The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of F(ST's, R(ST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

  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.

    Science.gov (United States)

    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. Capturing Thoughts, Capturing Minds?

    DEFF Research Database (Denmark)

    Nielsen, Janni

    2004-01-01

    Think Aloud is cost effective, promises access to the user's mind and is the applied usability technique. But 'keep talking' is difficult, besides, the multimodal interface is visual not verbal. Eye-tracking seems to get around the verbalisation problem. It captures the visual focus of attention...

  17. A Novel Vertex Affinity for Community Detection

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    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.

  18. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

    Directory of Open Access Journals (Sweden)

    Yu Myeong-Hee

    2010-03-01

    Full Text Available Abstract Background Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Methods Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. Results A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD, and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002. BTD levels were lowered in all cancer grades (I-IV except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940 and progesterone receptor status (p = 0.440 were not associated with the plasma BTD levels. Conclusions Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.

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

    Science.gov (United States)

    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. Reinvestigation of aminoacyl-tRNA synthetase core complex by affinity purification-mass spectrometry reveals TARSL2 as a potential member of the complex.

    Directory of Open Access Journals (Sweden)

    Kyutae Kim

    Full Text Available Twenty different aminoacyl-tRNA synthetases (ARSs link each amino acid to their cognate tRNAs. Individual ARSs are also associated with various non-canonical activities involved in neuronal diseases, cancer and autoimmune diseases. Among them, eight ARSs (D, EP, I, K, L, M, Q and RARS, together with three ARS-interacting multifunctional proteins (AIMPs, are currently known to assemble the multi-synthetase complex (MSC. However, the cellular function and global topology of MSC remain unclear. In order to understand the complex interaction within MSC, we conducted affinity purification-mass spectrometry (AP-MS using each of AIMP1, AIMP2 and KARS as a bait protein. Mass spectrometric data were funneled into SAINT software to distinguish true interactions from background contaminants. A total of 40, 134, 101 proteins in each bait scored over 0.9 of SAINT probability in HEK 293T cells. Complex-forming ARSs, such as DARS, EPRS, IARS, Kars, LARS, MARS, QARS and RARS, were constantly found to interact with each bait. Variants such as, AIMP2-DX2 and AIMP1 isoform 2 were found with specific peptides in KARS precipitates. Relative enrichment analysis of the mass spectrometric data demonstrated that TARSL2 (threonyl-tRNA synthetase like-2 was highly enriched with the ARS-core complex. The interaction was further confirmed by coimmunoprecipitation of TARSL2 with other ARS core-complex components. We suggest TARSL2 as a new component of ARS core-complex.

  1. Targeted capture sequencing in whitebark pine reveals range-wide demographic and adaptive patterns despite challenges of a large, repetitive genome

    Directory of Open Access Journals (Sweden)

    John eSyring

    2016-04-01

    Full Text Available Whitebark pine (Pinus albicaulis inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the tree to be listed as ‘globally endangered’ by the International Union for Conservation of Nature (IUCN and ‘endangered’ by the Canadian government. Conservation collections (in situ and ex situ are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 30+ GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp, and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits, targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect

  2. Purification and characterisation of immunoglobulins from the Australian black flying fox (Pteropus alecto using anti-fab affinity chromatography reveals the low abundance of IgA.

    Directory of Open Access Journals (Sweden)

    James W Wynne

    Full Text Available There is now an overwhelming body of evidence that implicates bats in the dissemination of a long list of emerging and re-emerging viral agents, often causing illnesses or death in both animals and humans. Despite this, there is a paucity of information regarding the immunological mechanisms by which bats coexist with highly pathogenic viruses. Immunoglobulins are major components of the adaptive immune system. Early studies found bats may have quantitatively lower antibody responses to model antigens compared to conventional laboratory animals. To further understand the antibody response of bats, the present study purified and characterised the major immunoglobulin classes from healthy black flying foxes, Pteropus alecto. We employed a novel strategy, where IgG was initially purified and used to generate anti-Fab specific antibodies. Immobilised anti-Fab specific antibodies were then used to capture other immunoglobulins from IgG depleted serum. While high quantities of IgM were successfully isolated from serum, IgA was not. Only trace quantities of IgA were detected in the serum by mass spectrometry. Immobilised ligands specific to IgA (Jacalin, Peptide M and staphylococcal superantigen-like protein also failed to capture P. alecto IgA from serum. IgM was the second most abundant serum antibody after IgG. A survey of mucosal secretions found IgG was the dominant antibody class rather than IgA. Our study demonstrates healthy P. alecto bats have markedly less serum IgA than expected. Higher quantities of IgG in mucosal secretions may be compensation for this low abundance or lack of IgA. Knowledge and reagents developed within this study can be used in the future to examine class-specific antibody response within this important viral host.

  3. Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives.

    Science.gov (United States)

    Graifer, D M; Babkina, G T; Matasova, N B; Vladimirov, S N; Karpova, G G; Vlassov, V V

    1989-07-01

    A systematic study of protein environment of tRNA in ribosomes in model complexes representing different translation steps was carried out using the affinity labelling of the ribosomes with tRNA derivatives bearing aryl azide groups scattered statistically over tRNA guanine residues. Analysis of the proteins crosslinked to tRNA derivatives showed that the location of the derivatives in the aminoacyl (A) site led to the labelling of the proteins S5 and S7 in all complexes studied, whereas the labelling of the proteins S2, S8, S9, S11, S14, S16, S17, S18, S19, S21 as well as L9, L11, L14, L15, L21, L23, L24, L29 depended on the state of tRNA in A site. Similarly, the location of tRNA derivatives in the peptidyl (P) site resulted in the labelling of the proteins L27, S11, S13 and S19 in all states, whereas the labelling of the proteins S5, S7, S9, S12, S14, S20, S21 as well as L2, L13, L14, L17, L24, L27, L31, L32, L33 depended on the type of complex. The derivatives of tRNA(fMet) were found to crosslink to S1, S3, S5, S7, S9, S14 and L1, L2, L7/L12, L27. Based on the data obtained, a general principle of the dynamic functioning of ribosomes has been proposed: (i) the formation of each type of ribosomal complex is accompanied by changes in mutual arrangement of proteins - 'conformational adjustment' of the ribosome - and (ii) a ribosome can dynamically change its internal structure at each step of initiation and elongation; on the 70 S ribosome there are no rigidly fixed structures forming tRNA-binding sites (primarily A and P sites).

  4. Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6.

    Science.gov (United States)

    Kempkens, Ozlem; Médina, Emmanuelle; Fernandez-Ballester, Gregorio; Ozüyaman, Susann; Le Bivic, André; Serrano, Luis; Knust, Elisabeth

    2006-08-01

    Formation of multiprotein complexes is a common theme to pattern a cell, thereby generating spatially and functionally distinct entities at specialised regions. Central components of these complexes are scaffold proteins, which contain several protein-protein interaction domains and provide a platform to recruit a variety of additional components. There is increasing evidence that protein complexes are dynamic structures and that their components can undergo various interactions depending on the cellular context. However, little is known so far about the factors regulating this behaviour. One evolutionarily conserved protein complex, which can be found both in Drosophila and mammalian epithelial cells, is composed of the transmembrane protein Crumbs/Crb3 and the scaffolding proteins Stardust/Pals1 and DPATJ/PATJ, respectively, and localises apically to the zonula adherens. Here we show by in vitro analysis that, similar as in vertebrates, the single PDZ domain of Drosophila DmPar-6 can bind to the four C-terminal amino acids (ERLI) of the transmembrane protein Crumbs. To further evaluate the binding capability of Crumbs to DmPar-6 and the MAGUK protein Stardust, analysis of the PDZ structural database and modelling of the interactions between the C-terminus of Crumbs and the PDZ domains of these two proteins were performed. The results suggest that both PDZ domains bind Crumbs with similar affinities. These data are supported by quantitative yeast two-hybrid interactions. In vivo analysis performed in cell cultures and in the Drosophila embryo show that the cytoplasmic domain of Crumbs can recruit DmPar-6 and DaPKC to the plasma membrane. The data presented here are discussed with respect to possible dynamic interactions between these proteins.

  5. Haplotype affinities resolve a major component of goat (Capra hircus MtDNA D-loop diversity and reveal specific features of the Sardinian stock.

    Directory of Open Access Journals (Sweden)

    Daniela Piras

    Full Text Available Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1 to provide an operational definition of meaningful mtDNA units within haplogroup A, 2 to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3 to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591 which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

  6. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock.

    Science.gov (United States)

    Piras, Daniela; Doro, Maria Grazia; Casu, Giuseppina; Melis, Paola Maria; Vaccargiu, Simona; Piras, Ignazio; Parracciani, Debora; Stradoni, Roberta; Frongia, Bruno; Lai, Graziano; Sale, Salvatore; Cattari, Walter; Piras, Roberto; Querci, Ombretta; Demuro, Piergiorgio; Cui, Sandro; Atzori, Franco; Mancosu, Marco; Marchiori, Francesca; Cammelli, Rossana; Spiga, Alessandra; Loddo, Pier Paolo; Pili, Gianfranco; Boi, Roberto; Argiolas, Giuseppe; Mereu, Paolo; Leoni, Giovanni Giuseppe; Naitana, Salvatore; Pirastu, Mario; Novelletto, Andrea

    2012-01-01

    Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

  7. Capture Matrices Handbook

    Science.gov (United States)

    2014-04-01

    changing the affinity ligand, we can use capture matrices to detect other chemicals such as chlorinated solvents, nerve and blister agents, pesticides...require significant chemical additives and complex equipment, generate a large secondary waste stream, and are difficult to automate. Magnetically...secondary wastes . 2 Other advantages are a large active surface area for a given mass of particles; the ability to process a solution that

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    González-González, Angélica; 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 inH. 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. oblique 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.

  10. Non-Zenoness of piecewise affine dynamical systems and affine complementarity systems with inputs

    Institute of Scientific and Technical Information of China (English)

    Le Quang THUAN

    2014-01-01

    In the context of continuous piecewise affine dynamical systems and affine complementarity systems with inputs, we study the existence of Zeno behavior, i.e., infinite number of mode transitions in a finite-length time interval, in this paper. The main result reveals that continuous piecewise affine dynamical systems with piecewise real-analytic inputs do not exhibit Zeno behavior. Applied the achieved result to affine complementarity systems with inputs, we also obtained a similar conclusion. A direct benefit of the main result is that one can apply smooth ordinary differential equations theory in a local manner for the analysis of continuous piecewise affine dynamical systems with inputs.

  11. Global affine differential geometry of hypersurfaces

    CERN Document Server

    Li, An-Min; Zhao, Guosong; Hu, Zejun

    2015-01-01

    This book draws a colorful and widespread picture of global affine hypersurface theory up to the most recent state. Moreover, the recent development revealed that affine differential geometry- as differential geometry in general- has an exciting intersection area with other fields of interest, like partial differential equations, global analysis, convex geometry and Riemann surfaces.

  12. Unexpected tolerance of glycosylation by UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase revealed by electron capture dissociation mass spectrometry: carbohydrate as potential protective groups.

    Science.gov (United States)

    Yoshimura, Yayoi; Matsushita, Takahiko; Fujitani, Naoki; Takegawa, Yasuhiro; Fujihira, Haruhiko; Naruchi, Kentarou; Gao, Xiao-Dong; Manri, Naomi; Sakamoto, Takeshi; Kato, Kentaro; Hinou, Hiroshi; Nishimura, Shin-Ichiro

    2010-07-20

    UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (ppGalNAcTs, EC 2.4.1.41), a family of key enzymes that initiate posttranslational modification with O-glycans in mucin synthesis by introduction of alpha-GalNAc residues, are structurally composed of a catalytic domain and a lectin domain. It has been known that multiple Ser/Thr residues are assigned in common mucin glycoproteins as potential O-glycosylation sites and more than 20 distinct isoforms of this enzyme family contribute to produce densely O-glycosylated mucin glycoproteins. However, it seems that the functional role of the lectin domain of ppGalNAcTs remains unclear. We considered that electron capture dissociation mass spectrometry (ECD-MS), a promising method for highly selective fragmentation at peptide linkages of glycopeptides to generate unique c and z series of ions, should allow for precise structural characterization to uncover the mechanism in O-glycosylation of mucin peptides by ppGalNAcTs. In the present study, it was demonstrated that a system composed of an electrospray source, a linear RFQ ion trap that isolates precursor ions, the ECD device, and a TOF mass spectrometer is a nice tool to identify the preferential O-glycosylation sites without any decomposition of the carbohydrate moiety. It should be noted that electrons used for ECD are accelerated within a range from 1.75 to 9.75 eV depending on the structures of glycopeptides of interest. We revealed for the first time that additional installation of a alpha-GalNAc residue at potential glycosylation sites by ppGalNAcT2 proceeds smoothly in various unnatural glycopeptides having alpha-Man, alpha-Fuc, and beta-Gal residues as well as alpha-GalNAc residues. The results may suggest that ppGalNAcT2 did not differentiate totally presubstituted sugar residues in terms of configuration of functional groups, d-, l-configuration, and even alpha-, beta-stereochemistry at an anomeric carbon atom when relatively short synthetic

  13. On affine rigidity

    Directory of Open Access Journals (Sweden)

    Steven J. Gortler

    2013-12-01

    Full Text Available We study the properties of affine rigidity of a hypergraph and prove a variety of fundamental results. First, we show that affine rigidity is a generic property (i.e., depends only on the hypergraph, not the particular embedding. Then we prove that a graph is generically neighborhood affinely rigid in d-dimensional space if it is (d+1-vertex-connected. We also show neighborhood affine rigidity of a graph implies universal rigidity of its squared graph.  Our results, and affine rigidity more generally, have natural applications in point registration and localization, as well as connections to manifold learning.

  14. Capture reactions

    NARCIS (Netherlands)

    Endt, P.M.

    1956-01-01

    Capture reactions will be considered here from the viewpoint of the nuclear spectroscopist. Especially important to him are the capture of neutrons, protons, and alpha particles, which may proceed through narrow resonances, offering a well defined initial state for the subsequent deexcitation proces

  15. Uncovering the secret lives of sewer rats (Rattus norvegicus): Movements, distribution and population dynamics revealed by a capture-mark-recapture study

    DEFF Research Database (Denmark)

    Heiberg, Ann-Charlotte; Sluydts, Vincent; Leirs, Herwig E.l.

    2012-01-01

    , half of these were juveniles. The median time an individual was present in the sewers was 4 months with maxima up to 22 months. Abundance ranged from 2 to 44 animals per sewer system and the dynamics showed no regular fluctuations. Rats were distributed throughout the study area, regardless of sewer...... dimensions. Juvenile rats were captured more in the smaller and drier sewer sections. Activity areas of rats of both sexes overlapped partially, and observations of bite wounds were rare, suggesting a high degree of tolerance. The average maximal distance covered by rats was ~200 m for both sexes. Day...... a surface area of 30 Ha. Multiple-capture live traps were placed in manholes in public sewers; animals were marked individually and data were collected every fourth week for a period of almost 3 years. Key results.: In total, 332 individual rats were trapped. Approximately one-third were only caught once...

  16. Affine Dynamics with Torsion

    CERN Document Server

    Gultekin, Kemal

    2015-01-01

    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 Schroedinger, we construct and analyze different affine gravities based on determinants of the Ricci tensor, torsion tensor, 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 construction of the affine connection in terms of curvature and torsion tensors. Our solutions of the dynamical equations show that curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor.

  17. Affinity in electrophoresis.

    Science.gov (United States)

    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.

  18. Affine dynamics with torsion

    Energy Technology Data Exchange (ETDEWEB)

    Gueltekin, Kemal [Izmir Institute of Technology, Department of Physics, Izmir (Turkey)

    2016-03-15

    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 Schroedinger, 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. (orig.)

  19. Affine and degenerate affine BMW algebras: Actions on tensor space

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2012-01-01

    The affine and degenerate affine Birman-Murakami-Wenzl (BMW) algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic quantum groups and Lie algebras, respectively. Cyclotomic BMW algebras, affine and cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper we explain how the affine and degenerate affine BMW algebras are tantalizers (tensor power centralizer algebras) by defining actions of the affine braid group and the degenerate affine braid algebra on tensor space and showing that, in important cases, these actions induce actions of the affine and degenerate affine BMW algebras. We then exploit the connection to quantum groups and Lie algebras to determine universal parameters for the affine and degenerate affine BMW algebras. Finally, we show that the universal parameters are central elements--the higher Casimir elements for orthogonal and symplectic enveloping algebras and quantum groups.

  20. Capturing appearance

    Science.gov (United States)

    Rushmeier, Holly E.

    2005-01-01

    For computer graphics applications, capturing the appearance parameters of objects (reflectance, transmittance and small scale surface structures), is as important as capturing the overall shape. We briefly review recent approaches developed by the computer graphics community to solve this problem. Excellent results have been obtained by various researchers measuring spatially varying reflectance functions for some classes of objects. We will consider some challenges from two of the remaining problematic classes of objects. First we will describe our experience scanning and modeling the throne of Tutankhamen. The major difficulties in this case were that the base shape was a highly detailed non-convex geometry with complex topology, and the shape was covered by optically uncooperative gold and silver. Then we will discuss some observations from our ongoing project to scan and model historic buildings on the Yale campus. The major difficulties in this second case are quantity of data and the lack of control over acquisition conditions.

  1. Out of sight, but still in mind: electrocortical correlates of attentional capture in spider phobia as revealed by a 'dot probe' paradigm.

    Science.gov (United States)

    Leutgeb, Verena; Sarlo, Michela; Schöngassner, Florian; Schienle, Anne

    2015-02-01

    The current investigation focused on attentional processes in spider phobia. Twenty phobics and 20 controls performed a dot-probe task while event-related potentials were recorded. In each trial they viewed a picture pair (a spider or a generally disgust eliciting picture that was paired with a neutral picture) for either 100 or 1500 ms. After the offset a visual probe (a dot) was presented either at the previous position of the emotionally relevant or the neutral slide and participants were asked to indicate with a button press whether the dot had been presented on the left or the right side of the screen. Results revealed a modulation of the centro-parietal P300 (340-500 ms after picture onset). Amplitudes were higher when the dot replaced a spider than when it replaced a neutral picture. This was phobia-specific, as it was only present in phobics and did not appear in response to disgust pictures. Moreover, the modulation could only be shown for short presentation times. The results are interpreted to reflect motivated attention in spider phobia, if disorder-relevant and neutral pictures are shown simultaneously. As the modulation of the P300 was found after picture offset, attentional allocation seems to be persist after the phobic object is no longer present.

  2. Graphene oxide capturing surface-fluorinated TiO2 nanosheets for advanced photocatalysis and the reveal of synergism reinforce mechanism.

    Science.gov (United States)

    Dai, Kai; Lu, Luhua; Liu, Qi; Zhu, Guangping; Liu, Qinzhuang; Liu, Zhongliang

    2014-02-07

    Surface-fluorinated TiO2 (F-TiO2) nanosheets with exposed (001) facets were synthesized from a scalable hydrothermal treatment assisted by a specific stabilization effect of fluorine ions on the (001) facets. Assembly of F-TiO2 on graphene oxide (GO) sheets into GO/F-TiO2 hybrid in aqueous solution was further achieved by making use of the surfactant role of GO. Photocatalytic properties of GO/F-TiO2 hybrid were evaluated under 365 nm UV light irradiation for photodegradation of methylene blue (MB). An optimal GO content has been determined to be 3 wt%, and the corresponding apparent pseudo-first-order rate constant Kapp is 0.0493 min(-1), 3 times and 4 times more than that of pure TiO2 nanosheets and commercial P25 photocatalyst, respectively. To reveal the synergism reinforce mechanism of GO/F-TiO2 hybrid, photo absorption, surface absorption, and the photoelectrochemical current properties have been intensively studied. We found that enhanced electron-hole separation has been the key issue for the reinforcement of photocatalytic performance. F-TiO2 with exposed (001) facet has stronger electron-hole separation resulting in a higher photoelectrochemical current than that of P25 photocatalyst. Moreover, hybridization of F-TiO2 with GO could further increase the photoelectrochemical current and the largest current for the optimal weight fraction of GO is in good accordance with the photocatalysis performance. The GO/F-TiO2 interface junction that favors the electron-hole separation was attributed to the photoelectrochemical current enhancement.

  3. Affine Sphere Relativity

    Science.gov (United States)

    Minguzzi, E.

    2016-11-01

    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.

  4. Affine stochastic mortality

    NARCIS (Netherlands)

    D.F. Schrager

    2006-01-01

    We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing m

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

    Science.gov (United States)

    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.

  6. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

    DEFF Research Database (Denmark)

    Domanski, Michal; Molloy, Kelly; Jiang, Hua;

    2012-01-01

    An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous......-level tagged proteins. Isolations of triple-FLAG and GFP-tagged fusion proteins involved in RNA metabolism are presented.......An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous...

  7. Affine and degenerate affine BMW algebras: The center

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2011-01-01

    The degenerate affine and affine BMW algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic Lie algebras and quantum groups, respectively. Cyclotomic BMW algebras, affine Hecke algebras, cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper the theory is unified by treating the orthogonal and symplectic cases simultaneously; we make an exact parallel between the degenerate affine and affine cases via a new algebra which takes the role of the affine braid group for the degenerate setting. A main result of this paper is an identification of the centers of the affine and degenerate affine BMW algebras in terms of rings of symmetric functions which satisfy a "cancellation property" or "wheel condition" (in the degenerate case, a reformulation of a result of Nazarov). Miraculously, these same rings also arise in Schubert calculus, as the cohomology and K-theory of isotropic Grassmanians and symplectic loop Grassmanians. We also establish new inte...

  8. Hierarchical Affinity Propagation

    CERN Document Server

    Givoni, Inmar; Frey, Brendan J

    2012-01-01

    Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the hierarchical clustering problem, which arises in a variety of domains including biology, sensor networks and decision making in operational research. We derive an inference algorithm that operates by propagating information up and down the hierarchy, and is efficient despite the high-order potentials required for the graphical model formulation. We demonstrate that our method outperforms greedy techniques that cluster one layer at a time. We show that on an artificial dataset designed to mimic the HIV-strain mutation dynamics, our method outperforms related methods. For real HIV sequences, where the ground truth is not available, we show our method achieves better results, in terms of the underlying objective function, and show the results correspond meaningfully to geographi...

  9. Artificial Affinity Proteins as Ligands of Immunoglobulins

    Directory of Open Access Journals (Sweden)

    Barbara Mouratou

    2015-01-01

    Full Text Available A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized.

  10. Affinity driven social networks

    Science.gov (United States)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  11. Purely affine Gravity

    CERN Document Server

    Skirzewski, Aureliano

    2014-01-01

    We develop a topological theory of gravity with torsion where metric has a dynamical rather than a kinematical origin. This approach towards gravity resembles pre-geometrical approaches in which a fundamental metric does not exist, but the affine connection gives place to a local inertial structure. Such feature reminds us of Mach's principle, that assumes the inertial forces should have dynamical origin. Additionally, a Newtonian gravitational force is obtained in the non-relativistic limit of the theory.

  12. Affine morphisms at zero level

    CERN Document Server

    Das, Paramita; Gupta, Ved Prakash

    2010-01-01

    Given a finite index subfactor, we show that the {\\em affine morphisms at zero level} in the affine category over the planar algebra associated to the subfactor is isomorphic to the fusion algebra of the subfactor as a *-algebra.

  13. On the Affine Isoperimetric Inequalities

    Indian Academy of Sciences (India)

    Wuyang Yu; Gangsong Leng

    2011-11-01

    We obtain an isoperimetric inequality which estimate the affine invariant -surface area measure on convex bodies. We also establish the reverse version of -Petty projection inequality and an affine isoperimetric inequality of $_{-p}K$.

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

    Science.gov (United States)

    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. High affinity retinoic acid receptor antagonists: analogs of AGN 193109.

    Science.gov (United States)

    Johnson, A T; Wang, L; Gillett, S J; Chandraratna, R A

    1999-02-22

    A series of high affinity retinoic acid receptor (RAR) antagonists were prepared based upon the known antagonist AGN 193109 (2). Introduction of various phenyl groups revealed a preference for substitution at the para-position relative to the meta-site. Antagonists with the highest affinities for the RARs possessed hydrophobic groups, however, the presence of polar functionality was also well tolerated.

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

    Science.gov (United States)

    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…

  17. A High-Affinity Adenosine Kinase from Anopheles Gambiae

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Affine Patches on Positroid Varieties and Affine Pipe Dreams (Thesis)

    CERN Document Server

    Snider, Michelle

    2010-01-01

    The objects of interest in this thesis are positroid varieties in the Grassmannian, which are indexed by juggling patterns. In particular, we study affine patches on these positroid varieties. Our main result corresponds these affine patches to Kazhdan-Lusztig varieties in the affine Grassmannian. We develop a new term order and study how these spaces are related to subword complexes and Stanley-Reisner ideals. We define an extension of pipe dreams to the affine case and conclude by showing how our affine pipe dreams are generalizations of Cauchon and Le diagrams.

  19. Affine and quasi-affine frames for rational dilations

    DEFF Research Database (Denmark)

    Bownik, Marcin; Lemvig, Jakob

    2011-01-01

    , the corresponding family of quasi-affine systems are frames with uniform frame bounds. We also prove a similar equivalence result between pairs of dual affine frames and dual quasi-affine frames. Finally, we uncover some fundamental differences between the integer and rational settings by exhibiting an example......In this paper we extend the investigation of quasi-affine systems, which were originally introduced by Ron and Shen [J. Funct. Anal. 148 (1997), 408-447] for integer, expansive dilations, to the class of rational, expansive dilations. We show that an affine system is a frame if, and only if...

  20. On Affine Fusion and the Phase Model

    Directory of Open Access Journals (Sweden)

    Mark A. Walton

    2012-11-01

    Full Text Available A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the su(n Wess-Zumino-Novikov-Witten (WZNW conformal field theories appears in a simple integrable system known as the phase model. The Yang-Baxter equation leads to the construction of commuting operators as Schur polynomials, with noncommuting hopping operators as arguments. The algebraic Bethe ansatz diagonalizes them, revealing a connection to the modular S matrix and fusion of the su(n WZNW model. The noncommutative Schur polynomials play roles similar to those of the primary field operators in the corresponding WZNW model. In particular, their 3-point functions are the su(n fusion multiplicities. We show here how the new phase model realization of affine fusion makes obvious the existence of threshold levels, and how it accommodates higher-genus fusion.

  1. Jacobi Structures on Affine Bundles

    Institute of Scientific and Technical Information of China (English)

    J. GRABOWSKI; D. IGLESIAS; J. C. MARRERO; E. PADR(O)N; P. URBA(N)SKI

    2007-01-01

    We study affine Jacobi structures (brackets) on an affine bundle π: A→M, i.e. Jacobi brackets that close on affine functions. We prove that if the rank of A is non-zero, there is a one-to- one correspondence between affine Jacobi structures on A and Lie algebroid structures on the vector bundle A+=∪p∈M Aff(Ap, R) of affine functionals. In the case rank A = 0, it is shown that there is a one-to-one correspondence between affins Jacobi structures on A and local Lie algebras on A+. Some examples and applications, also for the linear case, are discussed. For a special type of affine Jacobi structures which are canonically exhibited (strongly-affine or affine-homogeneous Jacobi structures) over a real vector space of finite dimension, we describe the leaves of its characteristic foliation as the orbits of an affine representation. These afline Jacobi structures can be viewed as an analog of the Kostant-Arnold-LiouviUe linear Poisson structure on the dual space of a real finite-dimensional Lie algebra.

  2. Routes to improve binding capacities of affinity resins demonstrated for Protein A chromatography.

    Science.gov (United States)

    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.

  3. Kernel Affine Projection Algorithms

    Directory of Open Access Journals (Sweden)

    José C. Príncipe

    2008-05-01

    Full Text Available 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.

  4. Kernel Affine Projection Algorithms

    Science.gov (United States)

    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.

  5. Capture of formaldehyde by adsorption on nanoporous materials.

    Science.gov (United States)

    Bellat, Jean-Pierre; Bezverkhyy, Igor; Weber, Guy; Royer, Sébastien; Averlant, Remy; Giraudon, Jean-Marc; Lamonier, Jean-François

    2015-12-30

    The aim of this work is to assess the capability of a series of nanoporous materials to capture gaseous formaldehyde by adsorption in order to develop air treatment process and gas detection in workspaces or housings. Adsorption-desorption isotherms have been accurately measured at room temperature by TGA under very low pressure (pmesoporous silica (SBA15), activated carbon (AC NORIT RB3) and metal organic framework (MOF, Ga-MIL-53), exhibiting a wide range of pore sizes and surface properties. Results reveal that the NaX, NaY and CuX faujasite (FAU) zeolites are materials which show strong adsorption capacity and high affinity toward formaldehyde. In addition, these materials can be completely regenerated by heating at 200°C under vacuum. These cationic zeolites are therefore promising candidates as adsorbents for the design of air depollution process or gas sensing applications.

  6. Adjoint affine fusion and tadpoles

    Science.gov (United States)

    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.

  7. Adjoint affine fusion and tadpoles

    CERN Document Server

    Urichuk, Andrew

    2016-01-01

    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.

  8. Mepanipyrim haptens and antibodies with nanomolar affinity

    OpenAIRE

    Esteve Turrillas, Francesc Albert; Mercader Badia, Josep Vicent; Agulló, Consuelo; Abad Somovilla, Antonio; Abad Fuentes, Antonio

    2013-01-01

    Mepanipyrim is an anilinopyrimidine fungicide used worldwide for crop protection. With the aim of developing useful immunoreagents for mepanipyrim immunoanalysis, two new functionalized derivatives were prepared and antibodies were generated. Affinity and specificity were assessed by direct and indirect competitive ELISA using homologous and heterologous conjugates. Although all antibodies were selective for the target analyte, the immunizing hapten structure was revealed as a determinant for...

  9. Ebolavirus nucleoprotein C-termini potently attract single domain antibodies enabling monoclonal affinity reagent sandwich assay (MARSA formulation.

    Directory of Open Access Journals (Sweden)

    Laura J Sherwood

    Full Text Available BACKGROUND: Antigen detection assays can play an important part in environmental surveillance and diagnostics for emerging threats. We are interested in accelerating assay formulation; targeting the agents themselves to bypass requirements for a priori genome information or surrogates. Previously, using in vitro affinity reagent selection on Marburg virus we rapidly established monoclonal affinity reagent sandwich assay (MARSA where one recombinant antibody clone was both captor and tracer for polyvalent nucleoprotein (NP. Hypothesizing that the closely related Ebolavirus genus may share the same Achilles' heel, we redirected the scheme to see whether similar assays could be delivered and began to explore their mechanism. METHODS AND FINDINGS: In parallel we selected panels of llama single domain antibodies (sdAb from a semi-synthetic library against Zaire, Sudan, Ivory Coast, and Reston Ebola viruses. Each could perform as both captor and tracer in the same antigen sandwich capture assay thereby forming MARSAs. All sdAb were specific for NP and those tested required the C-terminal domain for recognition. Several clones were cross-reactive, indicating epitope conservation across the Ebolavirus genus. Analysis of two immune shark sdAb revealed they also targeted the C-terminal domain, and could be similarly employed, yet were less sensitive than a comparable llama sdAb despite stemming from immune selections. CONCLUSIONS: The C-terminal domain of Ebolavirus NP is a strong attractant for antibodies and enables sensitive sandwich immunoassays to be rapidly generated using a single antibody clone. The polyvalent nature of nucleocapsid borne NP and display of the C-terminal region likely serves as a bountiful affinity sink during selections, and a highly avid target for subsequent immunoassay capture. Combined with the high degree of amino acid conservation through 37 years and across wide geographies, this domain makes an ideal handle for monoclonal

  10. Combination of hydrogel nanoparticles and proteomics to reveal secreted proteins associated with decidualization of human uterine stromal cells

    Directory of Open Access Journals (Sweden)

    Stephens Andrew N

    2011-09-01

    Full Text Available Abstract Background Identification of secreted proteins of low abundance is often limited by abundant and high molecular weight (MW proteins. We have optimised a procedure to overcome this limitation. Results Low MW proteins in the conditioned media of cultured cells were first captured using dual-size exclusion/affinity hydrogel nanoparticles and their identities were then revealed by proteomics. Conclusions This technique enables the analysis of secreted proteins of cultured cells low MW and low abundance.

  11. Crystal structure of IgE bound to its B-cell receptor CD23 reveals a mechanism of reciprocal allosteric inhibition with high affinity receptor FcεRI.

    Science.gov (United States)

    Dhaliwal, Balvinder; Yuan, Daopeng; Pang, Marie O Y; Henry, Alistair J; Cain, Katharine; Oxbrow, Amanda; Fabiane, Stella M; Beavil, Andrew J; McDonnell, James M; Gould, Hannah J; Sutton, Brian J

    2012-07-31

    The role of IgE in allergic disease mechanisms is performed principally through its interactions with two receptors, FcεRI on mast cells and basophils, and CD23 (FcεRII) on B cells. The former mediates allergic hypersensitivity, the latter regulates IgE levels, and both receptors, also expressed on antigen-presenting cells, contribute to allergen uptake and presentation to the immune system. We have solved the crystal structure of the soluble lectin-like "head" domain of CD23 (derCD23) bound to a subfragment of IgE-Fc consisting of the dimer of Cε3 and Cε4 domains (Fcε3-4). One CD23 head binds to each heavy chain at the interface between the two domains, explaining the known 2:1 stoichiometry and suggesting mechanisms for cross-linking membrane-bound trimeric CD23 by IgE, or membrane IgE by soluble trimeric forms of CD23, both of which may contribute to the regulation of IgE synthesis by B cells. The two symmetrically located binding sites are distant from the single FcεRI binding site, which lies at the opposite ends of the Cε3 domains. Structural comparisons with both free IgE-Fc and its FcεRI complex reveal not only that the conformational changes in IgE-Fc required for CD23 binding are incompatible with FcεRI binding, but also that the converse is true. The two binding sites are allosterically linked. We demonstrate experimentally the reciprocal inhibition of CD23 and FcεRI binding in solution and suggest that the mutual exclusion of receptor binding allows IgE to function independently through its two receptors.

  12. Realization of Fractal Affine Transformation

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper gives the definition of fractal affine transformation and presents a specific method for its realization and its cor responding mathematical equations which are essential in fractal image construction.

  13. Affinity chromatography of phosphorylated proteins.

    Science.gov (United States)

    Tchaga, Grigoriy S

    2008-01-01

    This chapter covers the use of immobilized metal ion affinity chromatography (IMAC) for enrichment of phosphorylated proteins. Some requirements for successful enrichment of these types of proteins are discussed. An experimental protocol and a set of application data are included to enable the scientist to obtain high-yield results in a very short time with pre-packed phospho-specific metal ion affinity resin (PMAC).

  14. Oriented angles in affine space

    Directory of Open Access Journals (Sweden)

    Włodzimierz Waliszewski

    2004-05-01

    Full Text Available The concept of a smooth oriented angle in an arbitrary affine space is introduced. This concept is based on a kinematics concept of a run. Also, a concept of an oriented angle in such a space is considered. Next, it is shown that the adequacy of these concepts holds if and only if the affine space, in question, is of dimension 2 or 1.

  15. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  16. Capture Their Attention: Capturing Lessons Using Screen Capture Software

    Science.gov (United States)

    Drumheller, Kristina; Lawler, Gregg

    2011-01-01

    When students miss classes for university activities such as athletic and academic events, they inevitably miss important class material. Students can get notes from their peers or visit professors to find out what they missed, but when students miss new and challenging material these steps are sometimes not enough. Screen capture and recording…

  17. Neutron Capture Nucleosynthesis

    CERN Document Server

    Kiss, Miklos

    2016-01-01

    Heavy elements (beyond iron) are formed in neutron capture nucleosynthesis processes. We have proposed a simple unified model to investigate the neutron capture nucleosynthesis in arbitrary neutron density environment. We have also investigated what neutron density is required to reproduce the measured abundance of nuclei assuming equilibrium processes. We found both of these that the medium neutron density has a particularly important role at neutron capture nucleosynthesis. About these results most of the nuclei can formed at medium neutron capture density environment e.g. in some kind of AGB stars. Besides these observations our model is capable to use educational purpose.

  18. Affine Contractions on the Plane

    Science.gov (United States)

    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.…

  19. Capture ready study

    Energy Technology Data Exchange (ETDEWEB)

    Minchener, A.

    2007-07-15

    There are a large number of ways in which the capture of carbon as carbon dioxide (CO{sub 2}) can be integrated into fossil fuel power stations, most being applicable for both gas and coal feedstocks. To add to the choice of technology is the question of whether an existing plant should be retrofitted for capture, or whether it is more attractive to build totally new. This miscellany of choices adds considerably to the commercial risk of investing in a large power station. An intermediate stage between the non-capture and full capture state would be advantageous in helping to determine the best way forward and hence reduce those risks. In recent years the term 'carbon capture ready' or 'capture ready' has been coined to describe such an intermediate stage plant and is now widely used. However a detailed and all-encompassing definition of this term has never been published. All fossil fuel consuming plant produce a carbon dioxide gas byproduct. There is a possibility of scrubbing it with an appropriate CO{sub 2} solvent. Hence it could be said that all fossil fuel plant is in a condition for removal of its CO{sub 2} effluent and therefore already in a 'capture ready' state. Evidently, the practical reality of solvent scrubbing could cost more than the rewards offered by such as the ETS (European Trading Scheme). In which case, it can be said that although the possibility exists of capturing CO{sub 2}, it is not a commercially viable option and therefore the plant could not be described as ready for CO{sub 2} capture. The boundary between a capture ready and a non-capture ready condition using this definition cannot be determined in an objective and therefore universally acceptable way and criteria must be found which are less onerous and less potentially contentious to assess. 16 refs., 2 annexes.

  20. CAPTURED India Country Evaluation

    NARCIS (Netherlands)

    O'Donoghue, R.; Brouwers, J.H.A.M.

    2012-01-01

    This report provides the findings of the India Country Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the End Evaluation has assessed that results are commendable. I-AIM was able to design an approach in which health fol

  1. Carbon Capture and Storage

    NARCIS (Netherlands)

    Benson, S.M.; Bennaceur, K.; Cook, P.; Davison, J.; Coninck, H. de; Farhat, K.; Ramirez, C.A.; Simbeck, D.; Surles, T.; Verma, P.; Wright, I.

    2012-01-01

    Emissions of carbon dioxide, the most important long-lived anthropogenic greenhouse gas, can be reduced by Carbon Capture and Storage (CCS). CCS involves the integration of four elements: CO 2 capture, compression of the CO2 from a gas to a liquid or a denser gas, transportation of pressurized CO 2

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

    Science.gov (United States)

    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.

  3. Electron affinity of chlorine dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Babcock, L.M.; Pentecost, T.; Koppenol, W.H. (Louisiana State Univ., Baton Rouge (USA))

    1989-12-14

    The flowing afterglow technique was used to determine the electron affinity of chlorine dioxide. A value of 2.37 {plus minus} 0.10 eV was found by bracketing between the electron affinities of HS* and SF{sub 4} as a lower limit and that of NO{sub 2} as an upper limit. This value is in excellent agreement with 2.32 eV predicted from a simple thermodynamic cycle involving the reduction potential of the ClO{sub 2}/ClO{sub 2}{sup {minus}} couple and a Gibbs hydration energy identical with that of SO{sub 2}{sup {sm bullet}{minus}}.

  4. Affine density in wavelet analysis

    CERN Document Server

    Kutyniok, Gitta

    2007-01-01

    In wavelet analysis, irregular wavelet frames have recently come to the forefront of current research due to questions concerning the robustness and stability of wavelet algorithms. A major difficulty in the study of these systems is the highly sensitive interplay between geometric properties of a sequence of time-scale indices and frame properties of the associated wavelet systems. This volume provides the first thorough and comprehensive treatment of irregular wavelet frames by introducing and employing a new notion of affine density as a highly effective tool for examining the geometry of sequences of time-scale indices. Many of the results are new and published for the first time. Topics include: qualitative and quantitative density conditions for existence of irregular wavelet frames, non-existence of irregular co-affine frames, the Nyquist phenomenon for wavelet systems, and approximation properties of irregular wavelet frames.

  5. Lectin affinity chromatography of glycolipids

    Energy Technology Data Exchange (ETDEWEB)

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  6. The Quasi—affine Maps and Fractals

    Institute of Scientific and Technical Information of China (English)

    LunhaiLONG; GangCHEN

    1997-01-01

    In this paper,we discuss the discretization of the affine maps in R2,that is ,we consider a class of maps in Z2,which are induced by affine maps and called the quasi-affine maps.We investigate the properties and the dynamical behaviour of such maps,and give a sort of construction of complicated fractals by using quasi-affine maps.

  7. Affine connections on involutive G-structures

    OpenAIRE

    Merkulov, Sergey A.

    1995-01-01

    This paper is a review of the twistor theory of irreducible G-structures and affine connections. Long ago, Berger presented a very restricted list of possible irreducibly acting holonomies of torsion-free affine connections. His list was complete in the part of metric connections, while the situation with holonomies of non-metric torsion-free affine connections was and remains rather unclear. One of the results discussed in this review asserts that any torsion-free holomorphic affine connecti...

  8. Marine turtle capture data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — To estimate abundance, growth, and survival rate and to collect tissue samples, marine turtles are captured at nesting beaches and foraging grounds through various...

  9. Manifolds with integrable affine shape operator

    Directory of Open Access Journals (Sweden)

    Daniel A. Joaquín

    2005-05-01

    Full Text Available This work establishes the conditions for the existence of vector fields with the property that theirs covariant derivative, with respect to the affine normal connection, be the affine shape operatorS in hypersurfaces. Some results are obtained from this property and, in particular, for some kind of affine decomposable hypersurfaces we explicitely get the actual vector fields.

  10. Carboxybetaine methacrylate-modified nylon surface for circulating tumor cell capture.

    Science.gov (United States)

    Wang, Huiyu; Yue, Guofeng; Dong, Chaoqun; Wu, Fenglei; Wei, Jia; Yang, Yang; Zou, Zhengyun; Wang, Lifeng; Qian, Xiaoping; Zhang, Tao; Liu, Baorui

    2014-03-26

    Conventional in vitro circulating tumor cell (CTC) detection methods are always limited by blood sample volume because of the requirement of a large amount of blood. The aim of this study was to overcome the limitation by designing and making an in vivo CTC capture device. In this study, we designed and prepared a kind of proper material to serve the purpose of intervention. A method employing 3-aminopropyltriethoxysilane (γ-APS) as the coupling reagent to graft carboxybetaine methacrylate (CBMA) and to immobilize an anti-epithelial cell adhesion molecular (EpCAM) antibody on Nylon was developed. The results of X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy proved the successful graft of γ-APS and CBMA to Nylon. Furthermore, the predicted improvement in the biocompatibilities of our modified Nylon was confirmed by water contact angle measurement, bovine serum albumin adhesion, platelet adhesion, plasma recalcification time determination, and cytotoxicity tests. The tumor cells adhesion experiment revealed that Nylon with the antibody immobilized on it had an affinity for EpCAM positive tumor cells higher than that of pristine Nylon. Additionally, the capture ability of the CTCs was demonstrated in a nude mouse tumor model using the interventional device made of the modified Nylon wire. The positive results suggest that CBMA-grafted and anti-EpCAM antibody-immobilized Nylon is a promising new material for in vivo CTC capture devices.

  11. Multiparameter cell affinity chromatography: separation and analysis in a single microfluidic channel.

    Science.gov (United States)

    Li, Peng; Gao, Yan; Pappas, Dimitri

    2012-10-02

    The ability to sort and capture more than one cell type from a complex sample will enable a wide variety of studies of cell proliferation and death and the analysis of disease states. In this work, we integrated a pneumatic actuated control layer to an affinity separation layer to create different antibody-coating regions on the same fluidic channel. The comparison of different antibody capture capabilities to the same cell line was demonstrated by flowing Ramos cells through anti-CD19- and anti-CD71-coated regions in the same channel. It was determined that the cell capture density on the anti-CD19 region was 2.44 ± 0.13 times higher than that on the anti-CD71-coated region. This approach can be used to test different affinity molecules for selectivity and capture efficiency using a single cell line in one separation. Selective capture of Ramos and HuT 78 cells from a mixture was also demonstrated using two antibody regions in the same channel. Greater than 90% purity was obtained on both capture areas in both continuous flow and stop flow separation modes. A four-region antibody-coated device was then fabricated to study the simultaneous, serial capture of three different cell lines. In this case the device showed effective capture of cells in a single separation channel, opening up the possibility of multiple cell sorting. Multiparameter sequential blood sample analysis was also demonstrated with high capture specificity (>97% for both CD19+ and CD4+ leukocytes). The chip can also be used to selectively treat cells after affinity separation.

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

    Science.gov (United States)

    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.

  13. Fluorous-assisted metal chelate affinity extraction technique for analysis of protein kinase activity.

    Science.gov (United States)

    Hayama, Tadashi; Kiyokawa, Ena; Yoshida, Hideyuki; Imakyure, Osamu; Yamaguchi, Masatoshi; Nohta, Hitoshi

    2016-08-15

    We have developed a fluorous affinity-based extraction method for measurement of protein kinase activity. In this method, a fluorescent peptide substrate was phosphorylated by a protein kinase, and the obtained phosphopeptide was selectively captured with Fe(III)-immobilized perfluoroalkyliminodiacetic acid reagent via a metal chelate affinity technique. Next, the captured phosphopeptide was selectively extracted into a fluorous solvent mixture, tetradecafluorohexane and 1H,1H,2H,2H-tridecafluoro-1-n-octanol (3:1, v/v), using the specificity of fluorous affinity (fluorophilicity). In contrast, the remained substrate peptide in the aqueous (non-fluorous) phase was easily measured fluorimetrically. Finally, the enzyme activity could be assayed by measuring the decrease in fluorescence. The feasibility of this method was demonstrated by applying the method for measurement of the activity of cAMP-dependent protein kinase (PKA) using its substrate peptide (kemptide) pre-labeled with carboxytetramethylrhodamine (TAMRA).

  14. Topological conjugacy classes of affine maps

    OpenAIRE

    2008-01-01

    A map $f: \\ff^n \\to \\ff^n$ over a field $\\ff$ is called affine if it is of the form $f(x)=Ax+b$, where the matrix $A \\in \\ff^{n\\times n}$ is called the linear part of affine map and $b \\in \\ff^n$. The affine maps over $\\ff=\\rr$ or $\\cc$ are investigated. We prove that affine maps having fixed points are topologically conjugate if and only if their linear parts are topologically conjugate. If affine maps have no fixed points and $n=1$ or 2, then they are topologically conjugate if and only if ...

  15. Using Affinity Diagrams to Evaluate Interactive Prototypes

    DEFF Research Database (Denmark)

    Lucero, Andrés

    2015-01-01

    Affinity diagramming is a technique used to externalize, make sense of, and organize large amounts of unstructured, far-ranging, and seemingly dissimilar qualitative data. HCI and interaction design practitioners have adopted and used affinity diagrams for different purposes. This paper discusses...... our particular use of affinity diagramming in prototype evaluations. We reflect on a decade’s experience using affinity diagramming across a number of projects, both in industry and academia. Our affinity diagramming process in interaction design has been tailored and consists of four stages: creating...

  16. Muon capture at PSI

    CERN Document Server

    Winter, Peter

    2010-01-01

    Measuring the rate of muon capture in hydrogen provides one of the most direct ways to study the axial current of the nucleon. The MuCap experiment uses a negative muon beam stopped in a time projection chamber operated with ultra-pure hydrogen gas. Surrounded by a decay electron detector, the lifetime of muons in hydrogen can be measured to determine the singlet capture rate Lambda_s to a final precision of 1%. The capture rate determines the nucleon's pseudoscalar form factor g_p. A first result, g_p = 7.3 +- 1.1, has been published and the final analysis of the full statistics will reduce the error by a factor of up to 3. Muon capture on the deuteron probes the weak axial current in the two-nucleon system. Within the framework of effective field theories the calculation of such two-nucleon processes involving the axial current requires the knowledge of one additional low energy constant which can be extracted from the doublet capture rate Lambda_d. The same constant then allows to model-independently calcu...

  17. Performance of a new protein A affinity membrane for the primary recovery of antibodies.

    Science.gov (United States)

    Boi, Cristiana; Dimartino, Simone; Sarti, Giulio C

    2008-01-01

    Recovery of antibodies with Protein A affinity chromatography columns has become the standard for the biotechnology industry. Membrane affinity chromatography has not yet experienced extensive application due to the lower capacity of membrane supports compared to chromatographic beads. In this work, new affinity membranes endowed with an interesting binding capacity for human IgG are studied in view of their application in the capturing step of a monoclonal antibody production process. The membranes have been extensively tested with pure IgG solutions and with a cell culture supernatant containing IgG1. The effects of feed flow rate and IgG concentration on the separation performances have been studied in detail, considering in particular binding capacity, selectivity and recovery. These new high capacity affinity membranes appear good candidates to avoid the throughput limitations and other well-known drawbacks of traditional bead-based chromatographic columns.

  18. Muon capture in deuterium

    Science.gov (United States)

    Ricci, P.; Truhlík, E.; Mosconi, B.; Smejkal, J.

    2010-06-01

    Model dependence of the capture rates of the negative muon capture in deuterium is studied starting from potential models and the weak two-body meson exchange currents constructed in the tree approximation and also from an effective field theory. The tree one-boson exchange currents are derived from the hard pion chiral Lagrangians of the NΔπρωa system. If constructed in conjunction with the one-boson exchange potentials, the capture rates can be calculated consistently. On the other hand, the effective field theory currents, constructed within the heavy baryon chiral perturbation theory, contain a low energy constant d that cannot be extracted from data at the one-particle level nor determined from the first principles. Comparative analysis of the results for the doublet transition rate allows us to extract the constant d.

  19. US Spacesuit Knowledge Capture

    Science.gov (United States)

    Chullen, Cinda; Thomas, Ken; McMann, Joe; Dolan, Kristi; Bitterly, Rose; Lewis, Cathleen

    2011-01-01

    The ability to learn from both the mistakes and successes of the past is vital to assuring success in the future. Due to the close physical interaction between spacesuit systems and human beings as users, spacesuit technology and usage lends itself rather uniquely to the benefits realized from the skillful organization of historical information; its dissemination; the collection and identification of artifacts; and the education of those in the field. The National Aeronautics and Space Administration (NASA), other organizations and individuals have been performing United States (U.S.) Spacesuit Knowledge Capture since the beginning of space exploration. Avenues used to capture the knowledge have included publication of reports; conference presentations; specialized seminars; and classes usually given by veterans in the field. More recently the effort has been more concentrated and formalized whereby a new avenue of spacesuit knowledge capture has been added to the archives in which videotaping occurs engaging both current and retired specialists in the field presenting technical scope specifically for education and preservation of knowledge. With video archiving, all these avenues of learning can now be brought to life with the real experts presenting their wealth of knowledge on screen for future learners to enjoy. Scope and topics of U.S. spacesuit knowledge capture have included lessons learned in spacesuit technology, experience from the Gemini, Apollo, Skylab and Shuttle programs, hardware certification, design, development and other program components, spacesuit evolution and experience, failure analysis and resolution, and aspects of program management. Concurrently, U.S. spacesuit knowledge capture activities have progressed to a level where NASA, the National Air and Space Museum (NASM), Hamilton Sundstrand (HS) and the spacesuit community are now working together to provide a comprehensive closed-looped spacesuit knowledge capture system which includes

  20. Neutron capture therapies

    Energy Technology Data Exchange (ETDEWEB)

    Yanch, Jacquelyn C. (Cambridge, MA); Shefer, Ruth E. (Newton, MA); Klinkowstein, Robert E. (Winchester, MA)

    1999-01-01

    In one embodiment there is provided an application of the .sup.10 B(n,.alpha.).sup.7 Li nuclear reaction or other neutron capture reactions for the treatment of rheumatoid arthritis. This application, called Boron Neutron Capture Synovectomy (BNCS), requires substantially altered demands on neutron beam design than for instance treatment of deep seated tumors. Considerations for neutron beam design for the treatment of arthritic joints via BNCS are provided for, and comparisons with the design requirements for Boron Neutron Capture Therapy (BNCT) of tumors are made. In addition, exemplary moderator/reflector assemblies are provided which produce intense, high-quality neutron beams based on (p,n) accelerator-based reactions. In another embodiment there is provided the use of deuteron-based charged particle reactions to be used as sources for epithermal or thermal neutron beams for neutron capture therapies. Many d,n reactions (e.g. using deuterium, tritium or beryllium targets) are very prolific at relatively low deuteron energies.

  1. Neutron capture therapies

    Energy Technology Data Exchange (ETDEWEB)

    Yanch, J.C.; Shefer, R.E.; Klinkowstein, R.E.

    1999-11-02

    In one embodiment there is provided an application of the {sup 10}B(n,{alpha}){sup 7}Li nuclear reaction or other neutron capture reactions for the treatment of rheumatoid arthritis. This application, called Boron Neutron Capture Synovectomy (BNCS), requires substantially altered demands on neutron beam design than for instance treatment of deep seated tumors. Considerations for neutron beam design for the treatment of arthritic joints via BNCS are provided for, and comparisons with the design requirements for Boron Neutron Capture Therapy (BNCT) of tumors are made. In addition, exemplary moderator/reflector assemblies are provided which produce intense, high-quality neutron beams based on (p,n) accelerator-based reactions. In another embodiment there is provided the use of deuteron-based charged particle reactions to be used as sources for epithermal or thermal neutron beams for neutron capture therapies. Many d,n reactions (e.g. using deuterium, tritium or beryllium targets) are very prolific at relatively low deuteron energies.

  2. CAPTURED End Evaluation Synthesis Report

    NARCIS (Netherlands)

    Brouwers, J.H.A.M.

    2012-01-01

    This report provides the findings of the Synthesis Study of the CAPTURED Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the three CAPTURED partners have achieved commendable results. Ten lessons learned are formulated th

  3. Capturing RNA-dependent pathways for cryo-EM analysis

    Directory of Open Access Journals (Sweden)

    Deborah F Kelly

    2012-04-01

    Full Text Available Cryo-Electron Microscopy (EM is a powerful technique to visualize biological processes at nanometer resolution. Structural studies of macromolecular assemblies are typically performed on individual complexes that are biochemically isolated from their cellular context. Here we present a molecular imaging platform to capture and view multiple components of cellular pathways within a functionally relevant framework. We utilized the bacterial protein synthesis machinery as a model system to develop our approach. By using modified Affinity Grid surfaces, we were able to recruit multiple protein assemblies bound to nascent strands of mRNA. The combined use of Affinity Capture technology and single particle electron microscopy provide the basis for visualizing RNA-dependent pathways in a remarkable new way.

  4. Ordinary differential equations in affine geometry

    Directory of Open Access Journals (Sweden)

    Salvador Gigena

    1996-05-01

    Full Text Available The method of qualitative analysis is used, as applied to a class of fourth order, nonlinear ordinary differential equations, in order to classify, both locally and globally, two classes of hypersurfaces of decomposable type in affine geometry: those with constant unimodular affine mean curvature L , and those with constant Riemannian scalar curvature R. This allows to provide a large number of new examples of hypersurfaces in affine geometry.

  5. Ordinary differential equations in affine geometry

    OpenAIRE

    Salvador Gigena

    1996-01-01

    The method of qualitative analysis is used, as applied to a class of fourth order, nonlinear ordinary differential equations, in order to classify, both locally and globally, two classes of hypersurfaces of decomposable type in affine geometry: those with constant unimodular affine mean curvature L , and those with constant Riemannian scalar curvature R. This allows to provide a large number of new examples of hypersurfaces in affine geometry.

  6. Multipole solutions in metric-affine gravity

    CERN Document Server

    Socorro, J; Macías, A; Mielke, E W; Socorro, José; Lämmerzahl, Claus; Macías, Alfredo; Mielke, Eckehard W.

    1998-01-01

    Above Planck energies, the spacetime might become non--Riemannian, as it is known fron string theory and inflation. Then geometries arise in which nonmetricity and torsion appear as field strengths, side by side with curvature. By gauging the affine group, a metric affine gauge theory emerges as dynamical framework. Here, by using the harmonic map ansatz, a new class of multipole like solutions in the metric affine gravity theory (MAG) is obtained.

  7. Measurement of the electron affinity of lanthanum

    Energy Technology Data Exchange (ETDEWEB)

    Covington, A.M.; Calabrese, D.; Thompson, J.S. [Department of Physics and Chemical Physics Programme, University of Nevada, Reno, NV 89557-0058 (United States); Kvale, T.J. [Department of Physics and Astronomy, University of Toledo, OH 43606-3390 (United States)

    1998-10-28

    The electron affinity of lanthanum has been measured using laser photoelectron energy spectroscopy. This is the first electron affinity measurement for lanthanum and one of the first measurements of an electron affinity of a rare-earth series element. The electron affinity of lanthanum was measured to be 0.47{+-}0.02 eV. At least one bound excited state of La{sup -} was also observed in the photoelectron spectra, and the binding energy relative to the ground state of lanthanum was measured as 0.17{+-}0.02 eV. The present experimental measurements are compared to a recent calculation. (author). Letter-to-the-editor.

  8. Affine connections, midpoint formation, and point reflection

    DEFF Research Database (Denmark)

    Kock, Anders

    2011-01-01

    We describe some differential-geometric structures in combinatorial terms: namely affine connections and their torsion and curvature, and we show that torsion free affine connections may equivalently be presented in terms of some simpler combinatorial structure: midpoint formation, and point refl...... reflection (geodesic symmetry). The method employed is that of synthetic differential geometry, which is briefly explained.......We describe some differential-geometric structures in combinatorial terms: namely affine connections and their torsion and curvature, and we show that torsion free affine connections may equivalently be presented in terms of some simpler combinatorial structure: midpoint formation, and point...

  9. Dynamic friction of self-affine surfaces

    Science.gov (United States)

    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

  10. Properties of an affine transport equation and its holonomy

    Science.gov (United States)

    Vines, Justin; Nichols, David A.

    2016-10-01

    An affine transport equation was used recently to study properties of angular momentum and gravitational-wave memory effects in general relativity. In this paper, we investigate local properties of this transport equation in greater detail. Associated with this transport equation is a map between the tangent spaces at two points on a curve. This map consists of a homogeneous (linear) part given by the parallel transport map along the curve plus an inhomogeneous part, which is related to the development of a curve in a manifold into an affine tangent space. For closed curves, the affine transport equation defines a "generalized holonomy" that takes the form of an affine map on the tangent space. We explore the local properties of this generalized holonomy by using covariant bitensor methods to compute the generalized holonomy around geodesic polygon loops. We focus on triangles and "parallelogramoids" with sides formed from geodesic segments. For small loops, we recover the well-known result for the leading-order linear holonomy (˜ Riemann × area), and we derive the leading-order inhomogeneous part of the generalized holonomy (˜ Riemann × area^{3/2}). Our bitensor methods let us naturally compute higher-order corrections to these leading results. These corrections reveal the form of the finite-size effects that enter into the holonomy for larger loops; they could also provide quantitative errors on the leading-order results for finite loops.

  11. Supernova electron capture rates

    CERN Document Server

    Martínez-Pinedo, G

    1999-01-01

    We have calculated the Gamow-Teller strength distributions for the ground states and low lying states of several nuclei that play an important role in the precollapse evolution of supernova. The calculations reproduce the experimental GT distributions nicely. The GT distribution are used to calculate electron capture rates for typical presupernova conditions. The computed rates are noticeably smaller than the presently adopted rates. The possible implications for the supernova evolution are discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Uhi Rinn, E-mail: uhrisu1@math.snu.ac.kr [Department of Mathematical Sciences, Seoul National University, GwanAkRo 1, Gwanak-Gu, Seoul 151-747 (Korea, Republic of)

    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.

  13. Dyes with high affinity for polylactide

    Institute of Scientific and Technical Information of China (English)

    Liang He; Shu Fen Zhang; Bing Tao Tang; Li Li Wang; Jin Zong Yang

    2007-01-01

    Attempts were made to develop dyes with high affinity for polylactide as an alternative to the existent commercial disperse dyes.The dyes synthesized according to the affinity concept of dye to polylactide exhibited excellent dyeing properties on polylactide compared with the commercial disperse dyes.

  14. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    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...

  15. Porosity of Self-affine Sets

    Institute of Scientific and Technical Information of China (English)

    Lifeng XI

    2008-01-01

    In this paper,it is proved that any self-affine set satisfying the strong separation condition is uniformly porous.The author constructs a self-affine set which is not porous,although the open set condition holds.Besides,the author also gives a C1 iterated function system such that its invariant set is not porous.

  16. On affine non-negative matrix factorization

    DEFF Research Database (Denmark)

    Laurberg, Hans; Hansen, Lars Kai

    2007-01-01

    We generalize the non-negative matrix factorization (NMF) generative model to incorporate an explicit offset. Multiplicative estimation algorithms are provided for the resulting sparse affine NMF model. We show that the affine model has improved uniqueness properties and leads to more accurate...

  17. Affine processes on positive semidefinite matrices

    CERN Document Server

    Cuchiero, Christa; Mayerhofer, Eberhard; Teichmann, Josef

    2009-01-01

    This paper provides the mathematical foundation for stochastically continuous affine processes on the cone of positive semidefinite symmetric matrices. These matrix-valued affine processes have arisen from a large and growing range of useful applications in finance, including multi-asset option pricing with stochastic volatility and correlation structures, and fixed-income models with stochastically correlated risk factors and default intensities.

  18. Capturing the Future: Direct and Indirect Probes of Neutron Capture

    Energy Technology Data Exchange (ETDEWEB)

    Couture, Aaron Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-31

    This report documents aspects of direct and indirect neutron capture. The importance of neutron capture rates and methods to determine them are presented. The following conclusions are drawn: direct neutron capture measurements remain a backbone of experimental study; work is being done to take increased advantage of indirect methods for neutron capture; both instrumentation and facilities are making new measurements possible; more work is needed on the nuclear theory side to understand what is needed furthest from stability.

  19. Reflectable bases for affine reflection systems

    CERN Document Server

    Azam, Saeid; Yousofzadeh, Malihe

    2011-01-01

    The notion of a "root base" together with its geometry plays a crucial role in the theory of finite and affine Lie theory. However, it is known that such a notion does not exist for the recent generalizations of finite and affine root systems such as extended affine root systems and affine reflection systems. As an alternative, we introduce the notion of a "reflectable base", a minimal subset $\\Pi$ of roots such that the non-isotropic part of the root system can be recovered by reflecting roots of $\\Pi$ relative to the hyperplanes determined by $\\Pi$. We give a full characterization of reflectable bases for tame irreducible affine reflection systems of reduced types, excluding types $E_{6,7,8}$. As a byproduct of our results, we show that if the root system under consideration is locally finite then any reflectable base is an integral base.

  20. Improving image segmentation by learning region affinities

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.

    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.

  1. Engineering an antibody with picomolar affinity to DOTA chelates of multiple radionuclides for pretargeted radioimmunotherapy and imaging

    Energy Technology Data Exchange (ETDEWEB)

    Orcutt, Kelly Davis; Slusarczyk, Adrian L. [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Cieslewicz, Maryelise [Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Ruiz-Yi, Benjamin [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Bhushan, Kumar R. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Frangioni, John V. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Wittrup, K. Dane, E-mail: wittrup@mit.ed [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2011-02-15

    Introduction: In pretargeted radioimmunotherapy (PRIT), a bifunctional antibody is administered and allowed to pre-localize to tumor cells. Subsequently, a chelated radionuclide is administered and captured by cell-bound antibody while unbound hapten clears rapidly from the body. We aim to engineer high-affinity binders to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelates for use in PRIT applications. Methods: We mathematically modeled antibody and hapten pharmacokinetics to analyze hapten tumor retention as a function of hapten binding affinity. Motivated by model predictions, we used directed evolution and yeast surface display to affinity mature the 2D12.5 antibody to DOTA, reformatted as a single chain variable fragment (scFv). Results: Modeling predicts that for high antigen density and saturating bsAb dose, a hapten-binding affinity of 100 pM is needed for near-maximal hapten retention. We affinity matured 2D12.5 with an initial binding constant of about 10 nM to DOTA-yttrium chelates. Affinity maturation resulted in a 1000-fold affinity improvement to biotinylated DOTA-yttrium, yielding an 8.2{+-}1.9 picomolar binder. The high-affinity scFv binds DOTA complexes of lutetium and gadolinium with similar picomolar affinity and indium chelates with low nanomolar affinity. When engineered into a bispecific antibody construct targeting carcinoembryonic antigen, pretargeted high-affinity scFv results in significantly higher tumor retention of a {sup 111}In-DOTA hapten compared to pretargeted wild-type scFv in a xenograft mouse model. Conclusions: We have engineered a versatile, high-affinity, DOTA-chelate-binding scFv. We anticipate it will prove useful in developing pretargeted imaging and therapy protocols to exploit the potential of a variety of radiometals.

  2. Inertial capture in flow through porous media

    Science.gov (United States)

    Andrade, J. S., Jr.; Araújo, A. D.; Vasconcelos, T. F.; Herrmann, H. J.

    2008-08-01

    We investigate through numerical calculation of non-Brownian particles transported by a fluid in a porous medium, the influence of geometry and inertial effects on the capture efficiency of the solid matrix. In the case of a periodic array of cylinders and under the action of gravity, our results reveal that δ ˜ St, where δ is the particle capture efficiency, and St is the Stokes number. In the absence of gravity, we observe a typical second order transition between non-trapping and trapping of particles that can be expressed as δ ˜ ( St - St c ) α , with an exponent α ≈ 0.5, where St c is the critical Stokes number. We also perform simulations for flow through a random porous structure and confirm that its capture behavior is consistent with the simple periodic model.

  3. Lunar Sulfur Capture System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sulfur Capture System (LSCS) is an innovative method to capture greater than 90 percent of sulfur gases evolved during thermal treatment of lunar soils....

  4. Capturing Near Earth Objects

    OpenAIRE

    Baoyin, Hexi; CHEN Yang; Li, Junfeng

    2011-01-01

    Recently, Near Earth Objects (NEOs) have been attracting great attention, and thousands of NEOs have been found to date. This paper examines the NEOs' orbital dynamics using the framework of an accurate solar system model and a Sun-Earth-NEO three-body system when the NEOs are close to Earth to search for NEOs with low-energy orbits. It is possible for such an NEO to be temporarily captured by Earth; its orbit would thereby be changed and it would become an Earth-orbiting object after a small...

  5. Metal organoclays with compacted structure for truly physical capture of hydrogen

    Science.gov (United States)

    Tahir, M. Nazir; Sennour, Radia; Arus, Vasilica Alisa; Sallam, Lamyaa M.; Roy, René; Azzouz, Abdelkrim

    2017-03-01

    Truly reversible capture of hydrogen was achieved at ambient conditions on Pd-loaded organo-montmorillonites obtained by photo-addition of different thiols on propargylated-TRIS cations already grafted on the clay surface. TEM insights showed that more than 90% of Pd0 incorporated occur as 0.3-0.5 nm subnanoparticles (PdSNPs). XPS and NMR analyses revealed simultaneous strong S:Pd0 and O:Pd0 interactions that "cement" the organic moiety around PdSNPs. The significant decrease in porosity suggests a compacted structure that impedes not only metal aggregation, but also hydrogen diffusion in the metal bulk. Thus, hydrogen appears to adsorb mainly via physical condensation around PdSNPs. These thiol-clay matrices showed hydrogen surface affinity factors of up to 0.51 mmol m-2 at ambient temperature and pressure. This is higher than those reported for much more sophisticated materials. DSC measurements showed very low desorption heat between 20 and 80 °C. Hydrogen release was achieved merely under vacuum or slight heating starting from 40 °C and was almost completed up to 85 °C. This provides a proof of concept of truly reversible capture of hydrogen for concentration and/or storage purposes. Such a performance has never been achieved at ambient temperature and pressure. These findings open new prospects to develop low-cost materials for reversible hydrogen storage without energy and safety constraints.

  6. DNA capture reveals transoceanic gene flow in endangered river sharks

    OpenAIRE

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T.; Naylor, Gavin J. P.

    2015-01-01

    The river sharks of the genus Glyphis, widely feared as man-eaters throughout India, remain very poorly known to science. The group constitutes five described species, all of which are considered highly endangered and restricted to freshwater systems in Australasia and Southeast Asia. DNA sequence data derived from 19th-century dried museum material augmented with contemporary samples indicates that only three of the five currently described species are valid; that there is a genetically dist...

  7. The Cutting Edge of Affinity Electrophoresis Technology

    Directory of Open Access Journals (Sweden)

    Eiji Kinoshita

    2015-03-01

    Full Text Available 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.

  8. The Cutting Edge of Affinity Electrophoresis Technology

    Science.gov (United States)

    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.

  9. Capturing enveloped viruses on affinity grids for downstream cryo-electron microscopy applications

    Science.gov (United States)

    Electron microscopy cryo-electron microscopy and cryo-electron tomography are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pa...

  10. Corner Transfer Matrices and Quantum Affine Algebras

    CERN Document Server

    Foda, O E; Foda, Omar; Miwa, Tetsuji

    1992-01-01

    Let H be the corner-transfer-matrix Hamiltonian for the six-vertex model in the anti-ferroelectric regime. It acts on the infinite tensor product W = V . V . V ....., where is the 2-dimensional irreducible representation of the quantum affine sl(2). We observe that H is the derivation of quantum affine sl(2), and conjecture that the eigenvectors of H form the level-1 vacuum representation of quantum affine sl(2). We report on checks in support of our conjecture.

  11. Affinization of category O for quantum groups

    CERN Document Server

    Young, C A S

    2012-01-01

    Let g be a simple Lie algebra. We consider the category O-hat of those modules over the affine quantum group Uq(g-hat) whose Uq(g)-weights have finite multiplicity and lie in a finite union of cones generated by negative roots. We show that many properties of the category of the finite-dimensional representations naturally extend to the category O-hat. In particular, we develop the theory of q-characters and define the minimal affinizations of parabolic Verma modules. In types ABCFG we classify these minimal affinizations and conjecture a Weyl denominator type formula for their characters.

  12. The ground and excited state electron affinities of cytosine and trans-azobenzene

    Science.gov (United States)

    Chen, Edward C. M.; Herder, Charles; Chen, Edward S.

    2007-06-01

    The electron capture detector, reduction potential, electron transfer and photon methods of determining electron affinities are compared. The adiabatic electron affinities are (in eV): t-azobenzene(O 2), 1.578(5); t-azobenzene, 1.378(5); cytosine, 1.043(5) from anion photoelectron spectra. The largest or ground state value for trans-azobenzene and an excited state electron affinity for cytosine, 0.70 eV are also determined by reduction potentials. Other excited state energies are (in eV): t-azobenzene, 0.328(5), 0.589(5), 0.690(5), 0.768(5), 0.954(5), 1.038(5), 1.150(5), 1.275(5) and cytosine, 0.089(5), 0.098(5), 0.198(5), 0.235(5). The cytosine values are consistent with electron transport and radiation damage and repair in DNA.

  13. Neutron capture reactions at DANCE

    Science.gov (United States)

    Bredeweg, T. A.

    2008-05-01

    The Detector for Advanced Neutron Capture Experiments (DANCE) is a 4π BaF2 array consisting of 160 active detector elements. The primary purpose of the array is to perform neutron capture cross section measurements on small (>~100 μg) and/or radioactive (DANCE we have performed neutron capture cross section measurements on a wide array of medium to heavy mass nuclides. Measurements to date include neutron capture cross sections on 241,243Am, neutron capture and neutron-induced fission cross sections and capture-to-fission ratio (α = σγ/σf) for 235U using a new fission-tagging detector as well as neutron capture cross sections for several astrophysics branch-point nuclei. Results from several of these measurements will be presented along with a discussion of additional physics information that can be extracted from the DANCE data.

  14. Innate immunity probed by lipopolysaccharides affinity strategy and proteomics.

    Science.gov (United States)

    Giangrande, Chiara; Colarusso, Lucia; Lanzetta, Rosa; Molinaro, Antonio; Pucci, Piero; Amoresano, Angela

    2013-01-01

    Lipopolysaccharides (LPSs) are ubiquitous and vital components of the cell surface of Gram-negative bacteria that have been shown to play a relevant role in the induction of the immune-system response. In animal and plant cells, innate immune defenses toward microorganisms are triggered by the perception of pathogen associated molecular patterns. These are conserved and generally indispensable microbial structures such as LPSs that are fundamental in the Gram-negative immunity recognition. This paper reports the development of an integrated strategy based on lipopolysaccharide affinity methodology that represents a new starting point to elucidate the molecular mechanisms elicited by bacterial LPS and involved in the different steps of innate immunity response. Biotin-tagged LPS was immobilized on streptavidin column and used as a bait in an affinity capture procedure to identify protein partners from human serum specifically interacting with this effector. The complex proteins/lipopolysaccharide was isolated and the protein partners were fractionated by gel electrophoresis and identified by mass spectrometry. This procedure proved to be very effective in specifically binding proteins functionally correlated with the biological role of LPS. Proteins specifically bound to LPS essentially gathered within two functional groups, regulation of the complement system (factor H, C4b, C4BP, and alpha 2 macroglobulin) and inhibition of LPS-induced inflammation (HRG and Apolipoproteins). The reported strategy might have important applications in the elucidation of biological mechanisms involved in the LPSs-mediated molecular recognition and anti-infection responses.

  15. Fatty acid and drug binding to a low-affinity component of human serum albumin, purified by affinity chromatography

    DEFF Research Database (Denmark)

    Vorum, H; Pedersen, A O; Honoré, B

    1992-01-01

    of two albumin components about 40% of the albumin having high affinity and about 60% having low affinity. By affinity chromatography we succeeded in purifying the low-affinity component from the mixture. The high-affinity component, however, could not be isolated. We further analyzed the fatty acid...

  16. Robust automated knowledge capture.

    Energy Technology Data Exchange (ETDEWEB)

    Stevens-Adams, Susan Marie; Abbott, Robert G.; Forsythe, James Chris; Trumbo, Michael Christopher Stefan; Haass, Michael Joseph; Hendrickson, Stacey M. Langfitt

    2011-10-01

    This report summarizes research conducted through the Sandia National Laboratories Robust Automated Knowledge Capture Laboratory Directed Research and Development project. The objective of this project was to advance scientific understanding of the influence of individual cognitive attributes on decision making. The project has developed a quantitative model known as RumRunner that has proven effective in predicting the propensity of an individual to shift strategies on the basis of task and experience related parameters. Three separate studies are described which have validated the basic RumRunner model. This work provides a basis for better understanding human decision making in high consequent national security applications, and in particular, the individual characteristics that underlie adaptive thinking.

  17. Capturing the uncultivated majority

    Energy Technology Data Exchange (ETDEWEB)

    Green, Brian D.; Keller, Martin

    2007-04-02

    The metagenomic analysis of environmental microbialcommunities continues to be a rapidly developing area of study. DNAisolation, the first step in capturing the uncultivated majority, hasseen many advances in recent years. Protocols have been developed todistinguish DNA from live versus dead cells and to separate extracellularfrom intracellular DNA. Looking to increase our understanding of the rolethat members of a microbial community play in ecological processes,several techniques have been developed that are enabling greater indepthanalysis of environmental metagenomes. These include the development ofenvironmental gene tags and the serial analysis of 16S rRNA gene sequencetags. In addition, new screening methods have been designed to select forspecific functional genes within metagenomic libraries. Finally, newcultivation methods continue to be developed to improve our ability tocapture a greater diversity of microorganisms within theenvironment.

  18. Capturing the Daylight Dividend

    Energy Technology Data Exchange (ETDEWEB)

    Peter Boyce; Claudia Hunter; Owen Howlett

    2006-04-30

    Capturing the Daylight Dividend conducted activities to build market demand for daylight as a means of improving indoor environmental quality, overcoming technological barriers to effective daylighting, and informing and assisting state and regional market transformation and resource acquisition program implementation efforts. The program clarified the benefits of daylight by examining whole building systems energy interactions between windows, lighting, heating, and air conditioning in daylit buildings, and daylighting's effect on the human circadian system and productivity. The project undertook work to advance photosensors, dimming systems, and ballasts, and provided technical training in specifying and operating daylighting controls in buildings. Future daylighting work is recommended in metric development, technology development, testing, training, education, and outreach.

  19. Scaling laws in phytoplankton nutrient uptake affinity

    DEFF Research Database (Denmark)

    Lindemann, Christian; Fiksen, Øyvind; Andersen, Ken Haste

    2016-01-01

    Nutrient uptake affinity affects the competitive ability of microbial organisms at low nutrient concentrations. From the theory of diffusion limitation it follows that uptake affinity scales linearly with the cell radius. This is in conflict with some observations suggesting that uptake affinity...... scales to a quantity that is closer to the square of the radius, i.e. to cell surface area. We show that this apparent conflict can be resolved by nutrient uptake theory. Pure diffusion limitation assumes that the cell is a perfect sink which means that it is able to absorb all encountered nutrients...... to volume ratio. We show that there are two reasons for this. First, because the small cells need a higher transporter density in order to maximize their affinity, and second because the relative cost of a transporter is higher for a small than for a large cell. We suggest that this might explain why...

  20. Protein purification using PDZ affinity chromatography.

    Science.gov (United States)

    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. Preparation and characterization of fluorophenylboronic acid-functionalized affinity monolithic columns for the selective enrichment of cis-diol-containing biomolecules.

    Science.gov (United States)

    Li, Qianjin; Liu, Zhen

    2015-01-01

    Boronate affinity monolithic columns have been developed into an important means for the selective recognition and capture of cis-diol-containing biomolecules, such as glycoproteins, nucleosides and saccharides. The ligands of boronic acids are playing an important role in boronate affinity monolithic columns. Although several boronate affinity monoliths with high affinity toward cis-diol-containing biomolecules have been reported, only few publications are focused on their detailed procedures for preparation and characterization. This chapter describes in detail the preparation and characterization of a boronate affinity monolithic column applying 2,4-difluoro-3-formyl-phenylboronic acid (DFFPBA) as a ligand. The DFFPBA-functionalized monolithic column not only exhibited an ultrahigh boronate affinity toward cis-diol-containing biomolecules, but also showed great potential for the selective enrichment of cis-diol-containing biomolecules in real samples.

  2. Craniodental affinities of Southeast Asia's "negritos" and the concordance with their genetic affinities.

    Science.gov (United States)

    Bulbeck, David

    2013-01-01

    Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology have revealed some hints of Southwest Pacific affinities in cranial shape, dental morphology, and dental metrical "shape." On the other hand, the Andamanese have been shown to resemble Africans in their craniometrics and South Asians in their dental morphology, while Philippine negritos resemble Mongoloid Southeast Asians in these respects and also in their dental metrics. This study expands the scope of negrito cranial comparisons by including Melayu Malays and additional coverage of South Asians. It highlights the distinction between the Mongoloid-like Philippine negritos and the Andamanese and Semang (and Senoi of Malaya) with their non-Mongoloid associations. It proposes that the early/mid-Holocene dispersal of the B4a1a mitochondrial DNA clade across Borneo, the Philippines, and Taiwan may be important for understanding the distinction between Philippine and other negritos.

  3. Molecular-level Insight into Unusual Low Pressure CO2 Affinity in Pillared Metal-Organic Frameworks

    NARCIS (Netherlands)

    Burtch, N.C.; Jasuja, H.; Dubbeldam, D.; Walton, K.S.

    2013-01-01

    Fundamental insight into how low pressure adsorption properties are affected by chemical functionalization is critical to the development of next-generation porous materials for postcombustion CO2 capture. In this work, we present a systematic approach to understanding low pressure CO2 affinity in i

  4. APPROXIMATE OUTPUT REGULATION FOR AFFINE NONLINEAR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    Yali DONG; Daizhan CHENG; Huashu QIN

    2003-01-01

    Output regulation for affine nonlinear systems driven by an exogenous signal is investigated in this paper. In the absence of the standard exosystem hypothesis, we assume availability of the instantaneous values of the exogenous signal and its first time-derivative for use in the control law.For affine nonlinear systems, the necessary and sufficient conditions of the solvability of approximate output regulation problem are obtained. The precise form of the control law is presented under some suitable assumptions.

  5. Applications of new affine invariant for polytopes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    To study the Schneider's projection problem,Lutwak,Yang and Zhang recently introduced a new .affine invariant functional U(P) for convex polytopes in Rn.In the paper,we obtain the analytic expression of the affine-invariant U(P) defined on a specific subclass of origin-symmetric convex polytopes in Rn and give an application of U(P) to the Lp-Minkowski problem.

  6. Fan affinity laws from a collision model

    CERN Document Server

    Bhattacharjee, Shayak

    2012-01-01

    The performance of a fan is usually estimated from hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this work 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 of air is incorporated. Our calculations prove the affinity laws and provide numerical estimates of the air delivery, thrust and drag on a rotating fan.

  7. A new series of emodin derivatives with bone affinity

    Institute of Scientific and Technical Information of China (English)

    Hong Chen; Ying Wang; Ling Leng; Mao Sheng Cheng; Peng Fei Yu; Jing Ze Zhang

    2007-01-01

    A new series of bone affinity compounds were synthesized by linking emodin with 5-fluorouracil derivatives. Their bone affinities were established by hydroxyapative (HA) affinity experiment in vitro, and their cytostatic effects were shown by the MTT assay.

  8. Synthesis of a New Series of Bone Affinity Compounds

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A new series of bone affinity compounds were synthesized by linking chrysophanol with 5-fluorouracil derivatives. Their bone affinity was established by hydroxyapafive (HA)affinity experiment in vitro, and their cytostatic effects were shown by the MTT assay.

  9. The connection between metal ion affinity and ligand affinity in integrin I domains

    DEFF Research Database (Denmark)

    Vorup-Jensen, Thomas; Waldron, TT; Astrof, N;

    2007-01-01

    Integrins are cell-surface heterodimeric proteins that mediate cell-cell, cell-matrix, and cell-pathogen interactions. Half of the known integrin alpha subunits contain inserted domains (I domains) that coordinate ligand through a metal ion. Although the importance of conformational changes within...... isolated I domains in regulating ligand binding has been reported, the relationship between metal ion binding affinity and ligand binding affinity has not been elucidated. Metal and ligand binding by several I domain mutants that are stabilized in different conformations are investigated using isothermal...... titration calorimetry and surface plasmon resonance studies. This work suggests an inverse relationship between metal ion affinity and ligand binding affinity (i.e. constructs with a high affinity for ligand exhibit a low affinity for metal). This trend is discussed in the context of structural studies...

  10. Trojan capture by terrestrial planets

    CERN Document Server

    Schwarz, Richard

    2016-01-01

    The paper is devoted to investigate the capture of asteroids by Venus, Earth and Mars into the 1:1 mean motion resonance especially into Trojan orbits. Current theoretical studies predict that Trojan asteroids are a frequent by-product of the planet formation. This is not only the case for the outer giant planets, but also for the terrestrial planets in the inner Solar System. By using numerical integrations, we investigated the capture efficiency and the stability of the captured objects. We found out that the capture efficiency is larger for the planets in the inner Solar System compared to the outer ones, but most of the captured Trojan asteroids are not long term stable. This temporary captures caused by chaotic behaviour of the objects were investigated without any dissipative forces. They show an interesting dynamical behaviour of mixing like jumping from one Lagrange point to the other one.

  11. The Generic Data Capture Facility

    Science.gov (United States)

    Connell, Edward B.; Barnes, William P.; Stallings, William H.

    The Generic Data Capture Facility, which can provide data capture support for a variety of different types of spacecraft while enabling operations costs to be carefully controlled, is discussed. The data capture functions, data protection, isolation of users from data acquisition problems, data reconstruction, and quality and accounting are addressed. The TDM and packet data formats utilized by the system are described, and the development of generic facilities is considered.

  12. Captured by Aliens

    Science.gov (United States)

    Achenbach, Joel

    2000-03-01

    Captured by Aliens is a long and twisted voyage from science to the supernatural and back again. I hung out in Roswell, N.M., spent time with the Mars Society, met a guy who was figuring out the best way to build a spaceship to go to Alpha Centauri. I visited the set of the X-Files and talked to Mulder and Scully. One day over breakfast I was told by NASA administrator Dan Goldin, We live in a fog, man! He wants the big answers to the big questions. I spent a night in the base of a huge radio telescope in the boondocks of West Virginia, awaiting the signal from the aliens. I was hypnotized in a hotel room by someone who suspected that I'd been abducted by aliens and that this had triggered my interest in the topic. In the last months of his life, I talked to Carl Sagan, who believed that the galaxy riots with intelligent civilizations. He's my hero, for his steadfast adherence to the scientific method. What I found in all this is that the big question that needs immediate attention is not what's out THERE, but what's going on HERE, on Earth, and why we think the way we do, and how we came to be here in the first place.

  13. Capture-recapture methodology

    Science.gov (United States)

    Gould, William R.; Kendall, William L.

    2013-01-01

    Capture-recapture methods were initially developed to estimate human population abundance, but since that time have seen widespread use for fish and wildlife populations to estimate and model various parameters of population, metapopulation, and disease dynamics. Repeated sampling of marked animals provides information for estimating abundance and tracking the fate of individuals in the face of imperfect detection. Mark types have evolved from clipping or tagging to use of noninvasive methods such as photography of natural markings and DNA collection from feces. Survival estimation has been emphasized more recently as have transition probabilities between life history states and/or geographical locations, even where some states are unobservable or uncertain. Sophisticated software has been developed to handle highly parameterized models, including environmental and individual covariates, to conduct model selection, and to employ various estimation approaches such as maximum likelihood and Bayesian approaches. With these user-friendly tools, complex statistical models for studying population dynamics have been made available to ecologists. The future will include a continuing trend toward integrating data types, both for tagged and untagged individuals, to produce more precise and robust population models.

  14. Inland capture fisheries.

    Science.gov (United States)

    Welcomme, Robin L; Cowx, Ian G; Coates, David; Béné, Christophe; Funge-Smith, Simon; Halls, Ashley; Lorenzen, Kai

    2010-09-27

    The reported annual yield from inland capture fisheries in 2008 was over 10 million tonnes, although real catches are probably considerably higher than this. Inland fisheries are extremely complex, and in many cases poorly understood. The numerous water bodies and small rivers are inhabited by a wide range of species and several types of fisher community with diversified livelihood strategies for whom inland fisheries are extremely important. Many drivers affect the fisheries, including internal fisheries management practices. There are also many drivers from outside the fishery that influence the state and functioning of the environment as well as the social and economic framework within which the fishery is pursued. The drivers affecting the various types of inland water, rivers, lakes, reservoirs and wetlands may differ, particularly with regard to ecosystem function. Many of these depend on land-use practices and demand for water which conflict with the sustainability of the fishery. Climate change is also exacerbating many of these factors. The future of inland fisheries varies between continents. In Asia and Africa the resources are very intensely exploited and there is probably little room for expansion; it is here that resources are most at risk. Inland fisheries are less heavily exploited in South and Central America, and in the North and South temperate zones inland fisheries are mostly oriented to recreation rather than food production.

  15. Gaussian and Affine Approximation of Stochastic Diffusion Models for Interest and Mortality Rates

    Directory of Open Access Journals (Sweden)

    Marcus C. Christiansen

    2013-10-01

    Full Text Available In the actuarial literature, it has become common practice to model future capital returns and mortality rates stochastically in order to capture market risk and forecasting risk. Although interest rates often should and mortality rates always have to be non-negative, many authors use stochastic diffusion models with an affine drift term and additive noise. As a result, the diffusion process is Gaussian and, thus, analytically tractable, but negative values occur with positive probability. The argument is that the class of Gaussian diffusions would be a good approximation of the real future development. We challenge that reasoning and study the asymptotics of diffusion processes with affine drift and a general noise term with corresponding diffusion processes with an affine drift term and an affine noise term or additive noise. Our study helps to quantify the error that is made by approximating diffusive interest and mortality rate models with Gaussian diffusions and affine diffusions. In particular, we discuss forward interest and forward mortality rates and the error that approximations cause on the valuation of life insurance claims.

  16. Resource capture by single leaves

    Energy Technology Data Exchange (ETDEWEB)

    Long, S.P.

    1992-05-01

    Leaves show a variety of strategies for maximizing CO{sub 2} and light capture. These are more meaningfully explained if they are considered in the context of maximizing capture relative to the utilization of water, nutrients and carbohydrates reserves. There is considerable variation between crops in their efficiency of CO{sub 2} and light capture at the leaf level. Understanding of these mechanisms indicate some ways in which efficiency of resource capture could be level cannot be meaningfully considered without simultaneous understanding of implications at the canopy level. 36 refs., 5 figs., 1 tab.

  17. Particle capture into the lung made simple?

    Science.gov (United States)

    de Vasconcelos, Talita Felipe; Sapoval, Bernard; Andrade, José S; Grotberg, James B; Hu, Yingying; Filoche, Marcel

    2011-06-01

    Understanding the impact distribution of particles entering the human respiratory system is of primary importance as it concerns not only atmospheric pollutants or dusts of various kinds but also the efficiency of aerosol therapy and drug delivery. To model this process, current approaches consist of increasingly complex computations of the aerodynamics and particle capture phenomena, performed in geometries trying to mimic lungs in a more and more realistic manner for as many airway generations as possible. Their capture results from the complex interplay between the details of the aerodynamic streamlines and the particle drag mechanics in the resulting flow. In contrast, the present work proposes a major simplification valid for most airway generations at quiet breathing. Within this context, focusing on particle escape rather than capture reveals a simpler structure in the entire process. When gravity can be neglected, we show by computing the escape rates in various model geometries that, although still complicated, the escape process can be depicted as a multiplicative escape cascade in which each elementary step is associated with a single bifurcation. As a net result, understanding of the particle capture may not require computing particle deposition in the entire lung structure but can be abbreviated in some regions using our simpler approach of successive computations in single realistic bifurcations. Introducing gravity back into our model, we show that this multiplicative model can still be successfully applied on up to nine generations, depending on particle type and breathing conditions.

  18. Classification of neocortical interneurons using affinity propagation

    Science.gov (United States)

    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

  19. Classification of neocortical interneurons using affinity propagation.

    Science.gov (United States)

    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.

  20. Proton Affinity Calculations with High Level Methods.

    Science.gov (United States)

    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.

  1. A novel thiol-affinity micropipette tip method using zinc(II)-cyclen-attached agarose beads for enrichment of cysteine-containing molecules.

    Science.gov (United States)

    Kusamoto, Hiroshi; Shiba, Akio; Koretake, Norinao; Fujioka, Haruto; Hieda, Yuhzo; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2016-09-15

    Cysteine-containing biomolecules are attractive targets in the study of thiol biology. Here we introduce a novel method for the selective enrichment of thiol-containing molecules using a thiol-capture zinc(II) complex of 1,4,7,10-tetraazacyclododecane (Zn(2+)-cyclen). Recognition of N-acetylcysteine amide by Zn(2+)-cyclen has been studied by potentiometric pH titration, revealing formation of a 1:1 thiolate-bound Zn(2+)-cyclen complex with a large thiolate-affinity constant of 10(6.2)M(-1) at 25°C and I=0.10M (NaCl). The Zn(2+)-bound thiolate anion is unexpectedly stable in aqueous solution at pH 7.8 under atmospheric conditions for a few days. These findings have contributed to the development of a convenient method for separation of thiol compounds by using a micropipette tip. A 200μL micropipette tip containing 10μL of hydrophilic cross-linked agarose beads attached to Zn(2+)-cyclen moieties was prepared. All steps for thiol-affinity separation (binding, washing, and eluting) are conducted using aqueous buffers at room temperature. The entire separation protocol requires less than 15min per sample. We demonstrate practical example separations of cysteine-containing molecules. This micropipette tip method would be used preferentially as an alternative to existing tools for reliable enrichment of thiol-containing molecules.

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

    Science.gov (United States)

    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…

  3. New opioid affinity labels containing maleoyl moiety.

    Science.gov (United States)

    Szatmári, I; Orosz, G; Rónai, A Z; Makó, E; Medzihradszky, K; Borsodi, A

    1999-01-01

    Opioid receptor binding properties and pharmacological profiles of novel peptides containing maleoyl function were determined in order to develop new affinity labels. Based on the enkephalin structure peptide ligands were synthesized and tested. Both in in vitro receptor binding experiments and pharmacological studies, all ligands showed agonist character with relatively high affinity (Ki values in the nanomolar range) and good to moderate selectivity. Replacement of Gly2 in the enkephalin frame with D-Ala led to higher affinities with a small decrease in selectivity. The longer peptide chains resulted in compounds with high percentage (up to 86%) of irreversible binding. The selectivity pattern of the ligands is in good agreement with the data obtained from the pharmacological assays (guinea pig ileum and mouse vas deferens bioassays). The newly synthesized peptides could be used in further studies in order to determine more detailed characteristics of the ligand-receptor interaction.

  4. Modelling and simulation of affinity membrane adsorption.

    Science.gov (United States)

    Boi, Cristiana; Dimartino, Simone; Sarti, Giulio C

    2007-08-24

    A mathematical model for the adsorption of biomolecules on affinity membranes is presented. The model considers convection, diffusion and adsorption kinetics on the membrane module as well as the influence of dead end volumes and lag times; an analysis of flow distribution on the whole system is also included. The parameters used in the simulations were obtained from equilibrium and dynamic experimental data measured for the adsorption of human IgG on A2P-Sartoepoxy affinity membranes. The identification of a bi-Langmuir kinetic mechanisms for the experimental system investigated was paramount for a correct process description and the simulated breakthrough curves were in good agreement with the experimental data. The proposed model provides a new insight into the phenomena involved in the adsorption on affinity membranes and it is a valuable tool to assess the use of membrane adsorbers in large scale processes.

  5. Carbon Capture: A Technology Assessment

    Science.gov (United States)

    2013-10-21

    monoethanolamine (MEA) and ammonia ; pre- combustion capture (also via chemical solvents) from the synthesis gas produced in an integrated coal gasification...71 D. Heaven et al., “ Synthesis Gas Purification in Gasification to Ammonia /Urea Plants,” Gasification Technologies...32 Ammonia -Based Capture Processes

  6. Muon capture on Chlorine-35

    CERN Document Server

    Arole, S; Gorringe, T P; Hasinoff, M D; Kovash, M A; Kuzmin, V; Moftah, B A; Sedlar, R; Stocki, T J; Tetereva, T

    2002-01-01

    We report measurements of $\\gamma$--ray spectra from muon capture on $^{35}$Cl. For the allowed Gamow--Teller transitions to the $^{35}$S$(2939, 3/2^+)$ state and the $^{35}$S$(3421, 5/2^+)$ state we obtained their capture rates, hyperfine dependences and $\\gamma$--$\

  7. On neutrinoless double electron capture

    CERN Document Server

    Drukarev, E G

    2016-01-01

    We found the probability for the neutrinoless double electron capture in the case of $KK$ capture. We clarified the mechanism of the energy transfer from the nucleus to the bound electrons. This enabled us to obtain the equations for the probability of the $2EC0\

  8. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives

    Directory of Open Access Journals (Sweden)

    Deborah A. Sarkes

    2016-11-01

    Full Text Available Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1 consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide–protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity, and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.

  9. Sub-barrier capture with quantum diffusion approach

    Directory of Open Access Journals (Sweden)

    Scheid W.

    2011-10-01

    Full Text Available With the quantum diffusion approach the behavior of capture cross sections and mean-square angular momenta of captured systems are revealed in the reactions with deformed and spherical nuclei at sub-barrier energies. With decreasing bombarding energy under the barrier the external turning point of the nucleus-nucleus potential leaves the region of short-range nuclear interaction and action of friction. Because of this change of the regime of interaction, an unexpected enhancement of the capture cross section is found at bombarding energies far below the Coulomb barrier. This effect is shown its worth in the dependence of mean-square angular momentum on the bombarding energy. From the comparison of calculated capture cross sections and experimental capture or fusion cross sections the importance of quasifission near the entrance channel is demonstrated for the actinidebased reactions and reactions with medium-heavy nuclei at extreme sub-barrier energies.

  10. Poisson Morphisms and Reduced Affine Poisson Group Actions

    Institute of Scientific and Technical Information of China (English)

    YANG Qi Lin

    2002-01-01

    We establish the concept of a quotient affine Poisson group, and study the reduced Poisson action of the quotient of an affine Poisson group G on the quotient of an affine Poisson G-variety V. The Poisson morphisms (including equivariant cases) between Poisson affine varieties are also discussed.

  11. Periodic cyclic homology of affine Hecke algebras

    CERN Document Server

    Solleveld, Maarten

    2009-01-01

    This is the author's PhD-thesis, which was written in 2006. The version posted here is identical to the printed one. Instead of an abstract, the short list of contents: Preface 5 1 Introduction 9 2 K-theory and cyclic type homology theories 13 3 Affine Hecke algebras 61 4 Reductive p-adic groups 103 5 Parameter deformations in affine Hecke algebras 129 6 Examples and calculations 169 A Crossed products 223 Bibliography 227 Index 237 Samenvatting 245 Curriculum vitae 253

  12. Control and estimation of piecewise affine systems

    CERN Document Server

    Xu, Jun

    2014-01-01

    As a powerful tool to study nonlinear systems and hybrid systems, piecewise affine (PWA) systems have been widely applied to mechanical systems. Control and Estimation of Piecewise Affine Systems presents several research findings relating to the control and estimation of PWA systems in one unified view. Chapters in this title discuss stability results of PWA systems, using piecewise quadratic Lyapunov functions and piecewise homogeneous polynomial Lyapunov functions. Explicit necessary and sufficient conditions for the controllability and reachability of a class of PWA systems are

  13. Einstein's gravity from an affine model

    CERN Document Server

    Castillo-Felisola, Oscar

    2015-01-01

    We show that the effective field equations for a recently formulated affine model of gravity, in the sector of a metric (torsion-free) connection, accept general Einstein manifolds --- with or without cosmological constant --- as solutions. Moreover, these effective field equations coincide with the ones obtained from a gravitational Yang--Mills theory known as Stephenson--Kilmister--Yang theory. Additionally, we find an equivalence between a minimally coupled massless scalar field in General Relativity with a "minimally" coupled scalar field in this affine model.

  14. Separation of Proteins by Electrophoretic Affinity Chromatography

    Institute of Scientific and Technical Information of China (English)

    邺韶骅; 刘铮; 丁富新; 袁乃驹

    1999-01-01

    A new kind of electrophoretic affinity chromatography (EAC) for bioseparation was proposed,Separation by EAC was conducted in a multicompartment electrolyzer in which the affinity gel media were packed in one of the central compartments.The presence of an electric field accelerated the migration of proteins inside the gel matrix during adsorption and descrption processes,This led to the increase of the overall speed of separation,The present study was focused on the effect of the strength of the electric field on adsorption and desorption processes.

  15. Adsorption affinity of anions on metal oxyhydroxides

    Science.gov (United States)

    Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.

    2013-03-01

    The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ≫ SO{4/2-}.

  16. Affine Invariant Character Recognition by Progressive Removing

    Science.gov (United States)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  17. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    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 Fe3+, Ga3+, Al3+, Zr4+, and Ti4+ 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...

  18. Iodine neutron capture therapy

    Science.gov (United States)

    Ahmed, Kazi Fariduddin

    A new technique, Iodine Neutron Capture Therapy (INCT) is proposed to treat hyperthyroidism in people. Present thyroid therapies, surgical removal and 131I treatment, result in hypothyroidism and, for 131I, involve protracted treatment times and excessive whole-body radiation doses. The new technique involves using a low energy neutron beam to convert a fraction of the natural iodine stored in the thyroid to radioactive 128I, which has a 24-minute half-life and decays by emitting 2.12-MeV beta particles. The beta particles are absorbed in and damage some thyroid tissue cells and consequently reduce the production and release of thyroid hormones to the blood stream. Treatment times and whole-body radiation doses are thus reduced substantially. This dissertation addresses the first of the several steps needed to obtain medical profession acceptance and regulatory approval to implement this therapy. As with other such programs, initial feasibility is established by performing experiments on suitable small mammals. Laboratory rats were used and their thyroids were exposed to the beta particles coming from small encapsulated amounts of 128I. Masses of 89.0 mg reagent-grade elemental iodine crystals have been activated in the ISU AGN-201 reactor to provide 0.033 mBq of 128I. This activity delivers 0.2 Gy to the thyroid gland of 300-g male rats having fresh thyroid tissue masses of ˜20 mg. Larger iodine masses are used to provide greater doses. The activated iodine is encapsulated to form a thin (0.16 cm 2/mg) patch that is then applied directly to the surgically exposed thyroid of an anesthetized rat. Direct neutron irradiation of a rat's thyroid was not possible due to its small size. Direct in-vivo exposure of the thyroid of the rat to the emitted radiation from 128I is allowed to continue for 2.5 hours (6 half-lives). Pre- and post-exposure blood samples are taken to quantify thyroid hormone levels. The serum T4 concentration is measured by radioimmunoassay at

  19. Electron capture dissociation of singly and multiply phosphorylated peptides

    DEFF Research Database (Denmark)

    Stensballe, A; Jensen, Ole Nørregaard; Olsen, J V

    2000-01-01

    Analysis of phosphotyrosine and phosphoserine containing peptides by nano-electrospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry established electron capture dissociation (ECD) as a viable method for phosphopeptide sequencing. In general, ECD spectra of synthetic...... and native phosphopeptides appeared less complex than conventional collision activated dissociation (CAD) mass spectra of these species. ECD of multiply protonated phosphopeptide ions generated mainly c- and z(.)-type peptide fragment ion series. No loss of water, phosphate groups or phosphoric acid from......(III)-affinity chromatography combined with nano-electrospray FTMS/ECD facilitated phosphopeptide analysis and amino acid sequencing from crude proteolytic peptide mixtures....

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

    Science.gov (United States)

    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.

  1. Crossing Chris: Some Markerian Affinities

    Directory of Open Access Journals (Sweden)

    Adrian Martin

    2010-01-01

    -pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

    Abstract (E: This essay creatively explores a group of artists, writers, and other special individuals whose work or life story can be described as having an intriguing affinity with the protean career of Chris Marker. Avoiding the ‘usual suspects’ (such as Godard or Sebald, it discusses gossip columnist Milt Machlin, record collector Harry Smith, painter Gianfranco Baruchello, writer-filmmaker Edgardo Cozarinsky, and several others. From this constellation, a particular view of Markerian poetics emerges, touching upon the meanings of anonymity, storytelling, history and archiving.

     

    Abstract (F: Cet essai brosse de manière créative le portrait d’un groupe d'artistes, d'écrivains et d'autres personnes particulières dont le travail ou la biographie peuvent être décrits comme montrant une étrange mais certaine connivence avec la carrière protéiforme de Chris Marker. Evitant les lieux communs (comme Godard ou Sebald, cet article trace des références moins attendues :

  2. Temporary Capture of Asteroids by a Planet: Dependence of Prograde/Retrograde Capture on Asteroids' Semimajor Axes

    CERN Document Server

    Higuchi, Arika

    2015-01-01

    We have investigated the dependence of the prograde/retrograde temporary capture of asteroids by a planet on their original heliocentric semimajor axes through analytical arguments and numerical orbital integrations in order to discuss the origins of irregular satellites of giant planets. We found that capture is mostly retrograde for the asteroids near the planetary orbit and is prograde for those from further orbits. An analytical investigation reveals the intrinsic dynamics of these dependences and gives boundary semimajor axes for the change in prograde/retrograde capture. The numerical calculations support the idea of deriving the analytical formulae and confirm their dependence. Our numerical results show that the capture probability is much higher for bodies from the inner region than for outer ones. These results imply that retrograde irregular satellites of Jupiter are most likely to be captured bodies from the nearby orbits of Jupiter that may have the same origin as Trojan asteroids, while prograde...

  3. Materials For Gas Capture, Methods Of Making Materials For Gas Capture, And Methods Of Capturing Gas

    KAUST Repository

    Polshettiwar, Vivek

    2013-06-20

    In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to materials that can be used for gas (e.g., CO.sub.2) capture, methods of making materials, methods of capturing gas (e.g., CO.sub.2), and the like, and the like.

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

    Science.gov (United States)

    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.

  5. Fan Affinity Laws from a Collision Model

    Science.gov (United States)

    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…

  6. Colliding waves in metric-affine gravity

    CERN Document Server

    García, A; Macías, A; Mielke, E W; Socorro, J; García, Alberto; Lämmerzahl, Claus; Macías, Alfredo; Mielke, Eckehard W.; Socorro, José

    1998-01-01

    We generalize the formulation of the colliding gravitational waves to metric-affine theories and present an example of such kind of exact solutions. The plane waves are equipped with five symmetries and the resulting geometry after the collision possesses two spacelike Killing vectors.

  7. Classification of neocortical interneurons using affinity propagation

    Directory of Open Access Journals (Sweden)

    Roberto eSantana

    2013-12-01

    Full Text Available In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. 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. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  8. Immunoproteomics Using Polyclonal Antibodies and Stable Isotope–labeled Affinity-purified Recombinant Proteins*

    Science.gov (United States)

    Edfors, Fredrik; Boström, Tove; Forsström, Björn; Zeiler, Marlis; Johansson, Henrik; Lundberg, Emma; Hober, Sophia; Lehtiö, Janne; Mann, Matthias; Uhlen, Mathias

    2014-01-01

    The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope–labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A–coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope–labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed. PMID:24722731

  9. Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.

    Science.gov (United States)

    Edfors, Fredrik; Boström, Tove; Forsström, Björn; Zeiler, Marlis; Johansson, Henrik; Lundberg, Emma; Hober, Sophia; Lehtiö, Janne; Mann, Matthias; Uhlen, Mathias

    2014-06-01

    The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope-labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A-coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope-labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed.

  10. High-Performance Sorbents for Carbon Dioxide Capture from Air

    Energy Technology Data Exchange (ETDEWEB)

    Sholl, David; Jones, Christopher

    2013-03-13

    This project has focused on capture of CO{sub 2} from ambient air (“air capture”). If this process is technically and economically feasible, it could potentially contribute to net reduction of CO{sub 2} emissions in ways that are complementary to better developed techniques for CO{sub 2} from concentrated point sources. We focused on cyclic adsorption processes for CO{sub 2} capture from air in which the entire cycle is performed at moderate temperatures. The project involved both experimental studies of sorbent materials and process level modeling of cyclic air capture processes. In our experimental work, a series of amine-functionalized silica adsorbents were prepared and characterized to determine the impact of molecular architecture on CO{sub 2} capture. Some key findings were: • Amine functionalized silicas can be prepared with high enough CO{sub 2} capacities under ambient conditions to merit consideration for use in air capture processes. • Primary amines are better candidates for CO{sub 2} capture than secondary or tertiary amines, both in terms of amine efficiency for CO{sub 2} adsorption and enhanced water affinity. • Mechanistic understanding of degradation of these materials can enable control of molecular architecture to significantly improve material stability. Our process modeling work provided the first publically available cost and energy estimates for cyclic adsorption processes for air capture of CO{sub 2}. Some key findings were: • Cycles based on diurnal ambient heating and cooling cannot yield useful purities or amounts of captured CO{sub 2}. • Cycles based on steam desorption at 110 oC can yield CO{sub 2} purities of ~88%. • The energy requirements for cycles using steam desorption are dominated by needs for thermal input, which results in lower costs than energy input in the form of electricity. Cyclic processes with operational costs of less than $100 tCO{sub 2}-net were described, and these results point to process and

  11. Provenance Datasets Highlighting Capture Disparities

    Science.gov (United States)

    2014-01-01

    the Web pages of the universities and institutes.1 Notes are made and links pasted in a variety of formats. Files are saved on a shared drive. When...institutions/ 3. Capture Methods There are several capture methods that are available for use [4]: • Manual capture. • Scraping of logs or...the high-level user desktop. Save links App: Word, SharePoint User: Alice Web Data Web Data Web Data Web Data Web Data Web Data Notes.txt Create

  12. Congophilicity (Congo red affinity) of different beta2-microglobulin conformations characterized by dye affinity capillary electrophoresis

    DEFF Research Database (Denmark)

    Heegaard, N H; Sen, J W; Nissen, Mogens Holst

    2000-01-01

    The amyloidogenic protein beta-microglobulin was characterized by affinity capillary electrophoresis (CE). CE could separate conformational variants of beta2-microglobulin and with the amyloid-specific dye Congo red as a buffer additive it was possible to measure different Congo red-affinities of......The amyloidogenic protein beta-microglobulin was characterized by affinity capillary electrophoresis (CE). CE could separate conformational variants of beta2-microglobulin and with the amyloid-specific dye Congo red as a buffer additive it was possible to measure different Congo red...

  13. Enzyme activity assay of glycoprotein enzymes based on a boronate affinity molecularly imprinted 96-well microplate.

    Science.gov (United States)

    Bi, Xiaodong; Liu, Zhen

    2014-12-16

    Enzyme activity assay is an important method in clinical diagnostics. However, conventional enzyme activity assay suffers from apparent interference from the sample matrix. Herein, we present a new format of enzyme activity assay that can effectively eliminate the effects of the sample matrix. The key is a 96-well microplate modified with molecularly imprinted polymer (MIP) prepared according to a newly proposed method called boronate affinity-based oriented surface imprinting. Alkaline phosphatase (ALP), a glycoprotein enzyme that has been routinely used as an indicator for several diseases in clinical tests, was taken as a representative target enzyme. The prepared MIP exhibited strong affinity toward the template enzyme (with a dissociation constant of 10(-10) M) as well as superb tolerance for interference. Thus, the enzyme molecules in a complicated sample matrix could be specifically captured and cleaned up for enzyme activity assay, which eliminated the interference from the sample matrix. On the other hand, because the boronate affinity MIP could well retain the enzymatic activity of glycoprotein enzymes, the enzyme captured by the MIP was directly used for activity assay. Thus, additional assay time and possible enzyme or activity loss due to an enzyme release step required by other methods were avoided. Assay of ALP in human serum was successfully demonstrated, suggesting a promising prospect of the proposed method in real-world applications.

  14. Tuning the Protein Corona of Hydrogel Nanoparticles: The Synthesis of Abiotic Protein and Peptide Affinity Reagents.

    Science.gov (United States)

    O'Brien, Jeffrey; Shea, Kenneth J

    2016-06-21

    Nanomaterials, when introduced into a complex, protein-rich environment, rapidly acquire a protein corona. The type and amount of proteins that constitute the corona depend significantly on the synthetic identity of the nanomaterial. For example, hydrogel nanoparticles (NPs) such as poly(N-isopropylacrylamide) (NIPAm) have little affinity for plasma proteins; in contrast, carboxylated poly(styrene) NPs acquire a dense protein corona. This range of protein adsorption suggests that the protein corona might be "tuned" by controlling the chemical composition of the NP. In this Account, we demonstrate that small libraries of synthetic polymer NPs incorporating a diverse pool of functional monomers can be screened for candidates with high affinity and selectivity to targeted biomacromolecules. Through directed synthetic evolution of NP compositions, one can tailor the protein corona to create synthetic organic hydrogel polymer NPs with high affinity and specificity to peptide toxins, enzymes, and other functional proteins, as well as to specific domains of large proteins. In addition, many NIPAm NPs undergo a change in morphology as a function of temperature. This transformation often correlates with a significant change in NP-biomacromolecule affinity, resulting in a temperature-dependent protein corona. This temperature dependence has been used to develop NP hydrogels with autonomous affinity switching for the protection of proteins from thermal stress and as a method of biomacromolecule purification through a selective thermally induced catch and release. In addition to temperature, changes in pH or buffer can also alter a NP protein corona composition, a property that has been exploited for protein purification. Finally, synthetic polymer nanoparticles with low nanomolar affinity for a peptide toxin were shown to capture and neutralize the toxin in the bloodstream of living mice. While the development of synthetic polymer alternatives to protein affinity reagents is

  15. Enzymes in CO2 Capture

    DEFF Research Database (Denmark)

    Fosbøl, Philip Loldrup; Gladis, Arne; Thomsen, Kaj

    of carbon capture is the application of enzymes for acceleration of typically slow ternary amines or inorganic carbonates. There is a hidden potential to revive currently infeasible amines which have an interesting low energy consumption for regeneration but too slow kinetics for viable CO2 capture. The aim......The enzyme Carbonic Anhydrase (CA) can accelerate the absorption rate of CO2 into aqueous solutions by several-fold. It exist in almost all living organisms and catalyses different important processes like CO2 transport, respiration and the acid-base balances. A new technology in the field...... of this work is to discuss the measurements of kinetic properties for CA promoted CO2 capture solvent systems. The development of a rate-based model for enzymes will be discussed showing the principles of implementation and the results on using a well-known ternary amine for CO2 capture. Conclusions...

  16. Methane capture from livestock manure.

    Science.gov (United States)

    Tauseef, S M; Premalatha, M; Abbasi, Tasneem; Abbasi, S A

    2013-03-15

    It has been estimated that livestock manure contributes about 240 million metric tons of carbon dioxide equivalent of methane to the atmosphere and represents one of the biggest anthropogenic sources of methane. Considering that methane is the second biggest contributor to global warming after carbon dioxide, it is imperative that ways and means are developed to capture as much of the anthropogenic methane as possible. There is a major associated advantage of methane capture: its use as a source of energy which is comparable in 'cleanness' to natural gas. The present review dwells upon the traditional ways of methane capture used in India, China, and other developing countries for providing energy to the rural poor. It then reviews the present status of methane capture from livestock manure in developed countries and touches upon the prevalent trends.

  17. Lunar Sulfur Capture System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sulfur Capture System (LSCS) is an innovative method to recover sulfur compounds from lunar soil using sorbents derived primarily from in-situ resources....

  18. Capture-stabilize approach for membrane protein SPR assays.

    Science.gov (United States)

    Chu, Ruiyin; Reczek, David; Brondyk, William

    2014-12-08

    Measuring the binding kinetics of antibodies to intact membrane proteins by surface plasmon resonance has been challenging largely because of the inherent difficulties in capturing membrane proteins on chip surfaces while retaining their native conformation. Here we describe a method in which His-tagged CXCR5, a GPCR, was purified and captured on a Biacore chip surface via the affinity tag. The captured receptor protein was then stabilized on the chip surface by limited cross-linking. The resulting chip surface retained ligand binding activity and was used for monoclonal antibody kinetics assays by a standard Biacore kinetics assay method with a simple low pH regeneration step. We demonstrate the advantages of this whole receptor assay when compared to available peptide-based binding assays. We further extended the application of the capture-stabilize approach to virus-like particles and demonstrated its utility analyzing antibodies against CD52, a GPI-anchored protein, in its native membrane environment. The results are the first demonstration of chemically stabilized chip surfaces for membrane protein SPR assays.

  19. Radiative muon capture on hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Bertl, W. (Paul Scherrer Inst. (PSI), Villigen (Switzerland)); Ahmad, S.; Chen, C.Q.; Gumplinger, P.; Hasinoff, M.D.; Larabee, A.J.; Sample, D.G.; Schott, W.; Wright, D.H. (British Columbia Univ., Vancouver (Canada)); Armstrong, D.S.; Blecher, M. (Virginia Polytechnic Inst., Blacksburg, VA (United States) Virginia State Univ., Blacksburg, VA (United States)); Azuelos, G. (British Columbia Univ., Vancouver (Canada). TRIUMF Facility Montreal Univ., Quebec (Canada)); Depommier, P.; Jonkmans, G. (Montreal Univ., Quebec (Canada)); Gorringe, T.P. (Kentucky Univ., Lexington, KY (United States)); Henderson, R. (British Columbia Univ., Vancouver (Canada). TRIUMF Facility Melbourne Univ., Parkville (Australia)); Macdonald, J.A.; Poutissou, J.M.; Poutissou, R.; Von Egidy, T.; Zhang, N.S. (British Columbia Univ., Vancouver (Canada). TRIUMF Facility); McDonald, S.C.; Taylor, G.N. (Melbourne Univ., Parkville (Australia)); Robertson, B.D. (Queen' s Univ., Kingston, Ontario (Canada))

    1992-01-01

    The radiative capture of negative muons by protons can be used to measure the weak induced pseudoscalar form factor. Brief arguments why this method is preferable to ordinary muon capture are given followed by a discussion of the experimental difficulties. The solution to these problems as attempted by experiment no. 452 at TRIUMF is presented together with preliminary results from the first run in August 1990. An outlook on the expected final precision and the experimental schedule is also given. (orig.).

  20. Toward transformational carbon capture systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, David C. [National Energy Technology Laboratory, U.S. Dept. of Energy, Pittsburgh PA (United States); Litynski, John T. [Office of Fossil Energy, U.S. Dept. of Energy, Washington DC (United States); Brickett, Lynn A. [National Energy Technology Laboratory, U.S. Dept. of Energy, Pittsburgh PA (United States); Morreale, Bryan D. [National Energy Technology Laboratory, U.S. Dept. of Energy, Pittsburgh PA (United States)

    2015-10-28

    This paper will briefly review the history and current state of Carbon Capture and Storage (CCS) research and development and describe the technical barriers to carbon capture. it will argue forcefully for a new approach to R&D, which leverages both simulation and physical systems at the laboratory and pilot scales to more rapidly move the best technoogies forward, prune less advantageous approaches, and simultaneously develop materials and processes.

  1. The Capture of Jupiter Trojans

    Science.gov (United States)

    Morbidelli, A.; Nesvorny, D.; Vokrouhlicky, D.

    2013-09-01

    The origin of Jupiter Trojans remained mysterious for decades. Particularly, it was difficult to explain the excitation of the inclinations of the Trojan population [1]. In 2005, Morbidelli et al. [2] proposed a scenario of capture from the trans-Neptunian disk, in the framework of the so-called "Nice model" [3,4]. This scenario explained in a natural way the observed orbital distribution of Trojans. The Nice model, however, evolved in the years, in order to satisfy an increasingly large number of constraints. It now appears that the dynamical evolution of the giant planets was different from that envisioned in [2]. Here, we assess again the process of capture of Trojans within this new evolution. We show that (6-8)×10 - 7 of the original trans-Neptunian planetesimals are captured in the Trojan region, with an orbital distribution consistent with the one observed. Relative to [2], the new capture mechanism has the potential of explaining the asymmetry between the L4 and L5 populations. Moreover, the resulting population of Trojans is consistent with that of the Irregular Satellites of Jupiter, which are captured in the same process; a few bodies from the main asteroid belt could also be captured in the Trojan cloud.

  2. Boronic acid lectin affinity chromatography (BLAC). 2. Affinity micropartitioning-mediated comparative glycosylation profiling.

    Science.gov (United States)

    Monzo, Alex; Olajos, Marcell; De Benedictis, Lorenzo; Rivera, Zuly; Bonn, Guenther K; Guttman, András

    2008-09-01

    As a continuation of our work on boronic acid lectin affinity chromatography (BLAC), in this paper we introduce an automated affinity micropartitioning approach using combined boronic acid and concanavalin A (BLAC/Con A) resin-filled micropipette tips to isolate and enrich human serum glycoproteins. The N-linked oligosaccharides of the partitioned glycoproteins were removed by PNGase F enzyme digestion, followed by 8-aminopyrene-1,3,6-trisulfonic acid labeling. Capillary gel electrophoresis with blue LED-induced fluorescence detection was applied in a multiplexed format for comparative glycan profiling. The efficiency of BLAC affinity micropartitioning was compared with that of the individual lectin and pseudolectin affinity enrichment. Finally, we report on our findings in glycosylation differences in human serum samples from healthy and prostate cancer patients by applying BLAC/Con A micropipette tip-based enrichment and comparative multicapillary gel electrophoresis analysis of the released and labeled glycans.

  3. Modulating the selectivity of affinity absorbents to multi-phosphopeptides by a competitive substitution strategy.

    Science.gov (United States)

    Liu, Zheyi; Wang, Fangjun; Chen, Jin; Zhou, Ye; Zou, Hanfa

    2016-08-26

    Although many affinity adsorbents have been developed for phosphopeptides enrichment, high-specifically capturing the multi-phosphopeptides is still a big challenge. Here, we investigated the mechanism of phosphate ion coordination and substitution on affinity adsorbents surfaces and modulated the selectivity of affinity adsorbents to multi-phosphopeptides based on the different capability of mono- and multi-phosphopeptides in competitively substituting the pre-coordinated phosphate ions at strong acidic condition. We demonstrated both the species of pre-coordinated phosphate ions and the substituting conditions played crucial roles in modulating the enrichment selectivity to multi-phosphopeptides, and the pre-coordinated affinity materials with relative more surfaces positive charges exhibited better enrichment efficiency due to the cooperative effect of electrostatic interaction and competitive substitution. Finally, an enrichment selectivity of 85% to multi-phosphopeptides was feasibly achieved with 66% improvement in identification numbers for complex protein sample extracted from HepG2 cells. Data are available via ProteomeXchange with identifier PXD004252.

  4. Local structure of self-affine sets

    CERN Document Server

    Bandt, Christoph

    2011-01-01

    The structure of a self-similar set with open set condition does not change under magnification. For self-affine sets the situation is completely different. We consider planar self-affine Cantor sets E of the type studied by Bedford, McMullen, Gatzouras and Lalley, for which the projection onto the horizontal axis is an interval. We show that within small square neighborhoods of almost each point x in E, with respect to many product measures on address space, E is well approximated by product sets of an interval and a Cantor set. Even though E is totally disconnected, the limit sets have the product structure with interval fibres, reminiscent to the view of attractors of chaotic differentiable dynamical systems.

  5. Introduction of structural affinity handles as a tool in selective nucleic acid separations

    Science.gov (United States)

    Willson, III, Richard Coale (Inventor); Cano, Luis Antonio (Inventor)

    2011-01-01

    The method is used for separating nucleic acids and other similar constructs. It involves selective introduction, enhancement, or stabilization of affinity handles such as single-strandedness in the undesired (or desired) nucleic acids as compared to the usual structure (e.g., double-strandedness) of the desired (or undesired) nucleic acids. The undesired (or desired) nucleic acids are separated from the desired (or undesired) nucleic acids due to capture by methods including but not limited to immobilized metal affinity chromatography, immobilized single-stranded DNA binding (SSB) protein, and immobilized oligonucleotides. The invention is useful to: remove contaminating genomic DNA from plasmid DNA; remove genomic DNA from plasmids, BACs, and similar constructs; selectively separate oligonucleotides and similar DNA fragments from their partner strands; purification of aptamers, (deoxy)-ribozymes and other highly structured nucleic acids; Separation of restriction fragments without using agarose gels; manufacture recombinant Taq polymerase or similar products that are sensitive to host genomic DNA contamination; and other applications.

  6. Real-time affine invariant gesture recognition for LED smart lighting control

    Science.gov (United States)

    Chen, Xu; Liao, Miao; Feng, Xiao-Fan

    2015-03-01

    Gesture recognition has attracted extensive research interest in the field of human computer interaction. Realtime affine invariant gesture recognition is an important and challenging problem. This paper presents a robust affine view invariant gesture recognition system for realtime LED smart light control. As far as we know, this is the first time that gesture recognition has been applied for control LED smart light in realtime. Employing skin detection, hand blobs captured from a top view camera are first localized and aligned. Subsequently, SVM classifiers trained on HOG features and robust shape features are then utilized for gesture recognition. By accurately recognizing two types of gestures ("gesture 8" and a "5 finger gesture"), a user is enabled to toggle lighting on/off efficiently and control light intensity on a continuous scale. In each case, gesture recognition is rotation- and translation-invariant. Extensive evaluations in an office setting demonstrate the effectiveness and robustness of the proposed gesture recognition algorithm.

  7. Target identification of natural products and bioactive compounds using affinity-based probes.

    Science.gov (United States)

    Pan, Sijun; Zhang, Hailong; Wang, Chenyu; Yao, Samantha C L; Yao, Shao Q

    2016-05-04

    Covering: 2010 to 2014.Advances in isolation, synthesis and screening strategies have made many bioactive substances available. However, in most cases their putative biological targets remain unknown. Herein, we highlight recent advances in target identification of natural products and bioactive compounds by using affinity-based probes. Aided by photoaffinity labelling, this strategy can capture potential cellular targets (on and off) of a natural product or bioactive compound in live cells directly, even when the compound-target interaction is reversible with moderate affinity. The knowledge of these targets may help uncover molecular pathways and new therapeutics for currently untreatable diseases. In this highlight, we will introduce the development of various photoactivatable groups, their synthesis and applications in target identification of natural products and bioactive compounds, with a focus on work done in recent years and from our laboratory. We will further discuss the strengths and weaknesses of each group and the outlooks for this novel proteome-wide profiling strategy.

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

    Science.gov (United States)

    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.

  9. Thermodynamics. Using Affinities to define reversible processes

    CERN Document Server

    Ritacco, Hernán A

    2016-01-01

    In this article a definition of reversible processes in terms of differences in intensive Thermodynamics properties (Affinities) is proposed. This definition makes it possible to both define reversible processes before introducing the concept of entropy and avoid the circularity problem that follows from the Clausius definition of entropy changes. The convenience of this new definition compared to those commonly found in textbooks is demonstrated with examples.

  10. Couplings in Affine Toda Field Theories

    OpenAIRE

    1992-01-01

    We present a systematic derivation for a general formula for the n-point coupling constant valid for affine Toda theories related to any simple Lie algebra {\\bf g}. All n-point couplings with $n \\geq 4$ are completely determined in terms of the masses and the three-point couplings. A general fusing rule, formulated in the root space of the Lie algebra, is derived for all n-point couplings.

  11. Folding defect affine Toda field theories

    CERN Document Server

    Robertson, C

    2013-01-01

    A folding process is applied to fused a^(1)_r defects to construct defects for the non-simply laced affi?ne Toda ?field theories of c^(1)_n, d^(2)_n and a^(2)_n at the classical level. Support for the hypothesis that these defects are integrable in the folded theories is provided by the observation that transmitted solitons retain their form. Further support is given by the demonstration that energy and momentum are conserved.

  12. AFFINE TRANSFORMATION IN RANDOM ITERATED FUNCTION SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    熊勇; 史定华

    2001-01-01

    Random iterated function systems (IFSs) is discussed, which is one of the methods for fractal drawing. A certain figure can be reconstructed by a random IFS. One approach is presented to determine a new random IFS, that the figure reconstructed by the new random IFS is the image of the origin figure reconstructed by old IFS under a given affine transformation. Two particular examples are used to show this approach.

  13. On constructing purely affine theories with matter

    Science.gov (United States)

    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.

  14. On constructing purely affine theories with matter

    CERN Document Server

    Cervantes-Cota, Jorge L

    2016-01-01

    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 Schroedinger's purely affine theory [21], 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.

  15. Overview of affinity biosensors in food analysis.

    Science.gov (United States)

    Patel, Pradip D

    2006-01-01

    The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field.

  16. Effect of surface modification of microfiltration membrane on capture of toxic heavy metal ions.

    Science.gov (United States)

    Madaeni, Sayed Siavash; Heidary, Farhad

    2012-01-01

    A novel complexing membrane containing 8-hydroxyquinoline groups was used for the removal of heavy metal ions (Cd2+ and Ni2+) from aqueous solution. The functionalized membranes were characterized by FTIR-ATR, SEM and EDAX for the presence of functional groups, the physical structure of the membranes and the analysis of the particles deposited on the membrane, respectively. The influence of 8-hydroxyquinoline concentration, feed concentration, pH and temperature of the solution on capture capability was studied. The modified membrane showed a higher affinity to Cd2+ cations than to Ni2+. The metal ion rejection was increased with an increase in concentration of 8-hydroxyquinoline from 0.5 to 2.0 wt%. However at a ligand concentration higher than 2.0 wt%, no significant change was observed in the metal rejection. The experimental results revealed that the metal rejection was decreased with an increase in metal ion concentration in the feed. Moreover the rejection depended on feed pH and is higher for elevated pH. By changing the temperature in the range of 23-28 degrees C, no considerable effect on metal rejection was observed. However, a higher temperature resulted in a decline in metal rejection. For filtration of a mixture of the two metal ions, the retention was similar to that of the single cations, i.e. Cd > Ni but with smaller absolute rejections.

  17. Experimental investigation of streamer affinity for dielectric surfaces

    NARCIS (Netherlands)

    Trienekens, D.J.M.; Nijdam, S.; Akkermans, G.; Plompen, I.; Christen, T.; Ebert, U.

    2015-01-01

    We have experimentally investigated the affinity of streamers for dielectric surfaces using stroboscopic imaging and stereo photography. Affinity of streamers for dielectric surfaces was found to depend on a wide set of parameters, including pressure, voltage, dielectric material and di

  18. Spatial model of affinity maturation in germinal centers

    NARCIS (Netherlands)

    Kesmir, C.; Boer, R.J. de

    2003-01-01

    Affinity maturation of humoral responses to T-cell-dependent antigens occurs in germinal centers (GC). In GCs antigen-specific B cells undergo rounds of somatic mutations that alter their affinity. High-affinity mutants take over GCs very soon after they appear; the replacement rate is as high as 4

  19. Affine Structures on a Ringed Space and Schemes

    Institute of Scientific and Technical Information of China (English)

    Fengwen AN

    2011-01-01

    The author first introduces the notion of affine structures on a ringed space and then obtains several related properties. Affine structures on a ringed space, arising from complex analytical spaces of algebraic schenes, behave like differential structures on a smooth nanifold.As one does for differential manifolds, pseudogroups of affine transformations are used to define affine atlases on a ringed space. An atlas on a space is said to be an affine structure if it is maximal. An affine structure is said to be admissible if there is a sheaf on the underlying space such that they are coincide on all affine charts, which are in deed affine open sets of a scheme. In a rigour manner, a scheme is defined to be a ringed space with a specified affine structure if the affine structures make a contribution to the cases such as analytical spaces of algebraic schemes. Particularly, by the whole of affine structures on a pace, two necessary and sufficient conditions, that two spaces are homeomorphic and that two schemes are isomorphic, coming from the main theorems of the paper, are obtained respectively. A conclusion is drawn that the whole of affine structures on a space and a scheme, as local data, encode and reflect the global properties of the space and the scheme,respectively.

  20. Glycation of the high affinity NGF-receptor and RAGE leads to reduced ligand affinity.

    Science.gov (United States)

    Bennmann, Dorit; Kannicht, Christoph; Fisseau, Claudine; Jacobs, Kathleen; Navarette-Santos, Alexander; Hofmann, Britt; Horstkorte, Rüdiger

    2015-09-01

    AGEs are posttranslational modifications generated by irreversible non-enzymatic crosslinking reactions between sugars and proteins - a reaction referred to as glycation. Glycation, a feature of ageing, can lead to non-degradable and less functional proteins and enzymes and can additionally induce inflammation and further pathophysiological processes such as neurodegeneration. In this study we investigated the influence of glycation on the high affinity NGF-receptor TrkA and the AGE-receptor RAGE. We quantified the binding affinity of the TrkA-receptor and RAGE to their ligands by surface plasmon resonance (SPR) and compared these to the binding affinity after glycation. At the same time, we established a glycation procedure using SPR. We found that glycation of TrkA reduced the affinity to NGF by a factor of three, which could be shown to lead to a reduction of NGF-dependent neurite outgrowth in PC12 cells. Glycation of RAGE reduced binding affinity of AGEs by 10-fold.

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

    Science.gov (United States)

    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.

  2. Uniform Orientation of Biotinylated Nanobody as an Affinity Binder for Detection of Bacillus thuringiensis (Bt) Cry1Ac Toxin

    Science.gov (United States)

    Li, Min; Zhu, Min; Zhang, Cunzheng; Liu, Xianjin; Wan, Yakun

    2014-01-01

    Nanobodies are the smallest natural fragments with useful properties such as high affinity, distinct paratope and high stability, which make them an ideal tool for detecting target antigens. In this study, we generated and characterized nanobodies against the Cry1Ac toxin and applied them in a biotin-streptavidin based double antibodies (nanobodies) sandwich-ELISA (DAS-ELISA) assay. After immunizing a camel with soluble Cry1Ac toxin, a phage displayed library was constructed to generate Nbs against the Cry1Ac toxin. Through successive rounds of affinity bio-panning, four nanobodies with greatest diversity in CDR3 sequences were obtained. After affinity determination and conjugating to HRP, two nanobodies with high affinity which can recognize different epitopes of the same antigen (Cry1Ac) were selected as capture antibody (Nb61) and detection antibody (Nb44). The capture antibody (Nb61) was biotinylated in vivo for directional immobilization on wells coated with streptavidin matrix. Both results of specificity analysis and thermal stability determination add support for reliability of the following DAS-ELISA with a minimum detection limit of 0.005 μg·mL−1 and a working range 0.010–1.0 μg·mL−1. The linear curve displayed an acceptable correlation coefficient of 0.9976. These results indicated promising applications of nanobodies for detection of Cry1Ac toxin with biotin-streptavidin based DAS-ELISA system. PMID:25474492

  3. Uniform Orientation of Biotinylated Nanobody as an Affinity Binder for Detection of Bacillus thuringiensis (Bt Cry1Ac Toxin

    Directory of Open Access Journals (Sweden)

    Min Li

    2014-12-01

    Full Text Available Nanobodies are the smallest natural fragments with useful properties such as high affinity, distinct paratope and high stability, which make them an ideal tool for detecting target antigens. In this study, we generated and characterized nanobodies against the Cry1Ac toxin and applied them in a biotin-streptavidin based double antibodies (nanobodies sandwich-ELISA (DAS-ELISA assay. After immunizing a camel with soluble Cry1Ac toxin, a phage displayed library was constructed to generate Nbs against the Cry1Ac toxin. Through successive rounds of affinity bio-panning, four nanobodies with greatest diversity in CDR3 sequences were obtained. After affinity determination and conjugating to HRP, two nanobodies with high affinity which can recognize different epitopes of the same antigen (Cry1Ac were selected as capture antibody (Nb61 and detection antibody (Nb44. The capture antibody (Nb61 was biotinylated in vivo for directional immobilization on wells coated with streptavidin matrix. Both results of specificity analysis and thermal stability determination add support for reliability of the following DAS-ELISA with a minimum detection limit of 0.005 μg·mL−1 and a working range 0.010–1.0 μg·mL−1. The linear curve displayed an acceptable correlation coefficient of 0.9976. These results indicated promising applications of nanobodies for detection of Cry1Ac toxin with biotin-streptavidin based DAS-ELISA system.

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

    Science.gov (United States)

    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.

  5. Dimerization capacities of FGF2 purified with or without heparin-affinity chromatography.

    Directory of Open Access Journals (Sweden)

    Natalia Platonova

    Full Text Available Fibroblast growth factor-2 (FGF2 is a pleiotropic growth factor exhibiting a variety of biological activities. In this article, we studied the capacity of FGF2 purified with or without heparin affinity chromatography to self-associate. Analyzing the NMR HSQC spectra for different FGF2 concentrations, heparin-affinity purified FGF2 showed perturbations that indicate dimerization and are a higher-order oligomerization state. HSQC perturbation observed with different FGF2 concentrations revealed a heparin-binding site and two dimer interfaces. Thus, with increasing protein concentrations, FGF2 monomers make contacts with each other and form dimers or higher order oligomers. On the contrary, FGF2 purified with ion-exchange chromatography did not show similar perturbation indicating that self-association of FGF2 is eliminated if purification is done without heparin-affinity chromatography. The HSQC spectra of heparin-affinity purified FGF2 can be reproduced to some extent by adding heparin tetra-saccharide to ion exchange chromatography purified FGF2. Heparin-affinity purified FGF2 bound to acceptor and donor beads in a tagged form using His-tagged or GST-tagged proteins, also dimerized in the AlphaScreen™ assay. This assay was further validated using different experimental conditions and competitors. The assay constitutes an interesting tool to study dimerization of other FGF forms as well.

  6. A TCR affinity threshold regulates memory CD4 T cell differentiation following vaccination.

    Science.gov (United States)

    Baumgartner, Christina K; Yagita, Hideo; Malherbe, Laurent P

    2012-09-01

    Diverse Ag-specific memory TCR repertoires are essential for protection against pathogens. Subunit vaccines that combine peptide or protein Ags with TLR agonists are very potent at inducing T cell immune responses, but their capacity to elicit stable and diverse memory CD4 T cell repertoires has not been evaluated. In this study, we examined the evolution of a complex Ag-specific population during the transition from primary effectors to memory T cells after peptide or protein vaccination. Both vaccination regimens induced equally diverse effector CD4 TCR repertoires, but peptide vaccines skewed the memory CD4 TCR repertoire toward high-affinity clonotypes whereas protein vaccines maintained low-affinity clonotypes in the memory compartment. CD27-mediated signaling was essential for the maintenance of low-affinity clonotypes after protein vaccination but was not sufficient to promote their survival following peptide vaccination. The rapid culling of the TCR repertoire in peptide-immunized mice coincided with a prolonged proliferation phase during which low-affinity clonotypes disappeared despite exhibiting no sign of enhanced apoptosis. Our study reveals a novel affinity threshold for memory CD4 T cell differentiation following vaccination and suggests a role for nonapoptotic cell death in the regulation of CD4 T cell clonal selection.

  7. Optic capture pars plana lensectomy

    Directory of Open Access Journals (Sweden)

    Lee JE

    2012-10-01

    Full Text Available Joo Eun LeeDepartment of Ophthalmology, Inje University College of Medicine, Busan, South KoreaObjective: To describe an optic capture pars plana lensectomy technique.Methods: After core vitrectomy, pars plana lensectomy is performed with preservation of the anterior capsule. Capsulorhexis is performed on the preserved anterior capsule through a 2.8 mm clear corneal incision. An intraocular lens (IOL is placed in the ciliary sulcus, and then the optic of the IOL is pushed back to the vitreous cavity so that the optic is captured by the surrounding capsulorhexis margin.Results: The captured IOL-capsule diaphragm remained stable during air–fluid exchange and prevented air prolapse to the anterior chamber. IOL stability and a clear visual axis were preserved during the follow-up period.Conclusion: With this modified pars plana lensectomy technique, stable IOL position and clear visual axis can be maintained when a pars plana approach is needed during combined cataract and vitreoretinal surgery.Keywords: lensectomy, optic capture, pars plana lensectomy, vitrectomy

  8. Metric-affine gravitation theory and superpotentials

    Energy Technology Data Exchange (ETDEWEB)

    Giachetta, G.; Mangiarotti, L.; Saltarelli, A. [Camerino, Univ. (Italy). Dipt. di Matematica e Fisica

    1997-05-01

    They consider a metric-affine theory of gravity in which the dynamical fields are the Lorentzian metrics and the non-symmetric linear connections on the worked manifold X. Working with a Lagrangian density which is invariant under general covariant transformations and using standard tools of the calculus of variations, they study the corresponding currents. They find that the superpotential takes a nice form involving the torsion of the linear connection in a simple way and generalizing the well-known Komar superpotential. A feature of our approach is the use of the Poincare`-Cartan form in relation to the first variational formula of the calculus of variations.

  9. Affinity chromatography with an immobilized RNA enzyme.

    OpenAIRE

    Vioque, A; Altman, S

    1986-01-01

    M1 RNA, the catalytic subunit of Escherichia coli RNase P, has been covalently linked at its 3' terminus to agarose beads. Unlike M1 RNA, which is active in solution in the absence of the protein component (C5) of RNase P, the RNA linked to the beads is active only in the presence of C5 protein. Affinity chromatography of crude extracts of E. coli on a column prepared from the beads to which the RNA has been crosslinked results in the purification of C5 protein in a single step. The protein h...

  10. Analysis of affinely equivalent Boolean functions

    Institute of Scientific and Technical Information of China (English)

    MENG QingShu; ZHANG HuanGuo; YANG Min; WANG ZhangYi

    2007-01-01

    By some basic transforms and invariant theory, we give two results: 1) an algorithm,which can be used to judge if two Boolean functions are affinely equivalent and to obtain the equivalence relationship if they are equivalent. This is useful in studying Boolean functions and in engineering. For example, we classify all 8-variable homogeneous bent functions of degree 3 into two classes; 2) Reed-Muller codes R(4,6)/R(1,6), R(3,7)/R(1,7) are classified efficiently.

  11. Affine Coherent States in Quantum Cosmology

    CERN Document Server

    Malkiewicz, Przemyslaw

    2015-01-01

    A brief summary of the application of coherent states in the examination of quantum dynamics of cosmological models is given. We discuss quantization maps, phase space probability distributions and semiclassical phase spaces. The implementation of coherent states based on the affine group resolves the hardest singularities, renders self-adjoint Hamiltonians without boundary conditions and provides a completely consistent semi-classical description of the involved quantum dynamics. We consider three examples: the closed Friedmann model, the anisotropic Bianchi Type I model and the deep quantum domain of the Bianchi Type IX model.

  12. Latest European coelacanth shows Gondwanan affinities.

    Science.gov (United States)

    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.

  13. Non-Statistical Effects in Neutron Capture

    Science.gov (United States)

    Koehler, P. E.; Bredeweg, T. A.; Guber, K. H.; Harvey, J. A.; O'Donnell, J. M.; Reifarth, R.; Rundberg, R. S.; Ullmann, J. L.; Vieira, D. J.; Wiarda, D.; Wouters, J. M.

    2009-01-01

    There have been many reports of non-statistical effects in neutron-capture measurements. However, reports of deviations of reduced-neutron-width (Γn0) distributions from the expected Porter-Thomas (PT) shape largely have been ignored. Most of these deviations have been reported for odd-A nuclides. Because reliable spin (J) assignments have been absent for most resonances for such nuclides, it is possible that reported deviations from PT might be due to incorrect J assignments. We recently developed a new method for measuring spins of neutron resonances by using the DANCE detector at the Los Alamos Neutron Science Center (LANSCE). Measurements made with a 147Sm sample allowed us to determine spins of almost all known resonances below 1 keV. Furthermore, analysis of these data revealed that the Γn0 distribution was in good agreement with PT for resonances below 350 eV, but in disagreement with PT for resonances between 350 and 700 eV. Our previous (n,α) measurements had revealed that the α strength function also changes abruptly at this energy. There currently is no known explanation for these two non-statistical effects. Recently, we have developed another new method for determining the spins of neutron resonances. To implement this technique required a small change (to record pulse-height information for coincidence events) to a much simpler apparatus: A pair of C6D6 γ-ray detectors which we have employed for many years to measure neutron-capture cross sections at the Oak Ridge Electron Linear Accelerator (ORELA). Measurements with a 95Mo sample revealed that not only does the method work very well for determining spins, but it also makes possible parity assignments. Taken together, these new techniques at LANSCE and ORELA could be very useful for further elucidation of non-statistical effects.

  14. Affine Fullerene C60 in a GS-Quasigroup

    Directory of Open Access Journals (Sweden)

    Vladimir Volenec

    2014-01-01

    Full Text Available It will be shown that the affine fullerene C60, which is defined as an affine image of buckminsterfullerene C60, can be obtained only by means of the golden section. The concept of the affine fullerene C60 will be constructed in a general GS-quasigroup using the statements about the relationships between affine regular pentagons and affine regular hexagons. The geometrical interpretation of all discovered relations in a general GS-quasigroup will be given in the GS-quasigroup C(1/2(1+5.

  15. 49 CFR 563.9 - Data capture.

    Science.gov (United States)

    2010-10-01

    ... frontal or side air bag deployment crash, capture and record the current deployment data, up to two events... 49 Transportation 6 2010-10-01 2010-10-01 false Data capture. 563.9 Section 563.9 Transportation..., DEPARTMENT OF TRANSPORTATION EVENT DATA RECORDERS § 563.9 Data capture. The EDR must capture and record...

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

    Science.gov (United States)

    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.

  17. Ambiguity Revealed

    OpenAIRE

    Subir Bose; Matthew Polisson; Ludovic Renou

    2012-01-01

    We derive necessary and suffcient conditions for data sets composed of state-contingent prices and consumption to be consistent with two prominent models of decision making under ambiguity: variational preferences and smooth ambiguity. The revealed preference conditions for the maxmin expected utility and subjective expected utility models are characterized as special cases.

  18. Ambiguity revealed

    OpenAIRE

    Bayer, Ralph-C; Bose, Subir; Polisson, Matthew; Renou, Ludovic

    2013-01-01

    We derive necessary and sufficient conditions for data sets composed of state-contingent prices and consumption to be consistent with two prominent models of decision making under uncertainty: variational preferences and smooth ambiguity. The revealed preference conditions for subjective expected utility, maxmin expected utility, and multiplier preferences are characterised as special cases. We implement our tests on data from a portfolio choice experiment.

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

    Science.gov (United States)

    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.

  20. Spherical functions on affine Lie groups

    CERN Document Server

    Etingof, P; Kirillov, A A; Pavel Etingof; Igor Frenkel; Alexander Kirillov Jr

    1994-01-01

    We show that the space of holomorphic functions of a fixed degree on an affine Lie group which take values in a finite-dimensional representation of this group and are equivariant with respect to (twisted) conjugacy coin- cides with the space of conformal blocks of the Wess-Zumino-Witten conformal field theory on an elliptic curve with punctures, or, equivalently,with the space of states of the Chern-Simons topological field theory in genus 1. This provides a group-theoretic realization of the Segal modular functor for elliptic curves. We also show that the the radial part of the second order Laplace operator on an affine Lie group acting in the space of equivariant functions coincides with the operator defining the Knizhnik-Zamolodchikov connection on conformal blocks on elliptic curves, and its eigenfunctions coincide with the correlation functions of conformal blocks. At the critical value of the degree (minus the dual Coxeter number of the underlying simple Lie algebra) there exist higher order Laplace op...

  1. Affine Mirkovi\\'c-Vilonen polytopes

    CERN Document Server

    Baumann, Pierre; Tingley, Peter

    2011-01-01

    Each integrable lowest weight representation of a symmetrizable Kac-Moody Lie algebra g has a crystal in the sense of Kashiwara, which describes its combinatorial properties. For a given g, there is a limit crystal, usually denoted by B(-\\infty), which contains all the other crystals. When g is finite dimensional, a convex polytope, called the Mirkovi\\'c-Vilonen polytope, can be associated to each element in B(-\\infty). This polytope sits in the dual space of a Cartan subalgebra of g, and its edges are parallel to the roots of g. In this paper, we generalize this construction to the case where g is a symmetric affine Kac-Moody algebra. The datum of the polytope must however be complemented by partitions attached to the edges parallel to the imaginary root \\delta. We prove that these decorated polytopes are characterized by conditions on their normal fans and on their 2-faces. In addition, we discuss how our polytopes provide an analog of the notion of Lusztig datum for affine Kac-Moody algebras. Our main tool...

  2. Affine conformal vectors in space-time

    Science.gov (United States)

    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.

  3. Cyclage, catabolism, and the affine Hecke algebra

    CERN Document Server

    Blasiak, Jonah

    2010-01-01

    We identify a subalgebra \\pH_n of the extended affine Hecke algebra \\eH_n of type A. The subalgebra \\pH_n is a \\u-analogue of the monoid algebra of \\S_n \\ltimes \\ZZ_{\\geq 0}^n and inherits a canonical basis from that of \\eH_n. We show that its left cells are naturally labeled by tableaux filled with positive integer entries having distinct residues mod n, which we term \\emph{positive affine tableaux} (PAT). We then exhibit a cellular subquotient \\R_{1^n} of \\pH_n that is a \\u-analogue of the ring of coinvariants \\CC[y_1,...,y_n]/(e_1,...,e_n) with left cells labeled by PAT that are essentially standard Young tableaux with cocharge labels. Multiplying canonical basis elements by a certain element \\pi \\in \\pH_n corresponds to rotations of words, and on cells corresponds to cocyclage. We further show that \\R_{1^n} has cellular quotients \\R_\\lambda that are \\u-analogues of the Garsia-Procesi modules R_\\lambda with left cells labeled by (a PAT version of) the \\lambda-catabolizable tableaux. We give a conjectural d...

  4. Focusing of the Flow Capture for Local Exhaust Ventilation Systems

    Directory of Open Access Journals (Sweden)

    S. Y. Spotar

    2010-01-01

    Full Text Available Problem statement: The extraction hoods commonly used as inlet element of the local ventilation systems exhibit limited emission capture over moderate distances from the source of the hazardous emissions. Proposed inclusion of a swirling peripheral jet was found to increase the effective length over which the extraction hood successfully captures harmful fumes. However information on a detailed pattern field of the vortex focused inflow was insufficient thus restricting the potential applications of the method. Approach: The numerical modeling study of the focusing by vortex inflow was accomplished to reveal the implication of the key operating parameters. In addition the visualization technique was applied to confirm the fume capturing features. Results: The simulated overall flow field patterns for an inflow of 10 m sec-1 value under sets of 0.5-1.5 swirl numbers and 0- 21 m sec-1 outcome velocities of peripheral jet showed the arrangement and contour of the capture stream. Under optimum parameters the capture zone derived from the vector velocity field yielded up to 4 inlet diameters near-axis distance from the extractor entrance. The complimentary observations using laser sheet visualization technique confirmed the enhanced capturing capacity from the mist or smoke sources of emission. Conclusion: Through numerical modeling study the capacity of peripheral vortex shielding to generate the more concentrated exhaust inflow comparing with action of the conventional hood has been elucidated.

  5. Affinity is an important determinant of the anti-trypanosome activity of nanobodies.

    Directory of Open Access Journals (Sweden)

    Guy Caljon

    Full Text Available BACKGROUND: The discovery of Nanobodies (Nbs with a direct toxic activity against African trypanosomes is a recent advancement towards a new strategy against these extracellular parasites. The anti-trypanosomal activity relies on perturbing the highly active recycling of the Variant-specific Surface Glycoprotein (VSG that occurs in the parasite's flagellar pocket. METHODOLOGY/PRINCIPAL FINDINGS: Here we expand the existing panel of Nbs with anti-Trypanosoma brucei potential and identify four categories based on their epitope specificity. We modified the binding properties of previously identified Nanobodies Nb_An05 and Nb_An33 by site-directed mutagenesis in the paratope and found this to strongly affect trypanotoxicity despite retention of antigen-targeting properties. Affinity measurements for all identified anti-trypanosomal Nbs reveal a strong correlation between trypanotoxicity and affinity (K(D, suggesting that it is a crucial determinant for this activity. Half maximal effective (50% affinity of 57 nM was calculated from the non-linear dose-response curves. In line with these observations, Nb humanizing mutations only preserved the trypanotoxic activity if the K(D remained unaffected. CONCLUSIONS/SIGNIFICANCE: This study reveals that the binding properties of Nanobodies need to be compatible with achieving an occupancy of >95% saturation of the parasite surface VSG in order to exert an anti-trypanosomal activity. As such, Nb-based approaches directed against the VSG target would require binding to an accessible, conserved epitope with high affinity.

  6. Preparation and characterization of polysulfone affinity membranes bearing a synthetic peptide ligand for the separation of murine immunoglobulins.

    Science.gov (United States)

    Boi, Cristiana; Algeri, Cristian; Sarti, Giulio C

    2008-01-01

    Affinity membranes have been prepared by immobilizing D-PAM, a synthetic ligand that exhibits affinity for the Fc portion of antibodies, onto poliethersulfone microporous membranes. The ligand density has been measured and the ligand utilization was evaluated and compared with literature data available for chromatographic beads. The resulting new affinity membranes have been experimentally characterized and tested by using pure murine IgG solutions and mouse serum. Equilibrium and kinetic parameters have been obtained in batch experiments using pure protein solutions. The highest binding capacity measured for murine IgG was 45 microg/cm(2) obtained at 1.2 mg/mL protein concentration at equilibrium, while the maximum static binding capacity calculated with the Langmuir model was 81 microg/cm(2). The adsorption of murine IgG on the affinity membranes was described using different isotherms: Freundlich and Temkin models have been considered and critically compared with the Langmuir adsorption model. A dynamic binding capacity of 21 microg/cm(2) was obtained by feeding a solution of 0.3 mg/mL of murine IgG, confirming the results obtained in batch experiments at the same concentration. The affinity membranes considered are endowed with good binding capacity for murine IgG and good selectivity for immunoglobulins and can be considered for the capturing step of an antibody production process.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Natural materials for carbon capture.

    Energy Technology Data Exchange (ETDEWEB)

    Myshakin, Evgeniy M. (National Energy Technology Laboratory, Pittsburgh, PA); Romanov, Vyacheslav N. (National Energy Technology Laboratory, Pittsburgh, PA); Cygan, Randall Timothy

    2010-11-01

    Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, carbon dioxide. Recent experimental studies have demonstrated the efficacy of intercalating carbon dioxide in the interlayer of layered clays but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 in the interlayer of montmorillonite clay and to help validate the models with experimental observation.

  10. Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine.

    Science.gov (United States)

    Golabi, Mohsen; Padiolleau, Laurence; Chen, Xi; Jafari, Mohammad Javad; Sheikhzadeh, Elham; Turner, Anthony P F; Jager, Edwin W H; Beni, Valerio

    2016-01-01

    Here we demonstrate the use of a functional dopant as a fast and simple way to tune the chemical affinity and selectivity of polypyrrole films. More specifically, a boronic-functionalised dopant, 4-N-Pentylphenylboronic Acid (PBA), was used to provide to polypyrrole films with enhanced affinity towards diols. In order to prove the proposed concept, two model systems were explored: (i) the capture and the electrochemical detection of dopamine and (ii) the adhesion of bacteria onto surfaces. The chemisensor, based on overoxidised polypyrrole boronic doped film, was shown to have the ability to capture and retain dopamine, thus improving its detection; furthermore the chemisensor showed better sensitivity in comparison with overoxidised perchlorate doped films. The adhesion of bacteria, Deinococcus proteolyticus, Escherichia coli, Streptococcus pneumoniae and Klebsiella pneumoniae, onto the boric doped polypyrrole film was also tested. The presence of the boronic group in the polypyrrole film was shown to favour the adhesion of sugar-rich bacterial cells when compared with a control film (Dodecyl benzenesulfonate (DBS) doped film) with similar morphological and physical properties. The presented single step synthesis approach is simple and fast, does not require the development and synthesis of functional monomers, and can be easily expanded to the electrochemical, and possibly chemical, fabrication of novel functional surfaces and interfaces with inherent pre-defined sensing and chemical properties.

  11. Carbon Capture and Sequestration (CCS)

    Science.gov (United States)

    2009-06-19

    for the pre-combustion capture of CO2 is the use of Integrated Gasification Combined-Cycle ( IGCC ) technology to generate electricity.14 There are...currently four commercial IGCC plants worldwide (two in the United States) each with a capacity of about 250 MW. The technology has yet to make a major... IGCC is an electric generating technology in which pulverized coal is not burned directly but mixed with oxygen and water in a high-pressure gasifier

  12. Affinity mesh screen materials for selective extraction and analysis of antibiotics using transmission mode desorption electrospray ionization mass spectrometry.

    Science.gov (United States)

    Yang, Samuel H; Wang, Evelyn H; Gurak, John A; Bhawal, Sumit; Deshmukh, Rajendrasing; Wijeratne, Aruna B; Edwards, Brian L; Foss, Frank W; Timmons, Richard B; Schug, Kevin A

    2013-06-25

    The extraction of active compounds from natural sources has shown to be an effective approach to drug discovery. However, the isolation and identification of natural products from complex extracts can be an arduous task. A novel approach to drug discovery is presented through the use of polymer screens functionalized with an l-lysine-d-alanine-d-alanine (Kaa) peptide to create new affinity capture mesh screen materials. The Kaa sequence is a well-characterized specific binding site for antibiotics that inhibit cell wall synthesis in Gram-positive bacteria. The detailed synthesis and characterization of these novel screen materials are presented in this work. Polypropylene mesh screens were first coated with a poly(acrylic acid) film by pulsed plasma polymerization. The synthesized Kaa peptide was then covalently attached to carboxylic acid groups through a condensation reaction. An analysis of captured compounds was performed in a rapid fashion with transmission-mode desorption electrospray ionization (TM-DESI) mass spectrometry. A proof of principle was demonstrated to show the ability of the novel affinity capture materials to select for a macrocyclic antibiotic, vancomycin, over a negative control compound, spectinomycin. With further development, this method may provide a rapid screening technique for new antibacterial compounds, for example, those extracted from natural product sources having a limited supply. Here, we show that the screen can capture vancomycin preferentially over spectinomycin in a spiked extract of tea leaves.

  13. 'The Strange Case of Angelica': affinity between Fantastic and Documental

    Directory of Open Access Journals (Sweden)

    Rita Benis

    2017-01-01

    Full Text Available In 2010, Manoel de Oliveira films The Strange Case of Angélica, a project from the early fifties of the past century. In it, the confrontation between the documentary side of the film (the sequences where the protagonist, Isaac, photographs the workers in the vineyards and the fantastic sequences (the episodes with the ghost of Angelica seems to indicate an affinity. That "shadow of resemblance" Petrarch spoke about to his close friend Giovanni Boccaccio: "... he who imitates must proceed in such a way that what he does is similar but not equal, and that the likeness is not that which exists between the original and the copy, that the more similar the more it is praiseworthy, but instead a likeness which one finds in the similarities between a father and a son, among which, though much difference is made in the aspect, there is, however, as a shadow of resemblance, which the painters call 'aire' (... "(apud Rodrigues 2003: 5. A "family air" as a living correlation that comes to our encounter and which is felt as an immediate understanding (and not as definable evidence. In the film, the shiver that assaults us through the apparition of Angelica seems to announce something that goes beyond this same vision: the eminence of the disappearance of the vineyard workers and their gestures, a loss of connection between Man and Nature. The present affinity - Angelica / diggers - is mirrored in Isaac's immense melancholy, the only person apparently capable of perceiving the landscape, the "air" that this relationship evokes. The whole film is crossed by the glimpse of this indefinable kinship, by the porosity between the sensitive world and the spectral world, the permanent interweaving of visibilities / invisibilities that allow us access to this other cinematographic space-time, more percept than visible, in which, according to Manoel de Oliveira, the phantom of physical reality reveals itself "more real, however, than reality itself" (Baecque and

  14. Development and characterization of high affinity leptins and leptin antagonists.

    Science.gov (United States)

    Shpilman, Michal; Niv-Spector, Leonora; Katz, Meirav; Varol, Chen; Solomon, Gili; Ayalon-Soffer, Michal; Boder, Eric; Halpern, Zamir; Elinav, Eran; Gertler, Arieh

    2011-02-11

    Leptin is a pleiotropic hormone acting both centrally and peripherally. It participates in a variety of biological processes, including energy metabolism, reproduction, and modulation of the immune response. So far, structural elements affecting leptin binding to its receptor remain unknown. We employed random mutagenesis of leptin, followed by selection of high affinity mutants by yeast surface display and discovered that replacing residue Asp-23 with a non-negatively charged amino acid leads to dramatically enhanced affinity of leptin for its soluble receptor. Rational mutagenesis of Asp-23 revealed the D23L substitution to be most effective. Coupling the Asp-23 mutation with alanine mutagenesis of three amino acids (L39A/D40A/F41A) previously reported to convert leptin into antagonist resulted in potent antagonistic activity. These novel superactive mouse and human leptin antagonists (D23L/L39A/D40A/F41A), termed SMLA and SHLA, respectively, exhibited over 60-fold increased binding to leptin receptor and 14-fold higher antagonistic activity in vitro relative to the L39A/D40A/F41A mutants. To prolong and enhance in vivo activity, SMLA and SHLA were monopegylated mainly at the N terminus. Administration of the pegylated SMLA to mice resulted in a remarkably rapid, significant, and reversible 27-fold more potent increase in body weight (as compared with pegylated mouse leptin antagonist), because of increased food consumption. Thus, recognition and mutagenesis of Asp-23 enabled construction of novel compounds that induce potent and reversible central and peripheral leptin deficiency. In addition to enhancing our understanding of leptin interactions with its receptor, these antagonists enable in vivo study of the role of leptin in metabolic and immune processes and hold potential for future therapeutic use in disease pathologies involving leptin.

  15. Development and Characterization of High Affinity Leptins and Leptin Antagonists*

    Science.gov (United States)

    Shpilman, Michal; Niv-Spector, Leonora; Katz, Meirav; Varol, Chen; Solomon, Gili; Ayalon-Soffer, Michal; Boder, Eric; Halpern, Zamir; Elinav, Eran; Gertler, Arieh

    2011-01-01

    Leptin is a pleiotropic hormone acting both centrally and peripherally. It participates in a variety of biological processes, including energy metabolism, reproduction, and modulation of the immune response. So far, structural elements affecting leptin binding to its receptor remain unknown. We employed random mutagenesis of leptin, followed by selection of high affinity mutants by yeast surface display and discovered that replacing residue Asp-23 with a non-negatively charged amino acid leads to dramatically enhanced affinity of leptin for its soluble receptor. Rational mutagenesis of Asp-23 revealed the D23L substitution to be most effective. Coupling the Asp-23 mutation with alanine mutagenesis of three amino acids (L39A/D40A/F41A) previously reported to convert leptin into antagonist resulted in potent antagonistic activity. These novel superactive mouse and human leptin antagonists (D23L/L39A/D40A/F41A), termed SMLA and SHLA, respectively, exhibited over 60-fold increased binding to leptin receptor and 14-fold higher antagonistic activity in vitro relative to the L39A/D40A/F41A mutants. To prolong and enhance in vivo activity, SMLA and SHLA were monopegylated mainly at the N terminus. Administration of the pegylated SMLA to mice resulted in a remarkably rapid, significant, and reversible 27-fold more potent increase in body weight (as compared with pegylated mouse leptin antagonist), because of increased food consumption. Thus, recognition and mutagenesis of Asp-23 enabled construction of novel compounds that induce potent and reversible central and peripheral leptin deficiency. In addition to enhancing our understanding of leptin interactions with its receptor, these antagonists enable in vivo study of the role of leptin in metabolic and immune processes and hold potential for future therapeutic use in disease pathologies involving leptin. PMID:21119198

  16. Reactive control of zoom while fixating using perspective and affine cameras.

    Science.gov (United States)

    Tordoff, Ben; Murray, David

    2004-01-01

    This paper describes reactive visual methods of controlling the zoom setting of the lens of an active camera while fixating upon an object. The first method assumes a perspective projection and adjusts zoom to preserve the ratio of focal length to scene depth. The active camera is constrained to rotate, permitting self-calibration from the image motion of points on the static background. A planar structure from motion algorithm is used to recover the depth of the foreground. The foreground-background segmentation exploits the properties of the two different interimage homographies which are observed. The fixation point is updated by transfer via the observed planar structure. The planar method is shown to work on real imagery, but results from simulated data suggest that its extension to general 3D structure is problematical under realistic viewing and noise regimes. The second method assumes an affine projection. It requires no self-calibration and the zooming camera may move generally. Fixation is again updated using transfer, but now via the affine structure recovered by factorization. Analysis of the projection matrices allows the relative scale of the affine bases in different views to be found in a number of ways and, hence, controlled to unity. The various ways are compared and the best used on real imagery captured from an active camera fitted with a controllable zoom lens in both look-move and continuous operation.

  17. Understanding ligand-protein interactions in affinity membrane chromatography for antibody purification.

    Science.gov (United States)

    Boi, Cristiana; Busini, Valentina; Salvalaglio, Matteo; Cavallotti, Carlo; Sarti, Giulio C

    2009-12-11

    Affinity chromatography with Protein A beads has become the conventional unit operation for the primary capture of monoclonal antibodies. However, Protein A activated supports are expensive and ligand leakage is an issue to be considered. In addition, the limited production capabilities of the chromatographic process drive the research towards feasible alternatives. The use of synthetic ligands as Protein A substitutes has been considered in this work. Synthetic ligands, that mimic the interaction between Protein A and the constant fragment (Fc) of immunoglobulins, have been immobilized on cellulosic membrane supports. The resulting affinity membranes have been experimentally characterized with pure immunoglobulin G (IgG). The effects of the membrane support and of the spacer arm on the ligand-ligate interaction have been studied in detail. Experimental data have been compared with molecular dynamic simulations with the aim of better understanding the interaction mechanisms. Molecular dynamic simulations were performed in explicit water, modelling the membrane as a matrix of overlapped glucopyranose units. Electrostatic charges of the ligand and spacer were calculated through ab initio methods to complete the force field used to model the membrane. The simulations enabled to elucidate how the interactions of surface, spacer and ligand with IgG, contribute to the formation of the bond between protein and affinity membrane.

  18. Spectromicroscopy in Boron Neutron Capture Therapy Research

    Science.gov (United States)

    Gilbert, Benjamin; Redondo, Jose; Andres, Roger; Suda, Takashi; Neumann, Michael; Steen, Steffi; Gabel, Detlef; Mercanti, Delio; Ciotti, Teresa; Perfetti, Paolo; Margaritondo, Giorgio; de Stasio, Gelsomina

    1998-03-01

    The MEPHISTO synchrotron imaging spectromicroscope can analyse ashed cells or tissue sections to reveal the microdistribution of trace elements. MEPHISTO performs core level x-ray absorption spectroscopy with synchrotron radiation, and uses an electron optics system to provide magnified photoelectron images. An application of the MEPHISTO spectromicroscope is in boron neutron capture therapy (BNCT). BNCT is a binary cancer therapy that will selectively destroy cancer cells provided that compounds containing a boron isotope are selectively accumulated in tumor tissue. Important factors for the success of BNCT include the ability to target every cancer cell, and the distribution of boron inside the cell. To investigate the boron distribution in tissue, sections of human glioblastoma containing a BNCT compound, and stained with nickel against a protein found in the nuclei of proliferating (cancer) cells, were studied with MEPHISTO.

  19. The mechanism of selective molecular capture in carbon nanotube networks.

    Science.gov (United States)

    Wan, Yu; Guan, Jun; Yang, Xudong; Zheng, Quanshui; Xu, Zhiping

    2014-07-28

    Recently, air pollution issues have drawn significant attention to the development of efficient air filters, and one of the most promising materials for this purpose is nanofibers. We explore here the mechanism of selective molecular capture of volatile organic compounds in carbon nanotube networks by performing atomistic simulations. The results are discussed with respect to the two key parameters that define the performance of nanofiltration, i.e. the capture efficiency and flow resistance, which demonstrate the advantages of carbon nanotube networks with high surface-to-volume ratio and atomistically smooth surfaces. We also reveal the important roles of interfacial adhesion and diffusion that govern selective gas transport through the network.

  20. Mercury capture by selected Bulgarian fly ashes: Influence of coal rank and fly ash carbon pore structure on capture efficiency

    Science.gov (United States)

    Kostova, I.J.; Hower, J.C.; Mastalerz, Maria; Vassilev, S.V.

    2011-01-01

    Mercury capture by fly ash C was investigated at five lignite- and subbituminous-coal-burning Bulgarian power plants (Republika, Bobov Dol, Maritza East 2, Maritza East 3, and Sliven). Although the C content of the ashes is low, never exceeding 1.6%, the Hg capture on a unit C basis demonstrates that the low-rank-coal-derived fly ash carbons are more efficient in capturing Hg than fly ash carbons from bituminous-fired power plants. While some low-C and low-Hg fly ashes do not reveal any trends of Hg versus C, the 2nd and, in particular, the 3rd electrostatic precipitator (ESP) rows at the Republika power plant do have sufficient fly ash C range and experience flue gas sufficiently cool to capture measurable amounts of Hg. The Republika 3rd ESP row exhibits an increase in Hg with increasing C, as observed in other power plants, for example, in Kentucky power plants burning Appalachian-sourced bituminous coals. Mercury/C decreases with an increase in fly ash C, suggesting that some of the C is isolated from the flue gas stream and does not contribute to Hg capture. Mercury capture increases with an increase in Brunauer-Emmett-Teller (BET) surface area and micropore surface area. The differences in Hg capture between the Bulgarian plants burning low-rank coal and high volatile bituminous-fed Kentucky power plants suggests that the variations in C forms resulting from the combustion of the different ranks also influence the efficiency of Hg capture. ?? 2010 Elsevier Ltd.

  1. Data Stream Clustering With Affinity Propagation

    KAUST Repository

    Zhang, Xiangliang

    2014-07-09

    Data stream clustering provides insights into the underlying patterns of data flows. This paper focuses on selecting the best representatives from clusters of streaming data. There are two main challenges: how to cluster with the best representatives and how to handle the evolving patterns that are important characteristics of streaming data with dynamic distributions. We employ the Affinity Propagation (AP) algorithm presented in 2007 by Frey and Dueck for the first challenge, as it offers good guarantees of clustering optimality for selecting exemplars. The second challenging problem is solved by change detection. The presented StrAP algorithm combines AP with a statistical change point detection test; the clustering model is rebuilt whenever the test detects a change in the underlying data distribution. Besides the validation on two benchmark data sets, the presented algorithm is validated on a real-world application, monitoring the data flow of jobs submitted to the EGEE grid.

  2. Affine and Projective Tree Metric Theorems

    CERN Document Server

    Harel, Matan; Pachter, Lior

    2011-01-01

    The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived from circular split systems (Kalmanson metrics). The tree metric theorem was first discovered in the context of phylogenetics and forms the basis of many tree reconstruction algorithms, whereas Kalmanson metrics were first considered by computer scientists, and are notable in that they are a non-trivial class of metrics for which the traveling salesman problem is tractable. We present a unifying framework for these theorems based on combinatorial structures that are used for graph planarity testing. These are (projective) PC-trees, and their affine analogs, PQ-trees. In the projective case, we generalize a number of concepts from clustering theory, including hierarchies, pyramids, ultrametrics and Robinsonian matrices, and the theorems that relate them. As with tree metric...

  3. Gravitational Goldstone fields from affine gauge theory

    CERN Document Server

    Tresguerres, R

    2000-01-01

    In order to facilitate the application of standard renormalization techniques, gravitation should be decribed, if possible, in pure connection formalism, as a Yang-Mills theory of a certain spacetime group, say the Poincare or the affine group. This embodies the translational as well as the linear connection. However, the coframe is not the standard Yang-Mills type gauge field of the translations, since it lacks the inhomogeneous gradient term in the gauge transformations. By explicitly restoring the "hidden" piece responsible for this behavior within the framework of nonlinear realizations, the usual geometrical interpretation of the dynamical theory becomes possible, and in addition one can avoid the metric or coframe degeneracy which would otherwise interfere with the integrations within the path integral. We claim that nonlinear realizations provide a general mathematical scheme clarifying the foundations of gauge theories of spacetime symmetries. When applied to construct the Yang-Mills theory of the aff...

  4. Automatic gesture analysis using constant affine velocity.

    Science.gov (United States)

    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.

  5. Affine trajectory correction for nonholonomic mobile robots

    CERN Document Server

    Pham, Quang-Cuong

    2011-01-01

    Planning trajectories for nonholonomic systems is difficult and computationally expensive. When facing unexpected events, it may therefore be preferable to deform in some way the initially planned trajectory rather than to re-plan entirely a new one. We suggest here a method based on affine transformations to make such deformations. This method is exact and fast: the deformations and the resulting trajectories can be computed algebraically, in one step, and without any trajectory re-integration. To demonstrate the possibilities offered by this new method, we use it to derive position correction, orientation correction, obstacle avoidance and feedback control algorithms for the general class of planar wheeled robots and for a tridimensional underwater vehicle.

  6. Self-affinity and nonextensivity of sunspots

    Energy Technology Data Exchange (ETDEWEB)

    Moret, M.A., E-mail: mamoret@gmail.com [Programa de Modelagem Computacional, SENAI, Cimatec, Av. Orlando Gomes, 1845, Piatã, 41650-010 Salvador, Bahia (Brazil); UNEB, Rua Silveira Martins, 2555, Cabula, 41150-000 Salvador, Bahia (Brazil)

    2014-01-24

    In this paper we study the time series of sunspots by using two different approaches, analyzing its self-affine behavior and studying its distribution. The long-range correlation exponent α has been calculated via Detrended Fluctuation Analysis and the power law vanishes to values greater than 11 years. On the other hand, the distribution of the sunspots obeys a q-exponential decay that suggests a non-extensive behavior. This observed characteristic seems to take an alternative interpretation of the sunspots dynamics. The present findings suggest us to propose a dynamic model of sunspots formation based on a nonlinear Fokker–Planck equation. Therefore its dynamic process follows the generalized thermostatistical formalism.

  7. Affine connection form of Regge calculus

    CERN Document Server

    Khatsymovsky, V M

    2015-01-01

    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 3-simplices which play a 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...

  8. New rht-Type Metal-Organic Frameworks Decorated with Acylamide Groups for Efficient Carbon Dioxide Capture and Chemical Fixation from Raw Power Plant Flue Gas.

    Science.gov (United States)

    Guo, Xiangyang; Zhou, Zhen; Chen, Cong; Bai, Junfeng; He, Cheng; Duan, Chunying

    2016-11-23

    The combination of carbon dioxide capture and chemical fixation in a one-pot process is attractive for both chemists and governments. The cycloaddition of carbon dioxide with epoxides to produce cyclic carbonates is an atomic economical reaction without any side products. By incorporating acylamide to enhance the binding affinity toward CO2, new rht-type metal-organic frameworks (MOFs) with (3, 28) and (3, 24) connected units were constructed. Zn-NTTA with two types of dinuclear paddlewheel building blocks-{Zn2(OOC(-))4} and {Zn2(OOC(-))3}. The high uptake of CO2 (115.6 cm(3)·g(-1)) and selectivity over N2 (30:1) at 273 K indicated that these MOFs are excellent candidates for postcombustion CO2 isolation and capture. The MOFs feature high catalytic activity, rapid dynamics of transformation and excellent stability with turnover number (TON) values up to 110 000 per paddlewheel unit after 5 × 6 rounds of recyclability, demonstrating that they are promising heterogeneous catalysts for CO2 cyclo-addition to value-added cyclic carbonates. The cycloaddition of epoxides with wet gases demonstrated that the catalyst activity was not affected by moisture, and the indices of the PXRD patterns of the bulk samples filtered from the catalytic reaction revealed that the crystallinities were maintained. The combination of the selective capture and catalytic transformation in one-pot enables the use of a negative-cost feedstock-raw power plant flue gas without any separation and purification-revealing the broad prospects of such MOFs for practical CO2 fixation in industry.

  9. Indefinite Affine Hyperspheres Admitting a Pointwise Symmetry. Part 2

    Directory of Open Access Journals (Sweden)

    Christine Scharlach

    2009-10-01

    Full Text Available An affine hypersurface M is said to admit a pointwise symmetry, if there exists a subgroup G of Aut(T_pM for all p in M, which preserves (pointwise the affine metric h, the difference tensor K and the affine shape operator S. Here, we consider 3-dimensional indefinite affine hyperspheres, i.e. S = HId (and thus S is trivially preserved. In Part 1 we found the possible symmetry groups G and gave for each G a canonical form of K. We started a classification by showing that hyperspheres admitting a pointwise Z_2 × Z_2 resp. R-symmetry are well-known, they have constant sectional curvature and Pick invariant J < 0 resp. J = 0. Here, we continue with affine hyperspheres admitting a pointwise Z_3- or SO(2-symmetry. They turn out to be warped products of affine spheres (Z_3 or quadrics (SO(2 with a curve.

  10. Classical affine W-algebras associated to Lie superalgebras

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Uhi Rinn, E-mail: uhrisu1@math.snu.ac.kr [Department of Mathematical Sciences, Seoul National University, GwanAkRo 1, Gwanak-Gu, Seoul 151-747 (Korea, Republic of)

    2016-02-15

    In this paper, we prove classical affine W-algebras associated to Lie superalgebras (W-superalgebras), which can be constructed in two different ways: via affine classical Hamiltonian reductions and via taking quasi-classical limits of quantum affine W-superalgebras. Also, we show that a classical finite W-superalgebra can be obtained by a Zhu algebra of a classical affine W-superalgebra. Using the definition by Hamiltonian reductions, we find free generators of a classical W-superalgebra associated to a minimal nilpotent. Moreover, we compute generators of the classical W-algebra associated to spo(2|3) and its principal nilpotent. In the last part of this paper, we introduce a generalization of classical affine W-superalgebras called classical affine fractional W-superalgebras. We show these have Poisson vertex algebra structures and find generators of a fractional W-superalgebra associated to a minimal nilpotent.

  11. Boronophenylalanine, a boron delivery agent for boron neutron capture therapy, is transported by ATB0,+, LAT1 and LAT2.

    Science.gov (United States)

    Wongthai, Printip; Hagiwara, Kohei; Miyoshi, Yurika; Wiriyasermkul, Pattama; Wei, Ling; Ohgaki, Ryuichi; Kato, Itsuro; Hamase, Kenji; Nagamori, Shushi; Kanai, Yoshikatsu

    2015-03-01

    The efficacy of boron neutron capture therapy relies on the selective delivery of boron carriers to malignant cells. p-Boronophenylalanine (BPA), a boron delivery agent, has been proposed to be localized to cells through transporter-mediated mechanisms. In this study, we screened aromatic amino acid transporters to identify BPA transporters. Human aromatic amino acid transporters were functionally expressed in Xenopus oocytes and examined for BPA uptake and kinetic parameters. The roles of the transporters in BPA uptake were characterized in cancer cell lines. For the quantitative assessment of BPA uptake, HPLC was used throughout the study. Among aromatic amino acid transporters, ATB(0,+), LAT1 and LAT2 were found to transport BPA with Km values of 137.4 ± 11.7, 20.3 ± 0.8 and 88.3 ± 5.6 μM, respectively. Uptake experiments in cancer cell lines revealed that the LAT1 protein amount was the major determinant of BPA uptake at 100 μM, whereas the contribution of ATB(0,+) became significant at 1000 μM, accounting for 20-25% of the total BPA uptake in MCF-7 breast cancer cells. ATB(0,+), LAT1 and LAT2 transport BPA at affinities comparable with their endogenous substrates, suggesting that they could mediate effective BPA uptake in vivo. The high and low affinities of LAT1 and ATB(0,+), respectively, differentiate their roles in BPA uptake. ATB(0,+), as well as LAT1, could contribute significantly to the tumor accumulation of BPA at clinical dose.

  12. Abacus models for parabolic quotients of affine Weyl groups

    CERN Document Server

    Hanusa, Christopher R H

    2011-01-01

    We introduce abacus diagrams that describe minimal length coset representatives in affine Weyl groups of types B, C, and D. These abacus diagrams use a realization of the affine Weyl group of type C due to Eriksson to generalize a construction of James for the symmetric group. We also describe several combinatorial models for these parabolic quotients that generalize classical results in affine type A related to core partitions.

  13. Fast Affinity Propagation Clustering based on Machine Learning

    OpenAIRE

    Shailendra Kumar Shrivastava; J. L. Rana; DR.R.C.JAIN

    2013-01-01

    Affinity propagation (AP) was recently introduced as an un-supervised learning algorithm for exemplar based clustering. In this paper a novel Fast Affinity Propagation clustering Approach based on Machine Learning (FAPML) has been proposed. FAPML tries to put data points into clusters based on the history of the data points belonging to clusters in early stages. In FAPML we introduce affinity learning constant and dispersion constant which supervise the clustering process. FAPML also enforces...

  14. Surfaces in 4-space from the affine differential geometry viewpoint

    OpenAIRE

    Luis Florial Espinoza Sánchez

    2014-01-01

    In this thesis, we study locally strictly convex surfaces from the affine differential viewpoint and generalize some tools for locally strictly submanifolds of codimension 2. We introduce a family of affine metrics on a locally strictly convex surface M in affine 4-space. Then, we define the symmetric and antisymmetric equiaffine planes associated with each metric. We show that if M is immersed in a locally atrictly convex hyperquadric, then the symmetric and the antisymmetric planes coincid...

  15. Impact of sulfur oxides on mercury capture by activated carbon.

    Science.gov (United States)

    Presto, Albert A; Granite, Evan J

    2007-09-15

    Recent field tests of mercury removal with activated carbon injection (ACI) have revealed that mercury capture is limited in flue gases containing high concentrations of sulfur oxides (SOx). In order to gain a more complete understanding of the impact of SOx on ACl, mercury capture was tested under varying conditions of SO2 and SO3 concentrations using a packed bed reactor and simulated flue gas (SFG). The final mercury content of the activated carbons is independent of the SO2 concentration in the SFG, but the presence of SO3 inhibits mercury capture even at the lowest concentration tested (20 ppm). The mercury removal capacity decreases as the sulfur content of the used activated carbons increases from 1 to 10%. In one extreme case, an activated carbon with 10% sulfur, prepared by H2SO4 impregnation, shows almost no mercury capacity. The results suggest that mercury and sulfur oxides are in competition for the same binding sites on the carbon surface.

  16. Realistic costs of carbon capture

    Energy Technology Data Exchange (ETDEWEB)

    Al Juaied, Mohammed (Harvard Univ., Cambridge, MA (US). Belfer Center for Science and International Affiaris); Whitmore, Adam (Hydrogen Energy International Ltd., Weybridge (GB))

    2009-07-01

    There is a growing interest in carbon capture and storage (CCS) as a means of reducing carbon dioxide (CO2) emissions. However there are substantial uncertainties about the costs of CCS. Costs for pre-combustion capture with compression (i.e. excluding costs of transport and storage and any revenue from EOR associated with storage) are examined in this discussion paper for First-of-a-Kind (FOAK) plant and for more mature technologies, or Nth-of-a-Kind plant (NOAK). For FOAK plant using solid fuels the levelised cost of electricity on a 2008 basis is approximately 10 cents/kWh higher with capture than for conventional plants (with a range of 8-12 cents/kWh). Costs of abatement are found typically to be approximately US$150/tCO2 avoided (with a range of US$120-180/tCO2 avoided). For NOAK plants the additional cost of electricity with capture is approximately 2-5 cents/kWh, with costs of the range of US$35-70/tCO2 avoided. Costs of abatement with carbon capture for other fuels and technologies are also estimated for NOAK plants. The costs of abatement are calculated with reference to conventional SCPC plant for both emissions and costs of electricity. Estimates for both FOAK and NOAK are mainly based on cost data from 2008, which was at the end of a period of sustained escalation in the costs of power generation plant and other large capital projects. There are now indications of costs falling from these levels. This may reduce the costs of abatement and costs presented here may be 'peak of the market' estimates. If general cost levels return, for example, to those prevailing in 2005 to 2006 (by which time significant cost escalation had already occurred from previous levels), then costs of capture and compression for FOAK plants are expected to be US$110/tCO2 avoided (with a range of US$90-135/tCO2 avoided). For NOAK plants costs are expected to be US$25-50/tCO2. Based on these considerations a likely representative range of costs of abatement from CCS

  17. Silica-templated melamine-formaldehyde resin derived adsorbents for CO{sub 2} capture

    Energy Technology Data Exchange (ETDEWEB)

    C. Pevida; T.C. Drage; C.E. Snape [University of Nottingham, Nottingham (United Kingdom). School of Chemical and Environmental Engineering

    2008-09-15

    Adsorption on porous solids is an emerging alternative for CO{sub 2} capture that seeks to reduce the costs associated to the capture step. The enhancement of a specific adsorption capacity may be carried out by increasing the affinity of the adsorbent surface to CO{sub 2}. Nitrogen enrichment is reported to be effective in introducing basic functionalties that enhances the specific adsorbent-adsorbate interaction for CO{sub 2}. In this work a templating technique was used to produce highly porous nitrogen enriched carbons from melamine-formaldehyde resins. Nitrogen incorporated into the polymer matrix results in the greater stability of the adsorbents in terms of volatile and thermal loss of nitrogen. CO{sub 2} capture performances were evaluated between 25{sup o}C and 75{sup o}C in a thermobalance. CO{sub 2} adsorption capacities up to 2.25 mmol g{sup -1} of CO{sub 2} at 25{sup o}C were achieved. Both texture and surface chemistry influence the CO{sub 2} capture performance of the adsorbents. The carbonisation temperature used during the synthesis step controls the nitrogen functional groups present, as determined by XPS, with the loss of triazine nitrogen with increasing carbonisation temperature proposed to account for the decreased CO{sub 2} affinity.

  18. Inhibition of Xanthine Oxidase Activity by Gnaphalium Affine Extract

    Institute of Scientific and Technical Information of China (English)

    Wei-qing Lin; Jian-xiang Xie; Xiao-mu Wu; Lin Yang; Hai-dong Wang

    2014-01-01

    Objective To evaluate the inhibitory effect of Gnaphalium affine extracts on xanthine oxidase (XO) activity in vitro and to analyze the mechanism of this effect. Methods In this in vitro study, Kinetic measurements were performed in 4 different inhibitor concentrations and 5 different xanthine concentrations (60, 100, 200, 300, 400 μmol/L). Dixon and Lineweaver-Burk plot analysis were used to determine Ki values and the inhibition mode for the compounds isolated from Gnaphalium affine extract. Results Four potent xanthine oxidase inhibitors were found in 95% ethanolic (v/v) Gnaphalium affine extract. Among them, the flavone Eupatilin exhibited the strongest inhibitory effect on XO with a inhibition constant (Ki) of 0.37μmol/L, lower than the Ki of allopurinol (4.56 mol/L), a known synthetic XO inhibitor. Apigenin (Ki of 0.56μmol/L, a proportion of 0.0053‰in Gnaphalium affine), luteolin (Ki of 2.63 μmol/L, 0.0032‰ in Gnaphalium affine) and 5-hydroxy-6,7,3’,4’-tetramethoxyflavone (Ki of 3.15μmol/L, 0.0043‰ in Gnaphalium affine) also contributed to the inhibitory effect of Gnaphalium affine extract on XO activity. Conclusions These results suggest that the use of Gnaphalium affine in the treatment of gout could be attributed to its inhibitory effect on XO. This study provides a rational basis for the traditional use of Gnaphalium affine against gout.

  19. Algal Energy Conversion and Capture

    Science.gov (United States)

    Hazendonk, P.

    2015-12-01

    We address the potential for energy conversions and capture for: energy generation; reduction in energy use; reduction in greenhouse gas emissions; remediation of water and air pollution; protection and enhancement of soil fertility. These processes have the potential to sequester carbon at scales that may have global impact. Energy conversion and capture strategies evaluate energy use and production from agriculture, urban areas and industries, and apply existing and emerging technologies to reduce and recapture energy embedded in waste products. The basis of biocrude production from Micro-algal feedstocks: 1) The nutrients from the liquid fraction of waste streams are concentrated and fed into photo bioreactors (essentially large vessels in which microalgae are grown) along with CO2 from flue gasses from down stream processes. 2) The algae are processed to remove high value products such as proteins and beta-carotenes. The advantage of algae feedstocks is the high biomass productivity is 30-50 times that of land based crops and the remaining biomass contains minimal components that are difficult to convert to biocrude. 3) The remaining biomass undergoes hydrothermal liquefaction to produces biocrude and biochar. The flue gasses of this process can be used to produce electricity (fuel cell) and subsequently fed back into the photobioreactor. The thermal energy required for this process is small, hence readily obtained from solar-thermal sources, and furthermore no drying or preprocessing is required keeping the energy overhead extremely small. 4) The biocrude can be upgraded and refined as conventional crude oil, creating a range of liquid fuels. In principle this process can be applied on the farm scale to the municipal scale. Overall, our primary food production is too dependent on fossil fuels. Energy conversion and capture can make food production sustainable.

  20. The cohomology of the affine Deligne-Lusztig varieties in the affine flag manifold of $GL_2$

    CERN Document Server

    Ivanov, Alexander

    2009-01-01

    This paper studies affine Deligne-Lusztig varieties in the affine flag manifold of GL_2. At first we determine all such varieties up to isomorphy. After this we investigate the representations of the sigma-stabilizer of an element b of the group on the etale cohomology of the affine Deligne-Lusztig variety X_w(b). We describe such representations as inductions from compact subgroups and in terms of noncuspidal representations.

  1. The Effectiveness of Classroom Capture Technology

    Science.gov (United States)

    Ford, Maire B.; Burns, Colleen E.; Mitch, Nathan; Gomez, Melissa M.

    2012-01-01

    The use of classroom capture systems (systems that capture audio and video footage of a lecture and attempt to replicate a classroom experience) is becoming increasingly popular at the university level. However, research on the effectiveness of classroom capture systems in the university classroom has been limited due to the recent development and…

  2. Marker-Free Human Motion Capture

    DEFF Research Database (Denmark)

    Grest, Daniel

    Human Motion Capture is a widely used technique to obtain motion data for animation of virtual characters. Commercial optical motion capture systems are marker-based. This book is about marker-free motion capture and its possibilities to acquire motion from a single viewing direction. The focus...

  3. Comparison among three anion exchange chromatographic supports to capture erythropoietin from cell culture supernatant

    Institute of Scientific and Technical Information of China (English)

    Lourdes HERNNDEZ; Diobel STEWART; Lourdes ZUMALACRREGUI; Daniel AMARO

    2015-01-01

    Affinity and ion exchange conventional chromatography have been used to capture erythropoietin ( EPO)from mammalian cell culture supernatant. Currently,chromatographic adsorbent perfusion is available, however a limited number of applications have been found in the literature. In this work,three anion exchange chromatographic supports( gel,membrane and monolithic)were evaluated in the capture step of the recombi-nant erythropoietin purification process. The influences of load and flow rate on each support performance were analyzed. Also the purity of the EPO molecules was determined. A productivity analysis,as a decision tool for larger scale implementation,was done. As a conclusion,the evaluated supports are technically suitable to cap-ture EPO with adequate recovery and good purity. However,the monolithic column admits high operating velocity,showing the highest adsorption capacity and productivity.

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

    Directory of Open Access Journals (Sweden)

    Thomas A. Munro

    2013-12-01

    Full Text Available 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. (Dimethylaminomethyl 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 [35S]GTPγS assay. No modulation was detected. As an alternative attachment point for bivalent derivatives, we prepared the 2-(hydroxyethoxymethyl ether, which retained high affinity for κ-OR. We discuss alternative design strategies for linked, fused or merged bivalent derivatives of 1.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. A bottleneck model of set-specific capture.

    Science.gov (United States)

    Moore, Katherine Sledge; Weissman, Daniel H

    2014-01-01

    Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters"). In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus) impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus). In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP) stream for up to three target letters (T1-T3) that could appear in any of three target colors (orange, green, or lavender). The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  10. Recent Advances in Carbon Capture with Metal-Organic Frameworks.

    Science.gov (United States)

    Stylianou, Kyriakos C; Queen, Wendy L

    2015-01-01

    The escalating level of CO(2) in the atmosphere is one of the most critical environmental issues of our age. The carbon capture and storage from pilot test plants represents an option for reducing CO(2) emissions, however, the energy cost associated with post-combustion carbon capture process alone is ∼30% of the total energy generated by the power plant. Thus, the generation of carbon capture adsorbents with high uptake capacities, great separation performance and low cost is of paramount importance. Metal-organic frameworks are infinite networks of metal-containing nodes bridged by organic ligands through coordination bonds into porous extended structures and several reports have revealed that they are ideal candidates for the selective capture of CO(2). In this review we summarize recent advances related to the synthesis of porous MOFs and the latest strategies to enhance the CO(2) adsorption enthalpies and capacities at low-pressures, increase hydrolytic and mechanical stabilities, and improve the ease of regeneration. Although they show great promise for post-combustion carbon capture, there are still major challenges that must be overcome before they can be used for such a large-scale application.

  11. Hypervelocity Capture of Meteoritic Particles in Nonsilica Aerogels

    Energy Technology Data Exchange (ETDEWEB)

    S Jones; G Flynn

    2011-12-31

    The Stardust mission captured particles from the comet 81P/Wild 2 in gradient density silica aerogel and returned the collected samples to earth in 2006. The analyses of these particles have revealed several new insights into the formation of our solar system. However, since the aerogel used as the capture material was silica, the elemental analyses of the silica-rich particles were made more complicated in certain ways due to the mixing of the silicon of the particles and that of the aerogel. By using a nonsilica aerogel, future elemental analyses of silica-rich particles captured in aerogel could be made more straightforward. Resorcinol/formaldehyde (RF), alumina, and zirconia aerogels were impact tested with meteoritic fragments and the captured fragments were mapped with synchrotron-based X-ray microprobe (XRM) and the particles were analyzed with X-ray fluorescence (XRF). The resorcinol/formaldehyde aerogel proved to be the best capture material, in that it could be keystoned and XRF could be used to locate and analyze particles that were less than 10 {micro}m.

  12. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available 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 emphasised 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.

  13. Non-Statistical Effects in Neutron Capture

    CERN Document Server

    Köhler, P E; Guber, K H; Harvey, J A; ODonnell, J M; Reifarth, R; Rundberg, R S; Ullmann, J L; Vieira, D J; Wiarda, D; Wouters, J M

    2008-01-01

    There have been many reports of non-statistical effects in neutron-capture measurements. However, reports of deviations of reduced-neutron-width distributions from the expected Porter-Thomas (PT) shape largely have been ignored. Most of these deviations have been reported for odd-A nuclides. Because reliable spin (J) assignments have been absent for most resonances for such nuclides, it is possible that reported deviations from PT might be due to incorrect J assignments. We recently developed a new method for measuring spins of neutron resonances by using the DANCE detector at LANSCE. Measurements made with a 147Sm sample allowed us to determine spins of almost all known resonances below 1 keV. Furthermore, analysis of these data revealed that the reduced-neutron-width distribution was in good agreement with PT for resonances below 350 eV, but in disagreement with PT for resonances between 350 and 700 eV. Our previous (n,alpha) measurements had revealed that the alpha strength function also changes abruptly a...

  14. Microstructured block copolymer surfaces for control of microbe capture and aggregation

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Ryan R [ORNL; Shubert, Katherine R [ORNL; Morrell, Jennifer L. [University of Tennessee, Knoxville (UTK); Lokitz, Bradley S [ORNL; Doktycz, Mitchel John [ORNL; Retterer, Scott T [ORNL

    2014-01-01

    The capture and arrangement of surface-associated microbes is influenced by biochemical and physical properties of the substrate. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe capture. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line or square grid patterns with 5 m wide features and varied edge spacing. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates captured was dependent on the pattern dimensions. Line patterns with edge spacing of 5 m or less led to the capture of individual microbes with minimal formation of aggregates, while grid patterns with the same spacing also captured individual microbes with further reduction in aggregation. Both geometries allowed for increases in aggregate size distribution with increased in edge spacing. These engineered surfaces combine spatial confinement with affinity-based microbe capture based on exopolysaccharide content to control the degree of microbe aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.

  15. Victim’s profile analysis reveals homicide affinity for minorities and the youth

    Directory of Open Access Journals (Sweden)

    Alan S. Whiteman

    2010-07-01

    Full Text Available BACKGROUND: In this study we have examined the risk of death by homicide in Miami-Dade County and Broward County (BC; and examined the association between socioeconomic status and homicide while describing victim's typical characteristics such as age, gender, race/ethnicity, and type of injury. METHODS: Data was collected from the County's Medical Examiner's Offices, Census Bureau, and Federal Bureau of Investigation between 2004 and 2007. RESULTS: There has been an increase in the risk of dying by homicide in the studied area; the homicide rate for the selected period was two times higher than the national average. Although Black Non-Hispanics count for 19% of the population of Miami-Dade County and 23% in Broward County, 56% and 53% of homicide victims are among this ethnic group in Miami-Dade County and Broward County respectively. Hispanics were more at risk of being a victim of homicide in 2007 than they were in 2004. CONCLUSIONS: A substantial proportion of the homicide victims were 22 years of age or younger. . In fact, the homicide victims' average age has been steadily decreasing in recent years. The drastic increase in the risk of death by gunshot among young Black non-Hispanic and Hispanic residents warrants cause for concern.

  16. Platelet affinity for burro aorta collagen

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, M.D.

    1977-10-01

    Despite ingenious concepts, there are no unequivocal clues as to what, when, and how some undefined biochemical factor(s) or constituent(s) that localizes in the arterial wall can precipitate a thromboatheromatous lesion or arterial disease. The present study focused on the extraction, partial purification, and characterization of a collagen-active platelet stimulator from the aortas of aged burros. The aggregator moiety in the aorta extracts invariably had a higher affinity for platelets in citrated platelet-rich plasma of human beings than for platelets of homologous burros. The platelet-aggregating factor(s) in the aorta extract was retained by incubation with ..cap alpha..-chymotrypsin. Platelet-aggregating activity was rapidly abolished after incubation with collagenase, as determined by platelet-aggregometry tests. Evidence based on light microscope and polysaccharide histochemical reactions indicates a probability that the intracellular amorphous matrix (PAS-positive) and filamentous components (PTAH-positive) expelled from smooth muscle cells disrupted during homogenization of the aorta may be a principal source of a precursor collagen species which is a potent inducer of platelet aggregation.

  17. Affine connection form of Regge calculus

    Science.gov (United States)

    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.

  18. Affinity of guanosine derivatives for polycytidylate revisited

    Science.gov (United States)

    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.

  19. Client/server approach to image capturing

    Science.gov (United States)

    Tuijn, Chris; Stokes, Earle

    1998-01-01

    The diversity of the digital image capturing devices on the market today is quite astonishing and ranges from low-cost CCD scanners to digital cameras (for both action and stand-still scenes), mid-end CCD scanners for desktop publishing and pre- press applications and high-end CCD flatbed scanners and drum- scanners with photo multiplier technology. Each device and market segment has its own specific needs which explains the diversity of the associated scanner applications. What all those applications have in common is the need to communicate with a particular device to import the digital images; after the import, additional image processing might be needed as well as color management operations. Although the specific requirements for all of these applications might differ considerably, a number of image capturing and color management facilities as well as other services are needed which can be shared. In this paper, we propose a client/server architecture for scanning and image editing applications which can be used as a common component for all these applications. One of the principal components of the scan server is the input capturing module. The specification of the input jobs is based on a generic input device model. Through this model we make abstraction of the specific scanner parameters and define the scan job definitions by a number of absolute parameters. As a result, scan job definitions will be less dependent on a particular scanner and have a more universal meaning. In this context, we also elaborate on the interaction of the generic parameters and the color characterization (i.e., the ICC profile). Other topics that are covered are the scheduling and parallel processing capabilities of the server, the image processing facilities, the interaction with the ICC engine, the communication facilities (both in-memory and over the network) and the different client architectures (stand-alone applications, TWAIN servers, plug-ins, OLE or Apple-event driven

  20. Halo Effect on Direct Neutron Capture Process

    Institute of Scientific and Technical Information of China (English)

    刘祖华; 周宏余

    2004-01-01

    We calculate the capture cross sections of the 10Be(n,γ) 11 Be reaction by means of the asymptotic normalization coefficient method and demonstrate the halo effects on the capture cross sections for the direct radiative neutron capture where a p-, s- or d-wave neutron is captured into an s-orbit or p-orbit in 11 Be by emitting an E1 γ-ray,respectively. The result shows that the enormous enhancement of the capture cross section is just due to the large overlap of the incident neutron wave with the extended tail of the halo, which is clearly illustrated by the reduced transition amplitude function.

  1. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because the textb......One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...... process for which process recordings are a valuable communication media in order to enhance the learning process. Student feedback indicates both high learning outcome and superior learning potential compared to traditional classroom teaching....

  2. Label-free detection and identification of protein ligands captured by receptors in a polymerized planar lipid bilayer using MALDI-TOF MS.

    Science.gov (United States)

    Liang, Boying; Ju, Yue; Joubert, James R; Kaleta, Erin J; Lopez, Rodrigo; Jones, Ian W; Hall, Henry K; Ratnayaka, Saliya N; Wysocki, Vicki H; Saavedra, S Scott

    2015-04-01

    Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) coupled with affinity capture is a well-established method to extract biological analytes from complex samples followed by label-free detection and identification. Many bioanalytes of interest bind to membrane-associated receptors; however, the matrices and high-vacuum conditions inherent to MALDI-TOF MS make it largely incompatible with the use of artificial lipid membranes with incorporated receptors as platforms for detection of captured proteins and peptides. Here we show that cross-linking polymerization of a planar supported lipid bilayer (PSLB) provides the stability needed for MALDI-TOF MS analysis of proteins captured by receptors embedded in the membrane. PSLBs composed of poly(bis-sorbylphosphatidylcholine) (poly(bis-SorbPC)) and doped with the ganglioside receptors GM1 and GD1a were used for affinity capture of the B subunits of cholera toxin, heat-labile enterotoxin, and pertussis toxin. The three toxins were captured simultaneously, then detected and identified by MS on the basis of differences in their molecular weights. Poly(bis-SorbPC) PSLBs are inherently resistant to nonspecific protein adsorption, which allowed selective toxin detection to be achieved in complex matrices (bovine serum and shrimp extract). Using GM1-cholera toxin subunit B as a model receptor-ligand pair, we estimated the minimal detectable concentration of toxin to be 4 nM. On-plate tryptic digestion of bound cholera toxin subunit B followed by MS/MS analysis of digested peptides was performed successfully, demonstrating the feasibility of using the PSLB-based affinity capture platform for identification of unknown, membrane-associated proteins. Overall, this work demonstrates that combining a poly(lipid) affinity capture platform with MALDI-TOF MS detection is a viable approach for capture and proteomic characterization of membrane-associated proteins in a label-free manner.

  3. Downstream processing of polysaccharide degrading enzymes by affinity chromatography.

    NARCIS (Netherlands)

    Somers, W.A.C.

    1992-01-01

    The objective of this study was the development of affinity matrices to isolate and purify a number of polysaccharide degrading enzymes and the application of these adsorbents in the large- scale purification of the enzymes from fermentation broths. Affinity adsorbents were developed for endo-polyga

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

    Energy Technology Data Exchange (ETDEWEB)

    Chou, Ching-Yi, E-mail: l2897107@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China); Ita, Eyo, E-mail: ita@usna.edu [Department of Physics, US Naval Academy, Annapolis, MD (United States); Soo, Chopin, E-mail: cpsoo@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China)

    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.

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

    Science.gov (United States)

    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.

  6. Self-affine roughness influence on redox reaction charge admittance

    NARCIS (Netherlands)

    Palasantzas, G

    2005-01-01

    In this work we investigate the influence of self-affine electrode roughness on the admittance of redox reactions during facile charge transfer kinetics. The self-affine roughness is characterized by the rms roughness amplitude w, the correlation length xi and the roughness exponent H (0

  7. Synthesis of tetracycline analogs and their bone affinities

    Institute of Scientific and Technical Information of China (English)

    Wen Cai Huang; Hu Zheng; Ling Ling Weng

    2008-01-01

    Tetracycline analogs were designed and synthesized and their bone affinities were tested on hydroxyapatite. The results showedthat the carbonyl-amide-enol structure in A ring and phenol-ketone structure in BCD ring may be responsible for tetracycline's highbone affinity and either A ring or BCD ring has a planar conformation is essential.

  8. The Affine Complete Hypersurfaces of Constant Gauss-Kronecker Curvature

    Institute of Scientific and Technical Information of China (English)

    Bao Fu WANG

    2009-01-01

    Given a bounded convex domain Ω with C∞ boundary and a function φ∈ C∞ ( partial deriv Ω), Li-Simon-Chen can construct an Euclidean complete and W-complete convex hypersurface M with constant affine Gauss-Kronecker curvature, and they guess the M is also affine complete. In this paper, we give a confirmation answer.

  9. Ordinary matter in nonlinear affine gauge theories of gravitation

    CERN Document Server

    Tiemblo, A; Tiemblo, A; Tresguerres, R

    1994-01-01

    We present a general framework to include ordinary fermionic matter in the metric--affine gauge theories of gravity. It is based on a nonlinear gauge realization of the affine group, with the Lorentz group as the classification subgroup of the matter and gravitational fields.

  10. Isolation of bovine serum albumin from whey using affinity chromatography

    NARCIS (Netherlands)

    Besselink, T.; Janssen, A.E.M.; Boom, R.M.

    2015-01-01

    The adsorption of bovine serum albumin (BSA) to a chromatography resin with immobilised llama antibody fragments as affinity ligands was investigated. The maximum adsorption capacity of the affinity resin was 21.6 mg mL-1 with a Langmuir equilibrium constant of 20.4 mg mg-1. Using packed bed chromat

  11. SHP-1 phosphatase activity counteracts increased T cell receptor affinity.

    Science.gov (United States)

    Hebeisen, Michael; Baitsch, Lukas; Presotto, Danilo; Baumgaertner, Petra; Romero, Pedro; Michielin, Olivier; Speiser, Daniel E; Rufer, Nathalie

    2013-03-01

    Anti-self/tumor T cell function can be improved by increasing TCR-peptide MHC (pMHC) affinity within physiological limits, but paradoxically further increases (K(d) affinity for the tumor antigen HLA-A2/NY-ESO-1, we investigated the molecular mechanisms underlying this high-affinity-associated loss of function. As compared with cells expressing TCR affinities generating optimal function (K(d) = 5 to 1 μM), those with supraphysiological affinity (K(d) = 1 μM to 15 nM) showed impaired gene expression, signaling, and surface expression of activatory/costimulatory receptors. Preferential expression of the inhibitory receptor programmed cell death-1 (PD-1) was limited to T cells with the highest TCR affinity, correlating with full functional recovery upon PD-1 ligand 1 (PD-L1) blockade. In contrast, upregulation of the Src homology 2 domain-containing phosphatase 1 (SHP-1/PTPN6) was broad, with gradually enhanced expression in CD8(+) T cells with increasing TCR affinities. Consequently, pharmacological inhibition of SHP-1 with sodium stibogluconate augmented the function of all engineered T cells, and this correlated with the TCR affinity-dependent levels of SHP-1. These data highlight an unexpected and global role of SHP-1 in regulating CD8(+) T cell activation and responsiveness and support the development of therapies inhibiting protein tyrosine phosphatases to enhance T cell-mediated immunity.

  12. Frame-independent mechanics:geometry on affine bundles

    OpenAIRE

    Grabowska, K.; Grabowski, J.; Urbanski, P.

    2005-01-01

    Main ideas of the differential geometry on affine bundles are presented. Affine counterparts of Lie algebroid and Poisson structures are introduced and discussed. The developed concepts are applied in a frame-independent formulation of the time-dependent and the Newtonian mechanics.

  13. Convergence of generic infinite products of affine operators

    Directory of Open Access Journals (Sweden)

    S. Reich

    1999-01-01

    Full Text Available We establish several results concerning the asymptotic behavior of random infinite products of generic sequences of affine uniformly continuous operators on bounded closed convex subsets of a Banach space. In addition to weak ergodic theorems we also obtain convergence to a unique common fixed point and more generally, to an affine retraction.

  14. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  15. Expression of recombinant West Nile virus prM protein fused to an affinity tag for use as a diagnostic antigen.

    Science.gov (United States)

    Setoh, Y X; Hobson-Peters, J; Prow, N A; Young, P R; Hall, R A

    2011-07-01

    Previous studies have concluded that the Flavivirus prM protein is a suitable viral antigen to distinguish serologically between infections with closely related Flaviviruses (Cardosa et al., 2002). To express the recombinant West Nile virus (WNV) prM antigen fused to a suitable affinity tag for purification, a series of prM-His-tag and prM-V5-tag fusion proteins were generated. Analysis of the prM-His-tag fusion proteins revealed that either prM epitopes were disrupted or the His-tag was not presented properly depending on the location of the His tag and the presence of the prM transmembrane domains in these constructs. This identified domains critical for proper folding of prM, and arrangements that allowed the correct presentation of the His-tag. However, the inclusion of the V5 epitope tag fused to the C terminus of prM allowed formation of the authentic antigenic structure of prM and the proper presentation of the V5 epitope. Capture of tagged recombinant WNV(NY99) prM antigen to the solid phase with anti-V5 antibody in ELISA enabled the detection of prM-specific antibodies in WNV(NY99)-immune horse serum, confirming its potential as a useful diagnostic reagent.

  16. Capture of Irregular Satellites at Jupiter

    CERN Document Server

    Nesvorny, D; Deienno, R

    2014-01-01

    The irregular satellites of outer planets are thought to have been captured from heliocentric orbits. The exact nature of the capture process, however, remains uncertain. We examine the possibility that irregular satellites were captured from the planetesimal disk during the early Solar System instability when encounters between the outer planets occurred (Nesvorny, Vokrouhlicky & Morbidelli 2007, AJ 133; hereafter NVM07). NVM07 already showed that the irregular satellites of Saturn, Uranus and Neptune were plausibly captured during planetary encounters. Here we find that the current instability models present favorable conditions for capture of irregular satellites at Jupiter as well, mainly because Jupiter undergoes a phase of close encounters with an ice giant. We show that the orbital distribution of bodies captured during planetary encounters provides a good match to the observed distribution of irregular satellites at Jupiter. The capture efficiency for each particle in the original transplanetary d...

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

    Science.gov (United States)

    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.

  18. IMPLEMENTASI ENKRIPSI DEKRIPSI ALGORITMA AFFINE CIPHER BERBASIS ANDROID

    Directory of Open Access Journals (Sweden)

    Sasono Wibowo

    2014-11-01

    Full Text Available Perkembangan Teknologi Informasi yang cukup pesat khususnya dalam bidang komunikasi menjadikan komunikasi sangat mudah namun dalam implementasinya perlu adanya keamanan tentang informasi yang disampaikan. Dalam komunikasi antar orang pasti memiliki pembicaraan informasi yang bersifat privat atau orang lain tidak boleh tahu tentang pembicaraan yang terjadi. Diperlukannya keamanan untuk menjaga kerahasiaan informasi pada saat komunikasi. Masyarakat lebih sering menggunakan komunikasi dengan telepon seluler karena dinilai mudah dibawa dan tidak repot menggunakannya. Kriptografi yang biasa dikenal sebagai ilmu yang mempelajari bagaimana cara menyembunyikan pesan bisa diterapkan dalam aplikasi pada telepon seluler sebagai contoh smartphone android. Dengan mengimplementasikan algoritma affine cipher maka aplikasi yang akan dibuat bisa mengubah isi pesan yang ada dan dapat mengamankan informasi yang ada. Algoritma affine cipher merupakan perkembangan dari algoritma caesar dimana algoritma affine cipher menggunakan dua kunci. Dengan mengimplementasikan algoritma affine cipher ke dalam android maka diharapkan kita bisa menyimpan informasi dari siapapun tanpa terbaca. Kata Kunci : Kriptografi, Affine Cipher, android, Implementasi, Informasi

  19. Duals of Affine Grassmann Codes and Their Relatives

    DEFF Research Database (Denmark)

    Beelen, P.; Ghorpade, S. R.; Hoholdt, T.

    2012-01-01

    Affine Grassmann codes are a variant of generalized Reed-Muller codes and are closely related to Grassmann codes. These codes were introduced in a recent work by Beelen Here, we consider, more generally, affine Grassmann codes of a given level. We explicitly determine the dual of an affine...... Grassmann code of any level and compute its minimum distance. Further, we ameliorate the results by Beelen concerning the automorphism group of affine Grassmann codes. Finally, we prove that affine Grassmann codes and their duals have the property that they are linear codes generated by their minimum......-weight codewords. This provides a clean analogue of a corresponding result for generalized Reed-Muller codes....

  20. Cage-based performance capture

    CERN Document Server

    Savoye, Yann

    2014-01-01

    Nowadays, highly-detailed animations of live-actor performances are increasingly easier to acquire and 3D Video has reached considerable attentions in visual media production. In this book, we address the problem of extracting or acquiring and then reusing non-rigid parametrization for video-based animations. At first sight, a crucial challenge is to reproduce plausible boneless deformations while preserving global and local captured properties of dynamic surfaces with a limited number of controllable, flexible and reusable parameters. To solve this challenge, we directly rely on a skin-detached dimension reduction thanks to the well-known cage-based paradigm. First, we achieve Scalable Inverse Cage-based Modeling by transposing the inverse kinematics paradigm on surfaces. Thus, we introduce a cage inversion process with user-specified screen-space constraints. Secondly, we convert non-rigid animated surfaces into a sequence of optimal cage parameters via Cage-based Animation Conversion. Building upon this re...

  1. Muon capture by silicon 28

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, D.S. [College of William and Mary, Williamsburg, VA (United States). Dept. of Physics; Bauer, J. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Evans, J. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Gorringe, T.P. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Johnson, B.L. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Kalvoda, S. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Porter, R. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Siebels, B. [Kentucky Univ., Lexington, KY (United States). Dept. of Physics; Gete, E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Physics; Measday, D.F. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Physics; Moftah, B.A. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Physics; Stanislaus, S. [Valparaiso Univ., IN (United States). Dept. of Physics

    1996-12-01

    A measurement has been made of the angular correlation of the neutrino with the 1229 keV {gamma}-ray from the de-excitation of the 2201 keV 1{sup +} level in aluminum-28, following muon capture in silicon-28. To suppress the neutron-induced background in the HPGe detector, a coincidence in a NaI array is required with the 942 keV {gamma}-ray in the de-excitation cascade. The lifetime of the 2201 keV level is found to be 61{+-}4{+-}9 fs. The correlation coefficient {alpha} is found to be 0.36{+-}0.06 implying g{sub P}/g{sub A}=0{sup +3.5}{sub -3}. (orig.).

  2. Workshop on neutron capture therapy

    Energy Technology Data Exchange (ETDEWEB)

    Fairchild, R.G.; Bond, V.P. (eds.)

    1986-01-01

    Potentially optimal conditions for Neutron Capture Therapy (NCT) may soon be in hand due to the anticipated development of band-pass filtered beams relatively free of fast neutron contaminations, and of broadly applicable biomolecules for boron transport such as porphyrins and monoclonal antibodies. Consequently, a number of groups in the US are now devoting their efforts to exploring NCT for clinical application. The purpose of this Workshop was to bring these groups together to exchange views on significant problems of mutual interest, and to assure a unified and effective approach to the solutions. Several areas of preclinical investigation were deemed to be necessary before it would be possible to initiate clinical studies. As neither the monomer nor the dimer of sulfhydryl boron hydride is unequivocally preferable at this time, studies on both compounds should be continued until one is proven superior.

  3. Experimental and theoretical proton affinities of methionine, methionine sulfoxide and their N- and C-terminal derivatives

    Science.gov (United States)

    Lioe, Hadi; O'Hair, Richard A. J.; Gronert, Scott; Austin, Allen; Reid, Gavin E.

    2007-11-01

    The proton affinities of methionine, methionine sulfoxide and their derivatives (methionine methyl ester, methionine sulfoxide methyl ester, methionine methyl amide, methionine sulfoxide methyl amide, N-acetyl methionine, N-acetyl methionine sulfoxide, N-acetyl methionine methyl ester, N-acetyl methionine sulfoxide methyl ester, N-acetyl methionine methyl amide and N-acetyl methionine sulfoxide methyl amide) were experimentally determined using the kinetic method, in which proton bound dimers formed via electrospray ionization (ESI) were subjected to collision induced dissociation (CID) in a triple quadrupole mass spectrometer. In addition, theoretical calculations carried out at the MP2/6-311 + G(2d,p)//B3LYP/6-31 + G(d,p) level of theory to determine the global minima of the neutral and protonated species of all derivatives studied, were used to predict theoretical proton affinities. The density function theory calculations not only support the experimental proton affinities, but also provide structural insights into the types of hydrogen bonding that stabilize the neutral and protonated methionine or methionine sulfoxide derivatives. Comparison of the proton affinities of the various methionine and methionine sulfoxide derivatives reveals that: (i) oxidation of methionine derivatives to methionine sulfoxide derivatives results in an increase in proton affinity due to higher intrinsic proton affinity and an increase in the ring size formed through charge complexation of the sulfoxide group, which allows more efficient hydrogen bonding compared to the sulfide group; (ii) C-terminal modification by methyl esterification or methyl amidation increases the proton affinity in the order of methyl amide > methyl ester > carboxylic acid due to improved charge stabilization; (iii) N-terminal modification by N-acetylation decreases proton affinity of the derivatives due to lower intrinsic proton affinity of the N-acetyl group as well as due to stabilization of the attached

  4. A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein.

    Science.gov (United States)

    Chang, Tsung-Che; Adak, Avijit K; Lin, Ting-Wei; Li, Pei-Jhen; Chen, Yi-Ju; Lai, Chain-Hui; Liang, Chien-Fu; Chen, Yu-Ju; Lin, Chun-Cheng

    2016-03-15

    The use of photo-crosslinking glycoprobes represents a powerful strategy for the covalent capture of labile protein complexes and allows detailed characterization of carbohydrate-mediated interactions. The selective release of target proteins from solid support is a key step in functional proteomics. We envisaged that light activation can be exploited for releasing labeled protein in a dual photo-affinity probe-based strategy. To investigate this possibility, we designed a trifunctional, galactose-based, multivalent glycoprobe for affinity labeling of carbohydrate-binding proteins. The resulting covalent protein-probe adduct is attached to a photo-cleavable biotin affinity tag; the biotin moiety enables specific presentation of the conjugate on streptavidin-coated beads, and the photolabile linker allows the release of the labeled proteins. This dual probe promotes both the labeling and the facile cleavage of the target protein complexes from the solid surfaces and the remainder of the cell lysate in a completely unaltered form, thus eliminating many of the common pitfalls associated with traditional affinity-based purification methods.

  5. Peptide-Based Protein Capture Agents with High Affinity, Selectivity, and Stability as Antibody Replacements in Biodetection Assays

    Science.gov (United States)

    2014-08-01

    The PCC agent oligopeptides are developed against known protein epitopes and can be mass produced using robotic methods. In this work, a PCC agent...are developed against known protein epitopes and can be mass produced using robotic methods. In this work, a PCC agent under development will be...of Anthrax Protective Antigen," ACS Nano , 7(10), 9452-9460 (2013). [16] Life Technologies, "ELISA Protocol (General Guidelines)," <http

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

    Science.gov (United States)

    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

  7. Generation of recombinant antibodies to rat GABAA receptor subunits by affinity selection on synthetic peptides.

    Directory of Open Access Journals (Sweden)

    Sujatha P Koduvayur

    Full Text Available The abundance and physiological importance of GABAA receptors in the central nervous system make this neurotransmitter receptor an attractive target for localizing diagnostic and therapeutic biomolecules. GABAA receptors are expressed within the retina and mediate synaptic signaling at multiple stages of the visual process. To generate monoclonal affinity reagents that can specifically recognize GABAA receptor subunits, we screened two bacteriophage M13 libraries, which displayed human scFvs, by affinity selection with synthetic peptides predicted to correspond to extracellular regions of the rat α1 and β2 GABAA subunits. We isolated three anti-β2 and one anti-α1 subunit specific scFvs. Fluorescence polarization measurements revealed all four scFvs to have low micromolar affinities with their cognate peptide targets. The scFvs were capable of detecting fully folded GABAA receptors heterologously expressed by Xenopus laevis oocytes, while preserving ligand-gated channel activity. Moreover, A10, the anti-α1 subunit-specific scFv, was capable of detecting native GABAA receptors in the mouse retina, as observed by immunofluorescence staining. In order to improve their apparent affinity via avidity, we dimerized the A10 scFv by fusing it to the Fc portion of the IgG. The resulting scFv-Fc construct had a Kd of ∼26 nM, which corresponds to an approximately 135-fold improvement in binding, and a lower detection limit in dot blots, compared to the monomeric scFv. These results strongly support the use of peptides as targets for generating affinity reagents to membrane proteins and encourage investigation of molecular conjugates that use scFvs as anchoring components to localize reagents of interest at GABAA receptors of retina and other neural tissues, for studies of receptor activation and subunit structure.

  8. Electrochemical Affinity Biosensors in Food Safety

    Directory of Open Access Journals (Sweden)

    Susana Campuzano

    2017-02-01

    Full Text Available Safety and quality are key issues of today’s food industry. Since the food chain is becoming more and more complex, powerful analytical methods are required to verify the performance of food safety and quality systems. Indeed, such methods require high sensitivity, selectivity, ability for rapid implementation and capability of automatic screening. Electroanalytical chemistry has, for decades, played a relevant role in food safety and quality assessment, taking more and more significance over time in the solution of analytical problems. At present, the implementation of electrochemical methods in the food is evident. This is in a large part due to the relevant results obtained by combining the attractive advantages of electrochemical transduction strategies (in terms of relatively simple hardware, versatility, interface with automatic logging and feasibility of application outside the laboratory environment with those from biosensors technology. Important examples of enzyme electrochemical biosensors are those dedicated to the determination of glucose, alcohol or cholesterol are important examples. In addition, other types of different electrochemical biosensing approaches have emerged strongly in the last years. Among these, the strategies involving affinity interactions have been shown to possess a large number of applications. Therefore, electrochemical immunosensors and DNA-based biosensors have been widely used to determine major and minor components in foodstuffs, providing sufficient data to evaluate food freshness, the quality of raw materials, or the origin of samples, as well as to determine a variety of compounds at trace levels related to food safety such as micotoxins, allergens, drugs residues or pathogen microorganisms. This review discusses some critical examples of the latest advances in this area, pointing out relevant methodologies related to the measurement techniques, including the use of nanostructured electrodes and

  9. Optimal affine-invariant matching: performance characterization

    Science.gov (United States)

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

    1992-04-01

    The geometric hashing scheme proposed by Lamdan and Wolfson can be 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. In a recent paper, we discussed errors that can occur with this method due to quantization, stability, symmetry, and noise problems. These errors make the original geometric hashing technique unsuitable for use on the factory floor. Beginning with an explicit noise model, which the original Lamdan and Wolfson technique lacks, we derived an optimal approach that overcomes these problems. We showed that the results obtained with the new algorithm are clearly better than the results from the original method. This paper addresses the performance characterization of the geometric hashing technique, more specifically the affine-invariant point matching, applied to the problem of recognizing and determining the pose of sheet metal parts. The experiments indicate that with a model having 10 to 14 points, with 2 points of the model undetected and 10 extraneous points detected, and with the model points perturbed by Gaussian noise of standard deviation 3 (0.58 of range), the average amount of computation required to obtain an answer is equivalent to trying 11 of the possible three-point bases. The misdetection rate, measured by the percentage of correct bases matches that fail to verify, is 0.9. The percentage of incorrect bases that successfully produced a match that did verify (false alarm rate) is 13. And, finally, 2 of the experiments failed to find a correct match and verify it. Results for experiments with real images are also presented.

  10. Affinity capillary electrophoresis: the theory of electromigration.

    Science.gov (United States)

    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).

  11. Convulsant bicuculline modifies CNS muscarinic receptor affinity

    Directory of Open Access Journals (Sweden)

    Rodríguez de Lores Arnaiz Georgina

    2006-04-01

    Full Text Available Abstract Background Previous work from this laboratory has shown that the administration of the convulsant drug 3-mercaptopropionic acid (MP, a GAD inhibitor, modifies not only GABA synthesis but also binding of the antagonist [3H]-quinuclidinyl benzilate ([3H]-QNB to central muscarinic receptors, an effect due to an increase in affinity without modifications in binding site number. The cholinergic system has been implicated in several experimental epilepsy models and the ability of acetylcholine to regulate neuronal excitability in the neocortex is well known. To study the potential relationship between GABAergic and cholinergic systems with seizure activity, we analyzed the muscarinic receptor after inducing seizure by bicuculline (BIC, known to antagonize the GABA-A postsynaptic receptor subtype. Results We analyzed binding of muscarinic antagonist [3H]-QNB to rat CNS membranes after i.p. administration of BIC at subconvulsant (1.0 mg/kg and convulsant (7.5 mg/kg doses. Subconvulsant BIC dose failed to develop seizures but produced binding alteration in the cerebellum and hippocampus with roughly 40% increase and 10% decrease, respectively. After convulsant BIC dose, which invariably led to generalized tonic-clonic seizures, binding increased 36% and 15% to cerebellar and striatal membranes respectively, but decreased 12% to hippocampal membranes. Kd value was accordingly modified: with the subconvulsant dose it decreased 27% in cerebellum whereas it increased 61% in hippocampus; with the convulsant dose, Kd value decreased 33% in cerebellum but increased 85% in hippocampus. No change in receptor number site was found, and Hill number was invariably close to unity. Conclusion Results indicate dissimilar central nervous system area susceptibility of muscarinic receptor to BIC. Ligand binding was modified not only by a convulsant BIC dose but also by a subconvulsant dose, indicating that changes are not attributable to the seizure process

  12. Genetic affinities of the central Indian tribal populations.

    Directory of Open Access Journals (Sweden)

    Gunjan Sharma

    Full Text Available BACKGROUND: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic. There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. METHODOLOGY/PRINCIPAL FINDINGS: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe with the Austroasiatic (Munda group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. CONCLUSIONS/SIGNIFICANCE: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.

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

    Science.gov (United States)

    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.

  14. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

    Directory of Open Access Journals (Sweden)

    Borkar Minal

    2007-04-01

    geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. Conclusion The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.

  15. Isolation of ubiquitinated substrates by tandem affinity purification of E3 ligase-polyubiquitin-binding domain fusions (ligase traps).

    Science.gov (United States)

    Mark, Kevin G; Loveless, Theresa B; Toczyski, David P

    2016-02-01

    Ubiquitination is an essential protein modification that influences eukaryotic processes ranging from substrate degradation to nonproteolytic pathway alterations, including DNA repair and endocytosis. Previous attempts to analyze substrates via physical association with their respective ubiquitin ligases have had some success. However, because of the transient nature of enzyme-substrate interactions and rapid protein degradation, detection of substrates remains a challenge. Ligase trapping is an affinity purification approach in which ubiquitin ligases are fused to a polyubiquitin-binding domain, which allows the isolation of ubiquitinated substrates. Immunoprecipitation is first used to enrich for proteins that are bound to the ligase trap. Subsequently, affinity purification is used under denaturing conditions to capture proteins conjugated with hexahistidine-tagged ubiquitin. By using this protocol, ubiquitinated substrates that are specific for a given ligase can be isolated for mass spectrometry or western blot analysis. After cells have been collected, the described protocol can be completed in 2-3 d.

  16. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

    KAUST Repository

    Wang, Xiaolei

    2014-12-12

    Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify

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

    Science.gov (United States)

    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.

  18. A deformation of quantum affine algebra in squashed Wess-Zumino-Novikov-Witten models

    Energy Technology Data Exchange (ETDEWEB)

    Kawaguchi, Io; Yoshida, Kentaroh [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan)

    2014-06-01

    We proceed to study infinite-dimensional symmetries in two-dimensional squashed Wess-Zumino-Novikov-Witten models at the classical level. The target space is given by squashed S³ and the isometry is SU(2){sub L}×U(1){sub R}. It is known that SU(2){sub L} is enhanced to a couple of Yangians. We reveal here that an infinite-dimensional extension of U(1){sub R} is a deformation of quantum affine algebra, where a new deformation parameter is provided with the coefficient of the Wess-Zumino term. Then we consider the relation between the deformed quantum affine algebra and the pair of Yangians from the viewpoint of the left-right duality of monodromy matrices. The integrable structure is also discussed by computing the r/s-matrices that satisfy the extended classical Yang-Baxter equation. Finally, two degenerate limits are discussed.

  19. The sodium ion affinities of asparagine, glutamine, histidine and arginine

    Science.gov (United States)

    Wang, Ping; Ohanessian, Gilles; Wesdemiotis, Chrys

    2008-01-01

    The sodium ion affinities of the amino acids Asn, Gln, His and Arg have been determined by experimental and computational approaches (for Asn, His and Arg). Na+-bound heterodimers with amino acid and peptide ligands (Pep1, Pep2) were produced by electrospray ionization. From the dissociation kinetics of these Pep1-Na+-Pep2 ions to Pep1-Na+ and Pep2-Na+, determined by collisionally activated dissociation, a ladder of relative affinities was constructed and subsequently converted to absolute affinities by anchoring the relative values to known Na+ affinities. The Na+ affinities of Asn, His and Arg, were calculated at the MP2(full)/6-311+G(2d,2p)//MP2/6-31G(d) level of ab initio theory. The resulting experimental and computed Na+ affinities are in excellent agreement with one another. These results, combined with those of our previous studies, yield the sodium ion affinities of 18 out of the 20 [alpha]-amino acids naturally occurring in peptides and proteins of living systems.

  20. Tetrahydroprotoberberine alkaloids with dopamine and σ receptor affinity.

    Science.gov (United States)

    Gadhiya, Satishkumar; Madapa, Sudharshan; Kurtzman, Thomas; Alberts, Ian L; Ramsey, Steven; Pillarsetty, Nagavara-Kishore; Kalidindi, Teja; Harding, Wayne W

    2016-05-01

    Two series of analogues of the tetrahydroprotoberberine (THPB) alkaloid (±)-stepholidine that (a) contain various alkoxy substituents at the C10 position and, (b) were de-rigidified with respect to (±)-stepholidine, were synthesized and evaluated for affinity at dopamine and σ receptors in order to evaluate effects on D3 and σ2 receptor affinity and selectivity. Small n-alkoxy groups are best tolerated by D3 and σ2 receptors. Among all compounds tested, C10 methoxy and ethoxy analogues (10 and 11 respectively) displayed the highest affinity for σ2 receptors as well as σ2 versus σ1 selectivity and also showed the highest D3 receptor affinity. De-rigidification of stepholidine resulted in decreased affinity at all receptors evaluated; thus the tetracyclic THPB framework is advantageous for affinity at dopamine and σ receptors. Docking of the C10 analogues at the D3 receptor, suggest that an ionic interaction between the protonated nitrogen atom and Asp110, a H-bond interaction between the C2 phenol and Ser192, a H-bond interaction between the C10 phenol and Cys181 as well as hydrophobic interactions of the aryl rings to Phe106 and Phe345, are critical for high affinity of the compounds.

  1. 谈辅导员工作中的亲和力%On Importance of Affinity in Counselors’Work

    Institute of Scientific and Technical Information of China (English)

    王晶

    2015-01-01

    亲和力是辅导员基本素质之一,提升辅导员亲和力,能够彰显辅导员人格魅力,有助于构建和谐人际关系,有助于增进凝聚力与向心力。%Affinity is one of the basic qualities of counselors.Enhancing the affinity of counselors can reveal the charisma of the counselors,helping to build harmonious interpersonal relationships,cohesion and solidarity.

  2. Affine structures and a tableau model for E_6 crystals

    CERN Document Server

    Jones, Brant

    2009-01-01

    We provide the unique affine crystal structure for type E_6^{(1)} Kirillov-Reshetikhin crystals corresponding to the multiples of fundamental weights s Lambda_1, s Lambda_2, and s Lambda_6 for all s \\geq 1 (in Bourbaki's labeling of the Dynkin nodes, where 2 is the adjoint node). Our methods introduce a generalized tableaux model for classical highest weight crystals of type E and use the order three automorphism of the affine E_6^{(1)} Dynkin diagram. In addition, we provide a conjecture for the affine crystal structure of type E_7^{(1)} Kirillov-Reshetikhin crystals corresponding to the adjoint node.

  3. ODE/IM correspondence and modified affine Toda field equations

    CERN Document Server

    Ito, Katsushi

    2014-01-01

    We study the two-dimensional affine Toda field equations for affine Lie algebra $\\hat{\\mathfrak{g}}$ modified by a conformal transformation and the associated linear equations. In the conformal limit, the associated linear problem reduces to a (pseudo-)differential equation. For classical affine Lie algebra $\\hat{\\mathfrak{g}}$, we obtain a (pseudo-)differential equation corresponding to the Bethe equations for the Langlands dual of the Lie algebra $\\mathfrak{g}$, which were found by Dorey et al. in study of the ODE/IM correspondence.

  4. Affinity Thresholds for Membrane Fusion Triggering by Viral Glycoproteins▿

    OpenAIRE

    Hasegawa, Kosei; Hu, Chunling; Nakamura, Takafumi; Marks, James D.; Russell, Stephen J.; Peng, Kah-Whye

    2007-01-01

    Enveloped viruses trigger membrane fusion to gain entry into cells. The receptor affinities of their attachment proteins vary greatly, from 10−4 M to 10−9 M, but the significance of this is unknown. Using six retargeted measles viruses that bind to Her-2/neu with a 5-log range in affinity, we show that receptor affinity has little impact on viral attachment but is nevertheless a key determinant of infectivity and intercellular fusion. For a given cell surface receptor density, there is an aff...

  5. Volatility Components, Affine Restrictions and Non-Normal Innovations

    DEFF Research Database (Denmark)

    Christoffersen, Peter; Jacobs, Kris; Dorian, Christian;

    Recent work by Engle and Lee (1999) shows that allowing for long-run and short-run components greatly enhances a GARCH model's ability fit daily equity return dynamics. Using the risk-neutralization in Duan (1995), we assess the option valuation performance of the Engle-Lee model and compare...... models to four conditionally non-normal versions. As in Hsieh and Ritchken (2005), we find that non-affine models dominate affine models both in terms of fitting return and in terms of option valuation. For the affine models we find strong evidence in favor of the component structure for both returns...

  6. Moment-Based Method to Estimate Image Affine Transform

    Institute of Scientific and Technical Information of China (English)

    FENG Guo-rui; JIANG Ling-ge

    2005-01-01

    The estimation of affine transform is a crucial problem in the image recognition field. This paper resorted to some invariant properties under translation, rotation and scaling, and proposed a simple method to estimate the affine transform kernel of the two-dimensional gray image. Maps, applying to the original, produce some correlative points that can accurately reflect the affine transform feature of the image. Furthermore, unknown variables existing in the kernel of the transform are calculated. The whole scheme only refers to one-order moment,therefore, it has very good stability.

  7. Identification of proteins associated with RNA polymerase III using a modified tandem chromatin affinity purification.

    Science.gov (United States)

    Nguyen, Ngoc-Thuy-Trinh; Saguez, Cyril; Conesa, Christine; Lefebvre, Olivier; Acker, Joël

    2015-02-01

    To identify the proteins associated with the RNA polymerase III (Pol III) machinery in exponentially growing yeast cells, we developed our own tandem chromatin affinity purification procedure (TChAP) after in vivo cross-link, allowing a reproducible and good recovery of the protein bait and its associated partners. In contrast to TFIIIA that could only be purified as a free protein, this protocol allows us to capture free Pol III together with Pol III bound on its target genes. Transcription factors, elongation factors, RNA-associated proteins and proteins involved in Pol III biogenesis were identified by mass spectrometry. Interestingly, the presence of all the TFIIIB subunits found associated with Pol III together with the absence of TFIIIC and chromatin factors including histones suggest that DNA-bound Pol III purified using TChAP is mainly engaged in transcription reinitiation.

  8. Experimental characterization of the transport phenomena, adsorption, and elution in a protein A affinity monolithic medium.

    Science.gov (United States)

    Herigstad, M Omon; Dimartino, Simone; Boi, Cristiana; Sarti, Giulio C

    2015-08-14

    A commercially available convective interaction media (CIM) Protein A monolithic column was fully characterized in view of its application for the affinity capture of IgG in monoclonal antibody production processes. By means of moment analysis, the interstitial porosity and axial dispersion coefficient were determined. The frontal analysis method of characteristic points was employed, for the first time with monolithic media, to determine the dynamic binding capacity. The effects of the flow rate and pH on the total recovery of polyclonal IgG and elution profile were evaluated. A comparison with literature data for Protein A chromatography beads demonstrate the superior bed utilization of monolithic media, which gave better performance at lower residence times.

  9. Techniques for capturing bighorn sheep lambs

    Science.gov (United States)

    Smith, Joshua B.; Walsh, Daniel P.; Goldstein, Elise J.; Parsons, Zachary D.; Karsch, Rebekah C.; Stiver, Julie R.; Cain, James W.; Raedeke, Kenneth J.; Jenks, Jonathan A.

    2014-01-01

    Low lamb recruitment is a major challenge facing managers attempting to mitigate the decline of bighorn sheep (Ovis canadensis), and investigations into the underlying mechanisms are limited because of the inability to readily capture and monitor bighorn sheep lambs. We evaluated 4 capture techniques for bighorn sheep lambs: 1) hand-capture of lambs from radiocollared adult females fitted with vaginal implant transmitters (VITs), 2) hand-capture of lambs of intensively monitored radiocollared adult females, 3) helicopter net-gunning, and 4) hand-capture of lambs from helicopters. During 2010–2012, we successfully captured 90% of lambs from females that retained VITs to ≤1 day of parturition, although we noted differences in capture rates between an area of high road density in the Black Hills (92–100%) of South Dakota, USA, and less accessible areas of New Mexico (71%), USA. Retention of VITs was 78% with pre-partum expulsion the main cause of failure. We were less likely to capture lambs from females that expelled VITs ≥1 day of parturition (range = 80–83%) or females that were collared without VITs (range = 60–78%). We used helicopter net-gunning at several sites in 1999, 2001–2002, and 2011, and it proved a useful technique; however, at one site, attempts to capture lambs led to lamb predation by golden eagles (Aquila chrysaetos). We attempted helicopter hand-captures at one site in 1999, and they also were successful in certain circumstances and avoided risk of physical trauma from net-gunning; however, application was limited. In areas of low accessibility or if personnel lack the ability to monitor females and/or VITs for extended periods, helicopter capture may provide a viable option for lamb capture.

  10. Radioactive proton capture on {sup 6}He

    Energy Technology Data Exchange (ETDEWEB)

    Sauvan, E.; Marques, F.M. [Caen Univ., 14 (France). Lab. de Physique Corpusculaire; Wilschut, H.W. [Kernfysich Versneller Instituut, Groningen (Netherlands)

    2001-03-01

    Radiative capture of protons is investigated as a probe of clustering in nuclei far from stability. The first such measurement on a halo nucleus is reported here for the reaction {sup 6}He(p,{gamma}) at 40 MeV. Capture into {sup 7}Li is observed as the strongest channel. In addition, events have been recorded that may be described by quasi-free capture on halo neutron, the {alpha} core and {sup 5}He. The possibility of describing such events by capture into the continuum of {sup 7}Li is also discussed. (authors)

  11. Design and optimization of a phosphopeptide anchor for specific immobilization of a capture protein on zirconium phosphonate modified supports.

    Science.gov (United States)

    Liu, Hao; Queffélec, Clémence; Charlier, Cathy; Defontaine, Alain; Fateh, Amina; Tellier, Charles; Talham, Daniel R; Bujoli, Bruno

    2014-11-25

    The attachment of affinity proteins onto zirconium phosphonate coated glass slides was investigated by fusing a short phosphorylated peptide sequence at one extremity to enable selective bonding to the active surface via the formation of zirconium phosphate coordinate covalent bonds. In a model study, the binding of short peptides containing zero to four phosphorylated serine units and a biotin end-group was assessed by surface plasmon resonance-enhanced ellipsometry (SPREE) as well as in a microarray format using fluorescence detection of AlexaFluor 647-labeled streptavidin. Significant binding to the zirconated surface was only observed in the case of the phosphopeptides, with the best performance, as judged by streptavidin capture, observed for peptides with three or four phosphorylation sites and when spotted at pH 3. When fusing similar phosphopeptide tags to the affinity protein, the presence of four phosphate groups in the tag allows efficient immobilization of the proteins and efficient capture of their target.

  12. Synthesis and characterization of pseudo-affinity ligand for penicillin acylase purification.

    Science.gov (United States)

    Keçili, Rüstem; Say, Ridvan; Yavuz, Handan

    2006-11-15

    The aim of this work was to test a chromatographic affinity support containing methacryloyl antipyrine (MAAP) for penicillin acylase (PA) purification by using pure penicillin acylase and crude extract. First, MAAP as a pseudo-specific ligand was synthesized by using methacryloyl chloride and 4-aminoantipyrine. Polymer beads (average size diameter: 40-120 micro m) were prepared by suspension polymerization of ethylene glycol dimethacrylate (EGDMA) and MAAP. This approach for the preparation of adsorbent has several advantages over conventional preparation protocols. An expensive and time consuming step in the preparation of adsorbent is immobilization of a ligand to the adsorption matrix. In this procedure, affinity ligand MAAP acts as comonomer without further modification steps. Poly(EGDMA-MAAP) beads were characterized by FTIR, NMR and screen analysis. Elemental analysis of MAAP for nitrogen was estimated as 89.3 micro mol/g. The prepared adsorbent was then used for the capture of penicillin acylase in batch system. The maximum penicillin acylase adsorption capacity of the poly(EGDMA-MAAP) beads was found to be 82.2 mg/g at pH 5.0. Chromatography with crude feedstock resulted in 23.2-fold purification and 93% recovery with 1.0 M NaOH.

  13. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    Science.gov (United States)

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  14. In-column ATR-FTIR spectroscopy to monitor affinity chromatography purification of monoclonal antibodies.

    Science.gov (United States)

    Boulet-Audet, Maxime; Kazarian, Sergei G; Byrne, Bernadette

    2016-07-29

    In recent years many monoclonal antibodies (mAb) have entered the biotherapeutics market, offering new treatments for chronic and life-threatening diseases. Protein A resin captures monoclonal antibody (mAb) effectively, but the binding capacity decays over repeated purification cycles. On an industrial scale, replacing fouled Protein A affinity chromatography resin accounts for a large proportion of the raw material cost. Cleaning-in-place (CIP) procedures were developed to extend Protein A resin lifespan, but chromatograms cannot reliably quantify any remaining contaminants over repeated cycles. To study resin fouling in situ, we coupled affinity chromatography and Fourier transform infrared (FTIR) spectroscopy for the first time, by embedding an attenuated total reflection (ATR) sensor inside a micro-scale column while measuring the UV 280 nm and conductivity. Our approach quantified the in-column protein concentration in the resin bed and determined protein conformation. Our results show that Protein A ligand leached during CIP. We also found that host cell proteins bound to the Protein A resin even more strongly than mAbs and that typical CIP conditions do not remove all fouling contaminants. The insights derived from in-column ATR-FTIR spectroscopic monitoring could contribute to mAb purification quality assurance as well as guide the development of more effective CIP conditions to optimise resin lifespan.

  15. Preparation and evaluation of spore-specific affinity- augmented bio-imprinted beads

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Scott D.; Mong, Gary M.; Ozanich, Rich M.; Mclean, Jeffrey S.; Goodwin, Shannon M.; Valentine, Nancy B.; Fredrickson, Jim K.

    2006-09-01

    The procedures previously described for imprinting bead surfaces with bacteria were applied to create novel affinity-augmented bacterial spore-imprinted beads. The imprinted beads are intended as a front-end spore capture/concentration stage of an integrated biological detection system. Our approach involves embedding bead surfaces with Bacillus thuringiensis kurstaki (Bt) spores (as a surrogate for Bacillus anthracis) during synthesis. Subsequent steps involved lithographic deactivation using a perfluoroether, spore removal to create imprint sites, and coating imprints with the lectin, concanavalin A, to provide general affinity. The synthesis of the intended material with the desired imprints was verified by scanning electron and confocal laser-scanning microscopy. The material was evaluated using spore-binding assays with either Bt or Bacillus subtilis (Bs) spores. The binding assays indicated strong spore-binding capability and a robust imprinting effect that accounted for 25 percent additional binding over nonimprinted controls. The binding assay results also indicated that further refinement of the surface deactivation procedure would enhance the performance of the imprinted substrate.

  16. Removal of PCR error products and unincorporated primers by metal-chelate affinity chromatography.

    Directory of Open Access Journals (Sweden)

    Indhu Kanakaraj

    Full Text Available Immobilized Metal Affinity Chromatography (IMAC has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and "histidine tags" genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu(2+-iminodiacetic acid (IDA agarose spin column, 94-99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu(2+-IDA agarose can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs.

  17. In-column ATR-FTIR spectroscopy to monitor affinity chromatography purification of monoclonal antibodies

    Science.gov (United States)

    Boulet-Audet, Maxime; Kazarian, Sergei G.; Byrne, Bernadette

    2016-07-01

    In recent years many monoclonal antibodies (mAb) have entered the biotherapeutics market, offering new treatments for chronic and life-threatening diseases. Protein A resin captures monoclonal antibody (mAb) effectively, but the binding capacity decays over repeated purification cycles. On an industrial scale, replacing fouled Protein A affinity chromatography resin accounts for a large proportion of the raw material cost. Cleaning-in-place (CIP) procedures were developed to extend Protein A resin lifespan, but chromatograms cannot reliably quantify any remaining contaminants over repeated cycles. To study resin fouling in situ, we coupled affinity chromatography and Fourier transform infrared (FTIR) spectroscopy for the first time, by embedding an attenuated total reflection (ATR) sensor inside a micro-scale column while measuring the UV 280 nm and conductivity. Our approach quantified the in-column protein concentration in the resin bed and determined protein conformation. Our results show that Protein A ligand leached during CIP. We also found that host cell proteins bound to the Protein A resin even more strongly than mAbs and that typical CIP conditions do not remove all fouling contaminants. The insights derived from in-column ATR-FTIR spectroscopic monitoring could contribute to mAb purification quality assurance as well as guide the development of more effective CIP conditions to optimise resin lifespan.

  18. Cellulose affinity purification of fusion proteins tagged with fungal family 1 cellulose-binding domain.

    Science.gov (United States)

    Sugimoto, Naohisa; Igarashi, Kiyohiko; Samejima, Masahiro

    2012-04-01

    N- or C-terminal fusions of red-fluorescent protein (RFP) with various fungal cellulose-binding domains (CBDs) belonging to carbohydrate binding module (CBM) family 1 were expressed in a Pichia pastoris expression system, and the resulting fusion proteins were used to examine the feasibility of large-scale affinity purification of CBD-tagged proteins on cellulose columns. We found that RFP fused with CBD from Trichoderma reesei CBHI (CBD(Tr)(CBHI)) was expressed at up to 1.2g/l in the culture filtrate, which could be directly injected into the cellulose column. The fusion protein was tightly adsorbed on the cellulose column in the presence of a sufficient amount of ammonium sulfate and was efficiently eluted with pure water. Bovine serum albumin (BSA) was not captured under these conditions, whereas both BSA and the fusion protein were adsorbed on a phenyl column, indicating that the cellulose column can be used for the purification of not only hydrophilic proteins but also for hydrophobic proteins. Recovery of various fusion proteins exceeded 80%. Our results indicate that protein purification by expression of a target protein as a fusion with a fungal family 1 CBD tag in a yeast expression system, followed by affinity purification on a cellulose column, is simple, effective and easily scalable.

  19. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    Science.gov (United States)

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

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

    Science.gov (United States)

    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.

  1. Taking Advantage: High Affinity B cells in the Germinal Center Have Lower Death Rates, But Similar Rates of Division Compared to Low Affinity Cells1

    OpenAIRE

    2009-01-01

    B lymphocytes producing high affinity antibodies (Abs) are critical for protection from extracellular pathogens, such as bacteria and parasites. The process by which high affinity B cells are selected during the immune response has never been elucidated. Though it has been shown that high affinity cells directly outcompete low affinity cells in the germinal center (GC)2, whether there are also intrinsic differences between these cells has not been addressed. It could be that higher affinity c...

  2. Dirac equation in gauge and affine-metric gravitation theories

    CERN Document Server

    Giachetta, G

    1995-01-01

    We show that the covariant derivative of Dirac fermion fields in the presence of a general linear connection on a world manifold is universal for Einstein's, gauge and affine-metric gravitation theories.

  3. Elective affinities and economic thought: 1870-1914

    Directory of Open Access Journals (Sweden)

    João Antônio de Paula

    2006-01-01

    Full Text Available This article seeks to demonstrate that the concept of "elective affinities" can be applied to the relations between economic thought, literature, and philosophy. Emphasis is given to Institutionalist thought, the German historical school, and neoclassical thought.

  4. REFINABLE DISTRIBUTIONS SUPPORTED ON SELF-AFFINE TILES

    Institute of Scientific and Technical Information of China (English)

    DaiXinrong

    2002-01-01

    In this paper,some conditions which assure the compactly supported refinable distributions supported on a self-affine tile to be Lebesgue-Stieltjes measures or absolutely continuous measures with respect to Lebesgue-Stieltjes measures are given.

  5. ASIFT: An Algorithm for Fully Affine Invariant Comparison

    Directory of Open Access Journals (Sweden)

    Guoshen Yu

    2011-02-01

    Full Text Available If a physical object has a smooth or piecewise smooth boundary, its images obtained by cameras in varying positions undergo smooth apparent deformations. These deformations are locally well approximated by affine transforms of the image plane. In consequence the solid object recognition problem has often been led back to the computation of affine invariant image local features. The similarity invariance (invariance to translation, rotation, and zoom is dealt with rigorously by the SIFT method The method illustrated and demonstrated in this work, Affine-SIFT (ASIFT, simulates a set of sample views of the initial images, obtainable by varying the two camera axis orientation parameters, namely the latitude and the longitude angles, which are not treated by the SIFT method. Then it applies the SIFT method itself to all images thus generated. Thus, ASIFT covers effectively all six parameters of the affine transform.

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

    Science.gov (United States)

    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.

  7. Aluminum-based water treatment residual use in a constructed wetland for capturing urban runoff phosphorus: Column study

    Science.gov (United States)

    Aluminum-based water treatment residuals (Al-WTR) have a strong affinity to sorb phosphorus. In a proof-of-concept greenhouse column study, Al-WTR was surface-applied at 0, 62, 124, and 248 Mg/ha to 15 cm of soil on top of 46 cm of sand; Al-WTR rates were estimated to capture 0, 10, 20, and 40 year...

  8. Some Inequalities for Lp-mixed Affine Surface Area

    Institute of Scientific and Technical Information of China (English)

    ZHU Xian-yang

    2012-01-01

    In this paper,the concepts of the ith Lp-mixed affine surface area and Lp-polar curvature images are introduced,some new inequalities connecting these new notions with Lp-centroid bodies and p-Blaschke bodies are showed.Moreover,a Blaschke-Santaló type inequality for Lp-mixed affine surface area is established.Our results also imply the similar to the inequalities for Marcus-Lopes,Bergstrom and Ky Fan.

  9. Affinity purification of sequence-specific DNA binding proteins.

    OpenAIRE

    1986-01-01

    We describe a method for affinity purification of sequence-specific DNA binding proteins that is fast and effective. Complementary chemically synthesized oligodeoxynucleotides that contain a recognition site for a sequence-specific DNA binding protein are annealed and ligated to give oligomers. This DNA is then covalently coupled to Sepharose CL-2B with cyanogen bromide to yield the affinity resin. A partially purified protein fraction is combined with competitor DNA and subsequently passed t...

  10. Affine A(1)3 N = 2 Monopole as the D Module and Affine ADHMN Sheaf

    Institute of Scientific and Technical Information of China (English)

    SONG Xiao-Shu; HOU Bo-Yu; GUO Yun-Dong; HOU Bo-Yuan; LING-HU Rong-Feng; L(U) Bing; CHENG Xin-Lu; YANG Xiang-Dong

    2008-01-01

    A Higgs-Yang-Mills monopole scattering spherical symmetrically Mong light cones is given. The left incoming anti-self-dual α plane fields are holomorphic, but the right outgoing SD fl plane fields are antiholomorphic, meanwhile the diffeomorphism symmetry is preserved with mutual inverse a/fine rapidity parameters μ and μ-1. The Dirac wave function scattering in this background also factorized respectively into the (anti)holomorphic amplitudes. The holomorphic anomaly is realized by the center term of a quasi Hopf algebra corresponding to an integrable conformal a/fine massive field. We find explicit Nahm transformation matrix (Fourier-Mukai transformation) between the Higgs YM BPS (fiat) bundles (D modules) and the affinized blow up ADHMN twistors (perverse sheafs). Thus we establish the algebra for the 't Hooft Hecke operators in the Hecke correspondence of the geometric Langfands program.

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

    Science.gov (United States)

    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.

  12. Structural basis for the high Ca2+ affinity of the ubiquitous SERCA2b Ca2+ pump.

    Science.gov (United States)

    Vandecaetsbeek, Ilse; Trekels, Mieke; De Maeyer, Marc; Ceulemans, Hugo; Lescrinier, Eveline; Raeymaekers, Luc; Wuytack, Frank; Vangheluwe, Peter

    2009-11-03

    Sarco(endo)plasmic reticulum Ca(2+) ATPase (SERCA) Ca(2+) transporters pump cytosolic Ca(2+) into the endoplasmic reticulum, maintaining a Ca(2+) gradient that controls vital cell functions ranging from proliferation to death. To meet the physiological demand of the cell, SERCA activity is regulated by adjusting the affinity for Ca(2+) ions. Of all SERCA isoforms, the housekeeping SERCA2b isoform displays the highest Ca(2+) affinity because of a unique C-terminal extension (2b-tail). Here, an extensive structure-function analysis of SERCA2b mutants and SERCA1a2b chimera revealed how the 2b-tail controls Ca(2+) affinity. Its transmembrane (TM) segment (TM11) and luminal extension functionally cooperate and interact with TM7/TM10 and luminal loops of SERCA2b, respectively. This stabilizes the Ca(2+)-bound E1 conformation and alters Ca(2+)-transport kinetics, which provides the rationale for the higher apparent Ca(2+) affinity. Based on our NMR structure of TM11 and guided by mutagenesis results, a structural model was developed for SERCA2b that supports the proposed 2b-tail mechanism and is reminiscent of the interaction between the alpha- and beta-subunits of Na(+),K(+)-ATPase. The 2b-tail interaction site may represent a novel target to increase the Ca(2+) affinity of malfunctioning SERCA2a in the failing heart to improve contractility.

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

    Science.gov (United States)

    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.

  14. Capture myopathy in an endangered sandhill crane (Grus canadensis pulla)

    Science.gov (United States)

    Carpenter, J.W.; Thomas, N.J.; Reeves, S.

    1991-01-01

    Despite precautions to protect cranes, a 3-year-old endangered Mississippi sandhill crane (Grus canadensis pulla) was found caught in a leghold trap in Gautier, Mississippi, on 11 November 1987. The bird could have been in the trap for up to 16 hr and was standing and struggling to escape when it was discovered. Serum chemistries of the crane on 12 November revealed elevated lactic dehydrogenase (2,880 IU/L), alanine aminotransferase (ALT) (152 IU/L), and aspartate aminotransferase (AST) (>1,000 IU/L) values. Following surgical amputation of a fractured toe, the bird never attempted to stand and was unable to stand even when manually supported. Radiographic and physical examination of both legs did not reveal any anatomical abnormalities. Despite medical care, including supportive therapy, no improvement was observed in the bird's ability to stand and to support itself, and the bird died on 19 November. Serum chemistries and the postmortem and histopathologic findings were compatible with capture myopathy described in other species. Because of the possible susceptibility of long-legged birds such as the Mississippi sandhill crane to capture myopathy, special care must be taken when trapping, handling, chemically immobilizing, and transporting these species. In addition, precautions must be taken when conducting a predator-control program to ensure that nontarget wildlife are unlikely to encounter traps. Capture myopathy has only rarely been observed in wild birds, and this case represents the first report in a Mississippi sandhill crane.

  15. Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy

    Science.gov (United States)

    Kuzmanov, Uros; Guo, Hongbo; Buchsbaum, Diana; Cosme, Jake; Abbasi, Cynthia; Isserlin, Ruth; Sharma, Parveen; Gramolini, Anthony O.; Emili, Andrew

    2016-01-01

    Phospholamban (PLN) plays a central role in Ca2+ homeostasis in cardiac myocytes through regulation of the sarco(endo)plasmic reticulum Ca2+-ATPase 2A (SERCA2A) Ca2+ pump. An inherited mutation converting arginine residue 9 in PLN to cysteine (R9C) results in dilated cardiomyopathy (DCM) in humans and transgenic mice, but the downstream signaling defects leading to decompensation and heart failure are poorly understood. Here we used precision mass spectrometry to study the global phosphorylation dynamics of 1,887 cardiac phosphoproteins in early affected heart tissue in a transgenic R9C mouse model of DCM compared with wild-type littermates. Dysregulated phosphorylation sites were quantified after affinity capture and identification of 3,908 phosphopeptides from fractionated whole-heart homogenates. Global statistical enrichment analysis of the differential phosphoprotein patterns revealed selective perturbation of signaling pathways regulating cardiovascular activity in early stages of DCM. Strikingly, dysregulated signaling through the Notch-1 receptor, recently linked to cardiomyogenesis and embryonic cardiac stem cell development and differentiation but never directly implicated in DCM before, was a prominently perturbed pathway. We verified alterations in Notch-1 downstream components in early symptomatic R9C transgenic mouse cardiomyocytes compared with wild type by immunoblot analysis and confocal immunofluorescence microscopy. These data reveal unexpected connections between stress-regulated cell signaling networks, specific protein kinases, and downstream effectors essential for proper cardiac function. PMID:27742792

  16. Affinity Solvents for Intensified Organics Extraction: Development Challenges and Prospects

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In most organics extraction processes, the commonly used solvents employ solely physical interactions. Therefore, for the recovery and purification of products from complex mixtures, the selectivity and/or capacity of classical solvents towards the desired solutes is usually insufficient, enforcing the need for complex and thus expensive separation schemes. Significant simplification and cost-reduction can be achieved when affinity solvents would be available that are able to recognize the solutes of interest by their molecular structure. The main development challenges to establish such affinity solvents are: Selection and incorporation of molecular recognition and complexation capabilities; Evaluation of extraction capabilities; Efficient recovery and recycling of the affinity solvents; Implementation in industrial extraction equipment. This paper presents how these development challenges are addressed at the University of Twente, going all the way from affinity solvent design and synthesis, via high throughput screening and characterization up to pilot plant evaluation. Essential in the successful development of affinity solvents are structural cooperations with molecular chemists and custom synthesis companies for their design and synthesis. The various aspects are illustrated by several examples where newly developed environmentally benign affinity solvents appeared able to create major breakthroughs. The applications addressed involve oxygenates, sugars, and pharmaceutical ingredients, such as optical isomers and biomolecules.

  17. High affinity ligands for 'diazepam-insensitive' benzodiazepine receptors.

    Science.gov (United States)

    Wong, G; Skolnick, P

    1992-01-14

    Structurally diverse compounds have been shown to possess high affinities for benzodiazepine receptors in their 'diazepam-sensitive' (DS) conformations. In contrast, only the imidazobenzodiazepinone Ro 15-4513 has been shown to exhibit a high affinity for the 'diazepam-insensitive' (DI) conformation of benzodiazepine receptors. We examined a series of 1,4-diazepines containing one or more annelated ring systems for their affinities at DI and DS benzodiazepine receptors, several 1,4-diazepinone carboxylates including Ro 19-4603, Ro 16-6028 and Ro 15-3505 were found to possess high affinities (Ki approximately 2.6-20 nM) for DI. Nonetheless, among the ligands examined, Ro 15-4513 was the only substance with a DI/DS potency ratio approximately 1; other substances had ratios ranging from 13 to greater than 1000. Ligands with high to moderate affinities at DI were previously classified as partial agonists, antagonists, or partial inverse agonists at DS benzodiazepine receptors, but behaved as 'GABA neutral' (antagonist) substances at DI. The identification of several additional high affinity ligands at DI benzodiazepine receptors may be helpful in elucidating the pharmacological and physiological importance of these sites.

  18. Quantitative screening of yeast surface-displayed polypeptide libraries by magnetic bead capture.

    Science.gov (United States)

    Yeung, Yik A; Wittrup, K Dane

    2002-01-01

    Magnetic bead capture is demonstrated here to be a feasible alternative for quantitative screening of favorable mutants from a cell-displayed polypeptide library. Flow cytometric sorting with fluorescent probes has been employed previously for high throughput screening for either novel binders or improved mutants. However, many laboratories do not have ready access to this technology as a result of the limited availability and high cost of cytometers, restricting the use of cell-displayed libraries. Using streptavidin-coated magnetic beads and biotinylated ligands, an alternative approach to cell-based library screening for improved mutants was developed. Magnetic bead capture probability of labeled cells is shown to be closely correlated with the surface ligand density. A single-pass enrichment ratio of 9400 +/- 1800-fold, at the expense of 85 +/- 6% binder losses, is achieved from screening a library that contains one antibody-displaying cell (binder) in 1.1 x 10(5) nondisplaying cells. Additionally, kinetic screening for an initial high affinity to low affinity (7.7-fold lower) mutant ratio of 1:95,000, the magnetic bead capture method attains a single-pass enrichment ratio of 600 +/- 200-fold with a 75 +/- 24% probability of loss for the higher affinity mutant. The observed high loss probabilities can be straightforwardly compensated for by library oversampling, given the inherently parallel nature of the screen. Overall, these results demonstrate that magnetic beads are capable of quantitatively screening for novel binders and improved mutants. The described methods are directly analogous to procedures in common use for phage display and should lower the barriers to entry for use of cell surface display libraries.

  19. Experience machines : Capturing and retrieving personal content

    NARCIS (Netherlands)

    Werkhoven, P.

    2005-01-01

    Fundamental to human existence is the ability to capture, memorise and retrieve personal experiences and to share them with others. Can systems help us to capture and retrieve experiences? After motors have supplemented our muscles and sensors have supplemented our senses, emerging computer systems

  20. Visual Field Asymmetry in Attentional Capture

    Science.gov (United States)

    Du, Feng; Abrams, Richard A.

    2010-01-01

    The present study examined the spatial distribution of involuntary attentional capture over the two visual hemi-fields. A new experiment, and an analysis of three previous experiments showed that distractors in the left visual field that matched a sought-for target in color produced a much larger capture effect than identical distractors in the…

  1. Radiative proton capture on He-6

    NARCIS (Netherlands)

    Sauvan, E; Marques, FM; Wilschut, HW; Orr, NA; Angelique, JC; Borcea, C; Catford, WN; Clarke, NM; Descouvemont, P; Diaz, J; Grevy, S; Kugler, A; Kravchuk, [No Value; Labiche, M; Le Brun, C; Lienard, E; Lohner, H; Mittig, W; Ostendorf, RW; Pietri, S; Roussel-Chomaz, P; Saint Laurent, MG; Savajols, H; Wagner, [No Value; Yahlali, N

    2001-01-01

    Radiative capture of protons is investigated as a probe of clustering in nuclei far from stability. The first such measurement on a halo nucleus is reported here for the reaction He-6(p, gamma) at 40 MeV. Capture into Li-7 is observed as the strongest channel. In addition, events have been recorded

  2. Screen captures to support switching attention

    NARCIS (Netherlands)

    Gellevij, Mark; Meij, van der Hans

    2002-01-01

    The study set out to validate the supportive role of screen captures for switching attention. Forty-two participants learned how to work with Microsoft Excel with a paper manual. There were three types of manuals: a textual manual, a visual manual with full-screen captures, and a visual manual with

  3. Seamless presentation capture, indexing, and management

    Science.gov (United States)

    Hilbert, David M.; Cooper, Matthew; Denoue, Laurent; Adcock, John; Billsus, Daniel

    2005-10-01

    Technology abounds for capturing presentations. However, no simple solution exists that is completely automatic. ProjectorBox is a "zero user interaction" appliance that automatically captures, indexes, and manages presentation multimedia. It operates continuously to record the RGB information sent from presentation devices, such as a presenter's laptop, to display devices, such as a projector. It seamlessly captures high-resolution slide images, text and audio. It requires no operator, specialized software, or changes to current presentation practice. Automatic media analysis is used to detect presentation content and segment presentations. The analysis substantially enhances the web-based user interface for browsing, searching, and exporting captured presentations. ProjectorBox has been in use for over a year in our corporate conference room, and has been deployed in two universities. Our goal is to develop automatic capture services that address both corporate and educational needs.

  4. Capture of Trojans by Jumping Jupiter

    CERN Document Server

    Nesvorny, David; Morbidelli, Alessandro

    2013-01-01

    Jupiter Trojans are thought to be survivors of a much larger population of planetesimals that existed in the planetary region when planets formed. They can provide important constraints on the mass and properties of the planetesimal disk, and its dispersal during planet migration. Here we tested a possibility that the Trojans were captured during the early dynamical instability among the outer planets (aka the Nice model), when the semimajor axis of Jupiter was changing as a result of scattering encounters with an ice giant. The capture occurs in this model when Jupiter's orbit and its Lagrange points become radially displaced in a scattering event and fall into a region populated by planetesimals (that previously evolved from their natal transplanetary disk to ~5 AU during the instability). Our numerical simulations of the new capture model, hereafter jump capture, satisfactorily reproduce the orbital distribution of the Trojans and their total mass. The jump capture is potentially capable of explaining the ...

  5. Encapsulated liquid sorbents for carbon dioxide capture.

    Science.gov (United States)

    Vericella, John J; Baker, Sarah E; Stolaroff, Joshuah K; Duoss, Eric B; Hardin, James O; Lewicki, James; Glogowski, Elizabeth; Floyd, William C; Valdez, Carlos A; Smith, William L; Satcher, Joe H; Bourcier, William L; Spadaccini, Christopher M; Lewis, Jennifer A; Aines, Roger D

    2015-02-05

    Drawbacks of current carbon dioxide capture methods include corrosivity, evaporative losses and fouling. Separating the capture solvent from infrastructure and effluent gases via microencapsulation provides possible solutions to these issues. Here we report carbon capture materials that may enable low-cost and energy-efficient capture of carbon dioxide from flue gas. Polymer microcapsules composed of liquid carbonate cores and highly permeable silicone shells are produced by microfluidic assembly. This motif couples the capacity and selectivity of liquid sorbents with high surface area to facilitate rapid and controlled carbon dioxide uptake and release over repeated cycles. While mass transport across the capsule shell is slightly lower relative to neat liquid sorbents, the surface area enhancement gained via encapsulation provides an order-of-magnitude increase in carbon dioxide absorption rates for a given sorbent mass. The microcapsules are stable under typical industrial operating conditions and may be used in supported packing and fluidized beds for large-scale carbon capture.

  6. Differential ligand binding affinities of human estrogen receptor-α isoforms.

    Directory of Open Access Journals (Sweden)

    Amanda H Y Lin

    Full Text Available Rapid non-genomic effects of 17β-estradiol are elicited by the activation of different estrogen receptor-α isoforms. Presence of surface binding sites for estrogen have been identified in cells transfected with full-length estrogen receptor-α66 (ER66 and the truncated isoforms, estrogen receptor-α46 (ER46 and estrogen receptor-α36 (ER36. However, the binding affinities of the membrane estrogen receptors (mERs remain unknown due to the difficulty of developing of stable mER-transfected cell lines with sufficient mER density, which has largely hampered biochemical binding studies. The present study utilized cell-free expression systems to determine the binding affinities of 17β-estradiol to mERs, and the relationship among palmitoylation, membrane insertion and binding affinities. Saturation binding assays of human mERs revealed that [³H]-17β-estradiol bound ER66 and ER46 with Kd values of 68.81 and 60.72 pM, respectively, whereas ER36 displayed no specific binding within the tested concentration range. Inhibition of palmitoylation or removal of the nanolipoprotein particles, used as membrane substitute, reduced the binding affinities of ER66 and ER46 to 17β-estradiol. Moreover, ER66 and ER46 bound differentially with some estrogen receptor agonists and antagonists, and phytoestrogens. In particular, the classical estrogen receptor antagonist, ICI 182,780, had a higher affinity for ER66 than ER46. In summary, the present study defines the binding affinities for human estrogen receptor-α isoforms, and demonstrates that ER66 and ER46 show characteristics of mERs. The present data also indicates that palmitoylation and membrane insertion of mERs are important for proper receptor conformation allowing 17β-estradiol binding. The differential binding of ER66 and ER46 with certain compounds substantiates the prospect of developing mER-selective drugs.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Briers, Yves [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium); Schmelcher, Mathias; Loessner, Martin J. [Institute of Food Science and Nutrition, ETH Zuerich, Schmelzbergstrasse 7, CH-8092 Zuerich (Switzerland); Hendrix, Jelle; Engelborghs, Yves [Laboratory of Biomolecular Dynamics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven (Belgium); Volckaert, Guido [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium); Lavigne, Rob, E-mail: rob.lavigne@biw.kuleuven.be [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium)

    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.

  9. Identification of proteins interacting with ammodytoxins in Vipera ammodytes ammodytes venom by immuno-affinity chromatography.

    Science.gov (United States)

    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.

  10. Affinity chromatography of chaperones based on denatured proteins: Analysis of cell lysates of different origin.

    Science.gov (United States)

    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.

  11. Purification to homogeneity of an active opioid receptor from rat brain by affinity chromatography.

    Science.gov (United States)

    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.

  12. The serotonin transporter: Examination of the changes in transporter affinity induced by ligand binding

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. In vitro evolution and affinity-maturation with Coliphage qβ display.

    Directory of Open Access Journals (Sweden)

    Claudia Skamel

    Full Text Available The Escherichia coli bacteriophage, Qβ (Coliphage Qβ, offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV. DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets.

  14. Metal binding affinity and selectivity in metalloproteins: insights from computational studies.

    Science.gov (United States)

    Dudev, Todor; Lim, Carmay

    2008-01-01

    This review highlights insights gained from computational studies on protein-metal recognition. We systematically dissect the various factors governing metal binding affinity and selectivity in proteins starting from (a) the intrinsic properties of the metal and neighboring metal cations (if present), to (b) the primary coordination sphere, (c) the second coordination shell, (d) the protein matrix, (e) the bulk solvent, and (f) competing non-protein ligands from the surrounding biological environment. The results herein reveal the fundamental principles and the molecular bases underlying protein-metal recognition, which serve as a guide to engineer novel metalloproteins with programmed properties.

  15. Innovation in chemistry courses in France in the mid-eighteenth century: experiments and affinities.

    Science.gov (United States)

    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.

  16. Charged Covalent Triazine Frameworks for CO2 Capture and Conversion.

    Science.gov (United States)

    Buyukcakir, Onur; Je, Sang Hyun; Talapaneni, Siddulu Naidu; Kim, Daeok; Coskun, Ali

    2017-03-01

    The quest for the development of new porous materials addressing both CO2 capture from various sources and its conversion into useful products is a very active research area and also critical in order to develop a more sustainable and environmentally-friendly society. Here, we present the first charged covalent triazine framework (cCTF) prepared by simply heating nitrile functionalized dicationic viologen derivatives under ionothermal reaction conditions using ZnCl2 as both solvent and trimerization catalyst. It has been demonstrated that the surface area, pore volume/size of cCTFs can be simply controlled by varying the synthesis temperature and the ZnCl2 content. Specifically, increasing the reaction temperature led to controlled increase in the mesopore content and facilitated the formation of hierarchical porosity, which is critical to ensure efficient mass transport within porous materials. The resulting cCTFs showed high specific surface areas up to 1247 m(2) g(-1), and high physicochemical stability. The incorporation of ionic functional moieties to porous organic polymers improved substantially their CO2 affinity (up to 133 mg g(-1), at 1 bar and 273 K) and transformed them into hierarchically porous organocatalysts for CO2 conversion. More importantly, the ionic nature of cCTFs, homogeneous charge distribution together with hierarchical porosity offered a perfect platform for the catalytic conversion of CO2 into cyclic carbonates in the presence of epoxides through an atom economy reaction in high yields and exclusive product selectivity. These results clearly demonstrate the promising aspect of incorporation of charged units into the porous organic polymers for the development of highly efficient porous organocatalysts for CO2 capture and fixation.

  17. Impact of automatic threshold capture on pulse generator longevity

    Institute of Scientific and Technical Information of China (English)

    CHEN Ruo-han; CHEN Ke-ping; WANG Fang-zheng; HUA Wei; ZHANG Shu

    2006-01-01

    Background The automatic, threshold tracking, pacing algorithm developed by St. Jude Medical, verifies ventricular capture beat by beat by recognizing the evoked response following each pacemaker stimulus. This function was assumed to be not only energy saving but safe. This study estimated the extension in longevity obtained by AutoCapture (AC) compared with pacemakers programmed to manually optimized, nominal output.Methods Thirty-four patients who received the St. Jude Affinity series pacemaker were included in the study.The following measurements were taken: stimulation and sensing threshold, impedance of leads, evoked response and polarization signals by 3501 programmer during followup, battery current and battery impedance under different conditions. For longevity comparison, ventricular output was programmed under three different conditions: (1) AC on; (2) AC off with nominal output, and (3) AC off with pacing output set at twice the pacing threshold with a minimum of 2.0 V. Patients were divided into two groups: chronic threshold is higher or lower than 1 V. The efficacy of AC was evaluated.Results Current drain in the AC on group, AC off with optimized programming or nominal output was (14.33±2.84) mA, (16.74±2.75) mA and (18.4±2.44) mA, respectively (AC on or AC off with optimized programming vs. nominal output, P < 0.01). Estimated longevity was significantly extended by AC on when compared with nominal setting [(103 ± 27) months, (80 ± 24) months, P < 0.01). Furthermore, compared with the optimized programming, AC extends the longevity when the pacing threshold is higher than 1 V.Conclusion AC could significantly prolong pacemaker longevity; especially in the patient with high pacing threshold.

  18. Analysis of allergens in tubeimu saponin extracts by using rat basophilic leukemia 2H3 cell-based affinity chromatography coupled to liquid chromatography and mass spectrometry.

    Science.gov (United States)

    Zhang, Tao; Han, Shengli; Liu, Qi; Guo, Ying; He, Langchong

    2014-11-01

    An affinity two-dimensional chromatography method was developed for the recognition, separation, and identification of allergic components from tubeimu saponin extracts, a preparation often injected to treat various conditions as indicated by traditional Chinese medicine. Rat basophilic leukemia-2H3 cell membranes were used as the stationary phase of a membrane affinity chromatography column to capture components with affinity for mast cells that could be involved in a degranulation reaction. The retained components were enriched and analyzed by membrane affinity chromatography with liquid chromatography and mass spectrometry via a port switch valve. Suitability and reliability of the method was investigated using appropriate standards, and then, the method was applied to identify components retained from tubeimu saponin extracts. Tubeimoside A was identified in this way as a potential allergen, and degranulation assays confirmed that tubeimoside A induces RBL-2H3 cell degranulation in a dose-dependent manner. An increase in Ca(2+) influx indicated that degranulation induced by tubeimoside A is likely Ca(2+) dependent. Coupled with the degranulation assay, RBL-2H3 cell-based affinity chromatography coupled with liquid chromatography and mass spectrometry is an effective method for screening and identifying allergic components from tubeimu saponin extracts.

  19. The Statistics of DNA Capture by a Solid-State Nanopore

    CERN Document Server

    Mihovilovic, Mirna; Stein, Derek

    2012-01-01

    A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

  20. Capture of irregular satellites at Jupiter

    Energy Technology Data Exchange (ETDEWEB)

    Nesvorný, David; Vokrouhlický, David; Deienno, Rogerio [Department of Space Studies, Southwest Research Institute, 1050 Walnut Street, Suite 300, Boulder, CO 80302 (United States)

    2014-03-20

    The irregular satellites of outer planets are thought to have been captured from heliocentric orbits. The exact nature of the capture process, however, remains uncertain. We examine the possibility that irregular satellites were captured from the planetesimal disk during the early solar system instability when encounters between the outer planets occurred. Nesvorný et al. already showed that the irregular satellites of Saturn, Uranus, and Neptune were plausibly captured during planetary encounters. Here we find that the current instability models present favorable conditions for capture of irregular satellites at Jupiter as well, mainly because Jupiter undergoes a phase of close encounters with an ice giant. We show that the orbital distribution of bodies captured during planetary encounters provides a good match to the observed distribution of irregular satellites at Jupiter. The capture efficiency for each particle in the original transplanetary disk is found to be (1.3-3.6) × 10{sup –8}. This is roughly enough to explain the observed population of jovian irregular moons. We also confirm Nesvorný et al.'s results for the irregular satellites of Saturn, Uranus, and Neptune.

  1. Covalent Organic Frameworks for CO2 Capture.

    Science.gov (United States)

    Zeng, Yongfei; Zou, Ruqiang; Zhao, Yanli

    2016-04-20

    As an emerging class of porous crystalline materials, covalent organic frameworks (COFs) are excellent candidates for various applications. In particular, they can serve as ideal platforms for capturing CO2 to mitigate the dilemma caused by the greenhouse effect. Recent research achievements using COFs for CO2 capture are highlighted. A background overview is provided, consisting of a brief statement on the current CO2 issue, a summary of representative materials utilized for CO2 capture, and an introduction to COFs. Research progresses on: i) experimental CO2 capture using different COFs synthesized based on different covalent bond formations, and ii) computational simulation results of such porous materials on CO2 capture are summarized. Based on these experimental and theoretical studies, careful analyses and discussions in terms of the COF stability, low- and high-pressure CO2 uptake, CO2 selectivity, breakthrough performance, and CO2 capture conditions are provided. Finally, a perspective and conclusion section of COFs for CO2 capture is presented. Recent advancements in the field are highlighted and the strategies and principals involved are discussed.

  2. Increased hsp70 of glucocorticoid receptor complex induced by scald and heat stress and its possible effect on the affinity of glucocorticoid receptor

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-hui; TANG Hong-tai; LU Jian; XIA Zhao-fan

    2010-01-01

    Background Glucocorticoid (GC) insensitivity/GC resistance is an important etiological and prognostic factor in multiple diseases and pathophysiological processes such as scald, shock and asthma. The function of GC was mediated by glucocorticoid receptor (GR). Scald not only decreased the expression of GR but also reduced the affinity of GR, which played an important role in GC resistance in scalded rats. Whereas the molecular mechanism responsible for the decrease of GR affinity resulted from scald remains unclear. Recent studies showed that the changes of heat shock proteins (hsp) especially hsp90 and hsp70 of GR heterocomplex were associated with GR low affinity in vitro. Methods The affinity of GR in hepatic cytosols and in the cytosols of SMMC-7721 cells were determined by radioligand binding assay and scatchard plot. GR heterocomplex in cytosols were captured by coimmunoprecipation and the levels of hsp90 and hsp70 of GR complex were detected by quantitative Western blotting.Results Similar with that of hepatic cytosol of scalded rats, a remarkable decrease of GR affinity was also found in the cytosol of heat stressed SMMC-7721 cells. The level of hsp70 of GR complex in hepatic cytosol of scalded rats (30% total body surface area immersion scald) and in cytosol of heat stressed human hepatocarcinoma cell line SMMC-7721 were both increased by 1.5 fold, whereas no change of hsp90 in GR heterocomplex was found. According to the correlation analysis, there may be a positive relationship between increased hsp70 of GR complex and decreased GR affinity in the cytosols.Conclusions The primary results indicated that the level of hsp70 of GR heterocomplex was increased in the hepatic cytosol of scalded rats and the cytosol of heat stressed SMMC-7721 cells. The increase of hsp70 of GR complex might be associated with the decrease of GR affinity.

  3. Neutron capture cross section of Am241

    Science.gov (United States)

    Jandel, M.; Bredeweg, T. A.; Bond, E. M.; Chadwick, M. B.; Clement, R. R.; Couture, A.; O'Donnell, J. M.; Haight, R. C.; Kawano, T.; Reifarth, R.; Rundberg, R. S.; Ullmann, J. L.; Vieira, D. J.; Wilhelmy, J. B.; Wouters, J. M.; Agvaanluvsan, U.; Parker, W. E.; Wu, C. Y.; Becker, J. A.

    2008-09-01

    The neutron capture cross section of Am241 for incident neutrons from 0.02 eV to 320 keV has been measured with the detector for advanced neutron capture experiments (DANCE) at the Los Alamos Neutron Science Center. The thermal neutron capture cross section was determined to be 665±33 b. Our result is in good agreement with other recent measurements. Resonance parameters for Enwell with the measured data, and the extracted averaged resonance parameters in the unresolved resonance region are consistent with those for the resolved resonances.

  4. Understanding Motion Capture for Computer Animation

    CERN Document Server

    Menache, Alberto

    2010-01-01

    The power of today's motion capture technology has taken animated characters and special effects to amazing new levels of reality. And with the release of blockbusters like Avatar and Tin-Tin, audiences continually expect more from each new release. To live up to these expectations, film and game makers, particularly technical animators and directors, need to be at the forefront of motion capture technology. In this extensively updated edition of Understanding Motion Capture for Computer Animation and Video Games, an industry insider explains the latest research developments in digital design

  5. Gravitational Capture of Asteroids by Gas Drag

    Directory of Open Access Journals (Sweden)

    E. Vieira Neto

    2009-01-01

    captured by the planet got its velocity reduced and could been trapped as an irregular satellite. It is well known that, depending on the time scale of the gas envelope, an asteroid will spiral and collide with the planet. So, we simulate the passage of the asteroid in the gas envelope with its density decreasing along the time. Using this approach, we found effective captures, and have a better understanding of the whole process. Finally, we conclude that the origin of the irregular satellites cannot be attributed to the gas drag capture mechanism alone.

  6. BAD-lectins: boronic acid-decorated lectins with enhanced binding affinity for the selective enrichment of glycoproteins.

    Science.gov (United States)

    Lu, Ying-Wei; Chien, Chih-Wei; Lin, Po-Chiao; Huang, Li-De; Chen, Chang-Yang; Wu, Sz-Wei; Han, Chia-Li; Khoo, Kay-Hooi; Lin, Chun-Cheng; Chen, Yu-Ju

    2013-09-03

    The weak and variable binding affinities exhibited by lectin-carbohydrate interactions have often compromised the practical utility of lectin in capturing glycoproteins for glycoproteomic applications. We report here the development and applications of a new type of hybrid biomaterial, namely a boronic acid-decorated lectin (BAD-lectin), for efficient bifunctional glycoprotein labeling and enrichment. Our binding studies showed an enhanced affinity by BAD-lectin, likely to be mediated via the formation of boronate ester linkages between the lectin and glycan subsequent to the initial recognition process and thus preserving its glycan-specificity. Moreover, when attached to magnetic nanoparticles (BAD-lectin@MNPs), 2 to 60-fold improvement on detection sensitivity and enrichment efficiency for specific glycoproteins was observed over the independent use of either lectin or BA. Tested at the level of whole cell lysates for glycoproteomic applications, three different types of BAD-lectin@MNPs exhibited excellent specificities with only 6% overlapping among the 295 N-linked glycopeptides identified. As many as 236 N-linked glycopeptides (80%) were uniquely identified by one of the BAD-lectin@MNPs. These results indicated that the enhanced glycan-selective recognition and binding affinity of BAD-lectin@MNPs will facilitate a complementary identification of the under-explored glycoproteome.

  7. Aptamer-based organic-silica hybrid affinity monolith prepared via "thiol-ene" click reaction for extraction of thrombin.

    Science.gov (United States)

    Wang, Zheng; Zhao, Jin-cheng; Lian, Hong-zhen; Chen, Hong-yuan

    2015-06-01

    A novel strategy for preparing aptamer-based organic-silica hybrid monolithic column was developed via "thiol-ene" click chemistry. Due to the large specific surface area of the hybrid matrix and the simplicity, rapidness and high efficiency of "thiol-ene" click reaction, the average coverage density of aptamer on the organic-silica hybrid monolith reached 420 pmol μL(-1). Human α-thrombin can be captured on the prepared affinity monolithic column with high specificity and eluted by NaClO4 solution. N-p-tosyl-Gly-Pro-Arg p-nitroanilide acetate was used as the sensitive chromogenic substrate of thrombin. The thrombin enriched by this affinity column was detected with a detection of limit of 0.01 μM by spectrophotometry. Furthermore, the extraction recovery of thrombin at 0.15 μM in human serum was 91.8% with a relative standard deviation of 4.0%. These results indicated that "thiol-ene" click chemistry provided a promising technique to immobilize aptamer on organic-inorganic hybrid monolith and the easily-assembled affinity monolithic material could be used to realize highly selective recognition of trace proteins.

  8. Affine kinematics in planar fibrous connective tissues: an experimental investigation.

    Science.gov (United States)

    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. Protein purification by aminosquarylium cyanine dye-affinity chromatography.

    Science.gov (United States)

    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.

  10. The proton affinities of saturated and unsaturated heterocyclic molecules

    Science.gov (United States)

    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.

  11. New Adsorption Cycles for Carbon Dioxide Capture and Concentration

    Energy Technology Data Exchange (ETDEWEB)

    James Ritter; Armin Ebner; Steven Reynolds Hai Du; Amal Mehrotra

    2008-07-31

    tested successfully against several cycle schedules taken from the literature, including a 2-bed 4-step Skarstrom cycle, a 4-bed 9-step process with 2 equalization steps, a 9-bed 11-step process with 3 equalization steps, and a 6-bed 13-step process with 4 equalization steps and 4 idle steps. With respect to CO{sub 2} capture and concentration by PSA, this new approach is now providing a very straightforward way to determine all the viable 3-bed, 4-bed, 5-bed, n-bed, etc. HR PSA cycle schedules to explore using both simulation and experimentation. This program also touted the use of K-promoted HTlc as a high temperature, reversible adsorbent for CO{sub 2} capture by PSA. This program not only showed how to use this material in HR PSA cycles, but it also proposed a new CO{sub 2} interaction mechanism in conjunction with a non-equilibrium kinetic model that adequately describes the uptake and release of CO{sub 2} in this material, and some preliminary fixed bed adsorption breakthrough and desorption elution experiments were carried out to demonstrate complete reversibility on a larger scale. This information was essentially missing from the literature and deemed invaluable toward promoting the use of K-promoted HTlc as a high temperature, reversible adsorbent for CO{sub 2} capture by PSA. Overall, the objectives of this project were met. It showed the feasibility of using K-promoted hydrotalcite (HTlc) as a high temperature, reversible adsorbent for CO{sub 2} capture by PSA. It discovered some novel HR PSA cycles that might be useful for this purpose. Finally, it revealed a mechanistic understanding of the interaction of CO{sub 2} with K-promoted HTlc.

  12. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

    Science.gov (United States)

    Tang, Yat T; Marshall, Garland R

    2011-02-28

    Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable

  13. Taking advantage: high-affinity B cells in the germinal center have lower death rates, but similar rates of division, compared to low-affinity cells.

    Science.gov (United States)

    Anderson, Shannon M; Khalil, Ashraf; Uduman, Mohamed; Hershberg, Uri; Louzoun, Yoram; Haberman, Ann M; Kleinstein, Steven H; Shlomchik, Mark J

    2009-12-01

    B lymphocytes producing high-affinity Abs are critical for protection from extracellular pathogens, such as bacteria and parasites. The process by which high-affinity B cells are selected during the immune response has never been elucidated. Although it has been shown that high-affinity cells directly outcompete low-affinity cells in the germinal center (GC), whether there are also intrinsic differences between these cells has not been addressed. It could be that higher affinity cells proliferate more rapidly or are more likely to enter cell cycle, thereby outgrowing lower affinity cells. Alternatively, higher affinity cells could be relatively more resistant to cell death in the GC. By comparing high- and low-affinity B cells for the same Ag, we show here that low-affinity cells have an intrinsically higher death rate than do cells of higher affinity, even in the absence of competition. This suggests that selection in the GC reaction is due at least in part to the control of survival of higher affinity B cells and not by a proliferative advantage conferred upon these cells compared with lower affinity B cells. Control over survival rather than proliferation of low- and high-affinity B cells in the GC allows greater diversity not only in the primary response but also in the memory response.

  14. Ethanol-Induced ADH Activity in Zebrafish: Differential Concentration-Dependent Effects on High- Versus Low-Affinity ADH Enzymes.

    Science.gov (United States)

    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.

  15. Reactive Capture of Carbon Dioxide Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this Phase I SBIR, Reactive Innovations, LLC (RIL) proposes to develop a compact and lightweight electrochemical to capture carbon dioxide in the martian...

  16. Carbon Dioxide Capture Adsorbents: Chemistry and Methods.

    Science.gov (United States)

    Patel, Hasmukh A; Byun, Jeehye; Yavuz, Cafer T

    2016-12-21

    Excess carbon dioxide (CO2 ) emissions and their inevitable consequences continue to stimulate hard debate and awareness in both academic and public spaces, despite the widespread lack of understanding on what really is needed to capture and store the unwanted CO2 . Of the entire carbon capture and storage (CCS) operation, capture is the most costly process, consisting of nearly 70 % of the price tag. In this tutorial review, CO2 capture science and technology based on adsorbents are described and evaluated in the context of chemistry and methods, after briefly introducing the current status of CO2 emissions. An effective sorbent design is suggested, whereby six checkpoints are expected to be met: cost, capacity, selectivity, stability, recyclability, and fast kinetics.

  17. Capture effeciency of a vegetative environmental buffer

    Science.gov (United States)

    Particulate matter emitted from tunnel-ventilated animal feeding operations (AFOs) is known to transport malodorous compounds. As a mitigation strategy, vegetative environmental buffers (VEBs) are often installed surrounding AFOs to capture particulates and induce lofting and dispersion. Currently, ...

  18. Model based adaptive control of a continuous capture process for monoclonal antibodies production.

    Science.gov (United States)

    Steinebach, Fabian; Angarita, Monica; Karst, Daniel J; Müller-Späth, Thomas; Morbidelli, Massimo

    2016-04-29

    A two-column capture process for continuous processing of cell-culture supernatant is presented. Similar to other multicolumn processes, this process uses sequential countercurrent loading of the target compound in order maximize resin utilization and productivity for a given product yield. The process was designed using a novel mechanistic model for affinity capture, which takes both specific adsorption as well as transport through the resin beads into account. Simulations as well as experimental results for the capture of an IgG antibody are discussed. The model was able to predict the process performance in terms of yield, productivity and capacity utilization. Compared to continuous capture with two columns operated batch wise in parallel, a 2.5-fold higher capacity utilization was obtained for the same productivity and yield. This results in an equal improvement in product concentration and reduction of buffer consumption. The developed model was used not only for the process design and optimization but also for its online control. In particular, the unit operating conditions are changed in order to maintain high product yield while optimizing the process performance in terms of capacity utilization and buffer consumption also in the presence of changing upstream conditions and resin aging.

  19. DC-SIGN plays a stronger role than DCIR in mediating HIV-1 capture and transfer.

    Science.gov (United States)

    Jin, Wei; Li, Chang; Du, Tao; Hu, Kai; Huang, Xin; Hu, Qinxue

    2014-06-01

    The C-type lectin receptors (CLRs) expressed on dendritic cells (DCs), in particular DC-SIGN and DCIR, likely play an important role in HIV-1 early infection. Here, we systematically compared the capture and transfer capability of DC-SIGN and DCIR using a wide range of HIV-1 isolates. Our results indicated that DC-SIGN plays a stronger role than DCIR in DC-mediated HIV-1 capture and transfer. This was further strengthened by the data from transient and stable transfectants, showing that DC-SIGN had better capability, compared with DCIR in HIV-1 capture and transfer. Following constructing and analyzing a series of soluble DC-SIGN and DCIR truncates and chimeras, we demonstrated that the neck domain, but not the CRD, renders DC-SIGN higher binding affinity to gp120 likely via the formation of tetramerization. Our findings provide insights into CLR-mediated HIV-1 capture and transfer, highlighting potential targets for intervention strategies against gp120-CLR interactions.

  20. Culturing captures members of the soil rare biosphere.

    Science.gov (United States)

    Shade, Ashley; Hogan, Clifford S; Klimowicz, Amy K; Linske, Matthew; McManus, Patricia S; Handelsman, Jo

    2012-09-01

    The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the 'rare biosphere') are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.

  1. Enhancing Community Detection By Affinity-based Edge Weighting Scheme

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    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.

  2. k-Schur functions and affine Schubert calculus

    CERN Document Server

    Lam, Thomas; Morse, Jennifer; Schilling, Anne; Shimozono, Mark; Zabrocki, Mike

    2014-01-01

    This book gives an introduction to the very active field of combinatorics of affine Schubert calculus, explains the current state of the art, and states the current open problems. Affine Schubert calculus lies at the crossroads of combinatorics, geometry, and representation theory. Its modern development is motivated by two seemingly unrelated directions. One is the introduction of k-Schur functions in the study of Macdonald polynomial positivity, a mostly combinatorial branch of symmetric function theory. The other direction is the study of the Schubert bases of the (co)homology of the affine Grassmannian, an algebro-topological formulation of a problem in enumerative geometry. This is the first introductory text on this subject. It contains many examples in Sage, a free open source general purpose mathematical software system, to entice the reader to investigate the open problems. This book is written for advanced undergraduate and graduate students, as well as researchers, who want to become familiar with ...

  3. REPRESENTATIONS OF AFFINE HECKE ALGEBRAS OF TYPE G2

    Institute of Scientific and Technical Information of China (English)

    Xi Nanhua

    2009-01-01

    Let k be a field and q a nonzero element in k such that the square roots of q are in k.We use Hq to denote an affine Hecke algebra over k of type G2 with parameter q.The purpose of this paper is to study representations of Hq by using based rings of two-sided cells of an affine Weyl group W of type G2.We shall give the classification of irreducible representations of Hq.We also remark that a calculation in [11] actually shows that Theorem 2 in [1] needs a modification, a fact is known to Grojnowski and Tanisaki long time ago.In this paper we also show an interesting relation between Hq and an Hecke algebra corresponding to a certain Coxeter group.Apparently the idea in this paper works for all affine Weyl groups, but that is the theme of another paper.

  4. Fast Affinity Propagation Clustering based on Machine Learning

    Directory of Open Access Journals (Sweden)

    Shailendra Kumar Shrivastava

    2013-01-01

    Full Text Available Affinity propagation (AP was recently introduced as an un-supervised learning algorithm for exemplar based clustering. In this paper a novel Fast Affinity Propagation clustering Approach based on Machine Learning (FAPML has been proposed. FAPML tries to put data points into clusters based on the history of the data points belonging to clusters in early stages. In FAPML we introduce affinity learning constant and dispersion constant which supervise the clustering process. FAPML also enforces the exemplar consistency and one of 'N constraints. Experiments conducted on many data sets such as Olivetti faces, Mushroom, Documents summarization, Thyroid, Yeast, Wine quality Red, Balance etc. show that FAPML is up to 54 % faster than the original AP with better Net Similarity.

  5. Single-cell measurement of red blood cell oxygen affinity

    CERN Document Server

    Caprio, Di; Higgins, John M; Schonbrun, Ethan

    2015-01-01

    Oxygen is transported throughout the body by hemoglobin in red blood cells. While the oxygen affinity of blood is well understood and is routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of red blood cell volume and hemoglobin concentration are taken millions of times per day by clinical hematology analyzers and are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume and hemoglobin concentration for individual red blood cells in high-throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.5%, which corresponds to the maximum slope of the oxygen-hemoglobin dissociation curve. In addition, single-cell oxygen affinity is positively correlated with hemoglobin concentr...

  6. Properties of the Affine Invariant Ensemble Sampler in high dimensions

    CERN Document Server

    Huijser, David; Brewer, Brendon J

    2015-01-01

    We present theoretical and practical properties of the affine-invariant ensemble sampler Markov chain Monte Carlo method. In high dimensions the affine-invariant ensemble sampler shows unusual and undesirable properties. We demonstrate this with an $n$-dimensional correlated Gaussian toy problem with a known mean and covariance structure, and analyse the burn-in period. The burn-in period seems to be short, however upon closer inspection we discover the mean and the variance of the target distribution do not match the expected, known values. This problem becomes greater as $n$ increases. We therefore conclude that the affine-invariant ensemble sampler should be used with caution in high dimensional problems. We also present some theoretical results explaining this behaviour.

  7. Super-Affine Hierarchies and their Poisson Embeddings

    CERN Document Server

    Toppan, F

    1998-01-01

    The link between (super)-affine Lie algebras as Poisson brackets structures and integrable hierarchies provides both a classification and a tool for obtaining superintegrable hierarchies. The lack of a fully systematic procedure for constructing matrix-type Lax operators, which makes the supersymmetric case essentially different from the bosonic counterpart, is overcome via the notion of Poisson embeddings (P.E.), i.e. Poisson mappings relating affine structures to conformal structures (in their simplest version P.E. coincide with the Sugawara construction). A full class of hierarchies can be recovered by using uniquely Lie-algebraic notions. The group-algebraic properties implicit in the super-affine picture allow a systematic derivation of reduced hierarchies by imposing either coset conditions or hamiltonian constraints (or possibly both).

  8. A fast quantum algorithm for the affine Boolean function identification

    Science.gov (United States)

    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.

  9. Mesozooplankton affinities in a recovering freshwater estuary

    Science.gov (United States)

    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 high predation pressure, NH3sbnd N toxicity, sensitivity to oxygen, etc.), there is no clear cause

  10. Data capture and processing. [for Space Station

    Science.gov (United States)

    Lyon, John; Smith, Gene; Carper, Richard

    1987-01-01

    A systems concept developed in response to the specific requirements imposed by the Space Station and affiliated instrumentation is described. Particular attention is given to those subsystems associated with initial data capture, handling, routing, and distribution control for return link data via the Tracking and Data Relay Satellite System. The conceived approach, designated the Customer Data and Operations System, includes a data interface facility and a data handling center whose functions are data capture, demultiplexing and routing, early preprocessing, and ancillary data handling.

  11. Neuroprotective effects of high affinity Σ1 receptor selective compounds.

    Science.gov (United States)

    Luedtke, Robert R; Perez, Evelyn; Yang, Shao-Hua; Liu, Ran; Vangveravong, Suwanna; Tu, Zhude; Mach, Robert H; Simpkins, James W

    2012-03-02

    We previously reported that the antipsychotic drug haloperidol, a multifunctional D2-like dopamine and sigma receptor subtype antagonist, has neuroprotective properties. In this study we further examined the association between neuroprotection and receptor antagonism by evaluating a panel of novel compounds with varying affinity at sigma and D2-like dopamine receptors. These compounds were evaluated using an in vitro cytotoxicity assay that utilizes a hippocampal-derived cell line, HT-22, in the presence or absence of varying concentrations (5 to 20 mM) of glutamate. While haloperidol was found to be a potent neuroprotective agent in this in vitro cell assay, the prototypic sigma 1 receptor agonist (+)-pentazocine was found not to be neuroprotective. Subsequently, the potency for the neuroprotection of HT-22 cells was evaluated for a) three SV series indoles which have nMolar affinity at D2-like receptors but varying affinity at sigma 1 receptor and b) two benzyl phenylacetamides sigma 1 receptor selective compounds which bind with low affinity at D2-like receptors but have nMolar affinity for the sigma 1 receptor. We observed that cytoprotection correlated with the affinity of the compounds for sigma 1 receptors. Based upon results from the HT-22 cell-based in vitro assay, two phenylacetamides, LS-127 and LS-137, were further evaluated in vivo using a transient middle cerebral artery occlusion (t-MCAO) model of stroke. At a dose of 100 μg/kg, both LS-127 and LS-137 attenuated infarct volume by approximately 50%. These studies provide further evidence that sigma 1 receptor selective compounds can provide neuroprotection in cytotoxic situations. These results also demonstrate that sigma 1 receptor selective benzyl phenylacetamides are candidate pharmacotherapeutic agents that could be used to minimize neuronal death after a stroke or head trauma.

  12. Gate manipulation of DNA capture into nanopores.

    Science.gov (United States)

    He, Yuhui; Tsutsui, Makusu; Fan, Chun; Taniguchi, Masateru; Kawai, Tomoji

    2011-10-25

    Understanding biophysics governing DNA capture into a nanopore and establishing a manipulation system for the capture process are essential for nanopore-based genome sequencing. In this work, the functionality of extended electric field and electroosmotic flow (EOF) during the capture stage and their dependence on gate voltage, U(G), are investigated. We demonstrate that while both the electric field and EOF within a cis chamber make long-distance contributions to DNA capture around the pore mouth, the former effect is always capturing, while the latter causes trapping or blocking of the molecule depending on the magnitude of the gate voltage, U(G): an anionic EOF induced by high U(G) is capable of doubling the DNA trapping speed and thus the absorption radius in the cis chamber, whereas a cationic EOF by low U(G) would substantially offset the trapping effort by the electric field and even totally block DNA entrance into the pore. Based on the analysis, a gate regulation is proposed with the objective of achieving a high DNA capture rate while maintaining a low error rate.

  13. Telescoping Sample Canister Capture Mechanism (TSCCM)

    Science.gov (United States)

    Kong, Kin Yuen; Gorevan, Stephen; Mukherjee, Suparna; Wilson, Jack

    2003-11-01

    Sample return from solar system bodies including planets, moons, comets and asteroids is of high importance within the space science community. A returned sample will allow much more elaborate and detailed analysis not feasible through remote robotic analysis. For this reason, Honeybee Robotics has developed a low-cost reusable, automated on-orbit sample canister capture mechanism. The purpose of the mechanism is to capture a full sample canister and transfer it to a storage cache, sample return spacecraft, or on-orbit laboratory for further scientific study. The current design allows for reliable misalignment-compensated capture for various sample container geometries in any initial orientation. After capture, the sample canister is aligned and presented for transfer. Honeybee has demonstrated the concept through tests of two- and three-dimensional telescopic capture mechanism breadboards. The telescopic capture mechanism design is scalable, minimizes volume and can be made of lightweight material to minmize mass, all of which are critical aspects of spacecraft design.

  14. Affine group representation formalism for four dimensional, Lorentzian, quantum gravity

    CERN Document Server

    Ching-Yi, Chou; Soo, Chopin

    2012-01-01

    The Hamiltonian constraint of 4-dimensional General Relativity is recast explicitly in terms of the Chern--Simons functional and the local volume operator. In conjunction with the algebraic quantization program, application of the affine quantization concept due to Klauder facilitates the construction of solutions to all of the the quantum constraints in the Ashtekar variables and their associated Hilbert space. A physical Hilbert space is constructed for Lorentzian signature gravity with nonzero cosmological constant in the form of unitary, irreducible representations of the affine group.

  15. Affine transformation crossed product like algebras and noncommutative surfaces

    CERN Document Server

    Arnlind, Joakim

    2009-01-01

    Several classes of *-algebras associated to the action of an affine transformation are considered, and an investigation of the interplay between the different classes of algebras is initiated. Connections are established that relate representations of *-algebras, geometry of algebraic surfaces, dynamics of affine transformations, graphs and algebras coming from a quantization procedure of Poisson structures. In particular, algebras related to surfaces being inverse images of fourth order polynomials (in R^3) are studied in detail, and a close link between representation theory and geometric properties is established for compact as well as non-compact surfaces.

  16. Affine diffusions and related processes simulation, theory and applications

    CERN Document Server

    Alfonsi, Aurélien

    2015-01-01

    This book gives an overview of affine diffusions, from Ornstein-Uhlenbeck processes to Wishart processes and it considers some related diffusions such as Wright-Fisher processes. It focuses on different simulation schemes for these processes, especially second-order schemes for the weak error. It also presents some models, mostly in the field of finance, where these methods are relevant and provides some numerical experiments. The book explains the mathematical background to understand affine diffusions and analyze the accuracy of the schemes.  

  17. Solid support resins and affinity purification mass spectrometry.

    Science.gov (United States)

    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.

  18. The growth rate of symplectic homology and affine varieties

    CERN Document Server

    McLean, Mark

    2010-01-01

    We will show that the cotangent bundle of an integrally hyperbolic manifold is not symplectomorphic to any smooth affine variety. We will also show that the unit cotangent bundle of such a manifold is not Stein fillable by a Stein domain whose completion is symplectomorphic to a smooth affine variety. For instance, these results hold when our manifolds are simply connected with at least one Betti number greater than the corresponding Betti number of the n torus. We use an invariant called the growth rate of symplectic homology to prove this result.

  19. Ferromagnetic Levan Composite: An Affinity Matrix to Purify Lectin

    Directory of Open Access Journals (Sweden)

    Renata Angeli

    2009-01-01

    Full Text Available A simple and inexpensive procedure used magnetite and levan to synthesize a composite recovered by a magnetic field. Lectins from Canavalia ensiformis (Con A and Cratylia mollis (Cramoll 1 and Cramoll 1,4 did bind specifically to composite. The magnetic property of derivative favored washing out contaminating proteins and recovery of pure lectins with glucose elution. Cramoll 1 was purified by this affinity binding procedure in two steps instead of a previous three-step protocol with ammonium sulfate fractionation, affinity chromatography on Sephadex G-75, and ion exchange chromatography through a CM-cellulose column.

  20. Low concentration CO2 capture using physical adsorbents: Are Metal-Organic Frameworks becoming the new benchmark materials?

    KAUST Repository

    Belmabkhout, Youssef

    2016-03-30

    The capture and separation of traces and concentrated CO2 from important commodities such as CH4, H2, O2 and N2, is becoming important in many areas related to energy security and environmental sustainability. While trace CO2 concentration removal applications have been modestly studied for decades, the spike in interest in the capture of concentrated CO2 was motivated by the need for new energy vectors to replace highly concentrated carbon fuels and the necessity to reduce emissions from fossil fuel-fired power plants. CO2 capture from various gas streams, at different concentrations, using physical adsorbents, such as activated carbon, zeolites, and metal-organic frameworks (MOFs), is attractive. However, the adsorbents must be designed with consideration of many parameters including CO2 affinity, kinetics, energetics, stability, capture mechanism, in addition to cost. Here, we perform a systematic analysis regarding the key technical parameters that are required for the best CO2 capture performance using physical adsorbents. We also experimentally demonstrate a suitable material model of Metal Organic Framework as advanced adsorbents with unprecedented properties for CO2 capture in a wide range of CO2 concentration. These recently developed class of MOF adsorbents represent a breakthrough finding in the removal of traces CO2 using physical adsorption. This platform shows colossal tuning potential for more efficient separation agents.

  1. Relative binding affinity does not predict biological response to xenoestrogens in rat endometrial adenocarcinoma cells.

    Science.gov (United States)

    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

  2. Identification and measurement of chlorinated organic pesticides in water by electron-capture gas chromatography

    Science.gov (United States)

    Lamar, William L.; Goerlitz, Donald F.; Law, LeRoy M.

    1965-01-01

    Pesticides, in minute quantities, may affect the regimen of streams, and because they may concentrate in sediments, aquatic organisms, and edible aquatic foods, their detection and their measurement in the parts-per-trillion range are considered essential. In 1964 the U.S. Geological Survey at Menlo Park, Calif., began research on methods for monitoring pesticides in water. Two systems were selected--electron-capture gas chromatography and microcoulometric-titration gas chromatography. Studies on these systems are now in progress. This report provides current information on the development and application of an electron-capture gas chromatographic procedure. This method is a convenient and extremely sensitive procedure for the detection and measurement of organic pesticides having high electron affinities, notably the chlorinated organic pesticides. The electron-affinity detector is extremely sensitive to these substances but it is not as sensitive to many other compounds. By this method, the chlorinated organic pesticide may be determined on a sample of convenient size in concentrations as low as the parts-per-trillion range. To insure greater accuracy in the identifications, the pesticides reported were separated and identified by their retention times on two different types of gas chromatographic columns.

  3. U.S. Spacesuit Knowledge Capture Status and Initiatives

    Science.gov (United States)

    Chullen, Cinda; Woods, Ron; Jairala, Juniper; Bitterly, Rose; McMann, Joe; Lewis, Cathleen

    2012-01-01

    The National Aeronautics and Space Administration (NASA), other organizations and individuals have been performing United States (U.S.) spacesuit knowledge capture since the beginning of space exploration via publication of reports, conference presentations, specialized seminars, and classes instructed by veterans in the field. Recently, the effort has been more concentrated and formalized whereby a new avenue of spacesuit knowledge capture has been added to the archives through which videotaping occurs, engaging both current and retired specialists in the field presenting technical scope specifically for education and preservation of knowledge or being interviewed to archive their significance to NASA's history. Now with video archiving, all these avenues of learning are brought to life with the real experts presenting their wealth of knowledge on screen for future learners to enjoy. U.S. spacesuit knowledge capture topics have included lessons learned in spacesuit technology, experience from the Gemini, Apollo, Skylab and Shuttle programs, hardware certification, design, development and other program components, spacesuit evolution and experience, failure analysis and resolution, aspects of program management, and personal interviews. These archives of actual spacesuit legacy now reflect its rich history and will provide a wealth of knowledge which will greatly enhance the chances for the success of future and more ambitious spacesuit system programs. In this paper, NASA s formal spacesuit knowledge capture efforts will be reviewed and a status will be provided to reveal initiatives and accomplishments since the inception of the more formal U.S. spacesuit knowledge program. A detail itemization of the actual archives will be addressed along with topics that are now available to the general NASA community and the public. Additionally, the latest developments in the archival relationship with the Smithsonian will be discussed.

  4. Neutron capture cross section and capture gamma-ray spectra of 89Y

    Directory of Open Access Journals (Sweden)

    Katabuchi Tatsuya

    2016-01-01

    Full Text Available The neutron capture cross section of 89Y was measured by the time-of-flight method in an energy range from 15 to 100 keV. A pulse-height weighting technique was applied to derive the capture yield. The absolute cross section was determined based on the standard reaciotn 197 Au(n, γ198 Au reaction. The neutron capture γ-ray spectrum was derived by unfolding the pulse-height spectrum with detector response functions.

  5. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  6. Development and evaluation of IgY ImmunoCapture PCR ELISA for detection of Staphylococcus aureus enterotoxin A devoid of protein A interference.

    Science.gov (United States)

    Reddy, Prakash; Ramlal, Shylaja; Sripathy, Murali Harishchandra; Batra, Harsh Vardhan

    2014-06-01

    In the present study, a sensitive and specific IgY mediated ImmunoCapture-PCR-ELISA (IC-PCR-ELISA) was developed for the detection of staphylococcal enterotoxin A (SEA) from culture supernatants and suspected contaminated samples. Due to the virtue of avian immunoglobulins (IgY) to have the least affinity towards staphylococcal protein A (SpA) responsible for false positives, we employed anti-SEA IgY for capture of SEA toxin and revealed with SEA specific rabbit antibodies conjugated to a 524bp DNA marker. Biotin-11-dUTP was incorporated during PCR amplification and post PCR analysis was performed by PCR-ELISA. Unlike IgG immunocapture, IgY mediated immunocapture of SEA was free from false positives due to protein A. The developed assay was specific to SEA except for minor cross reactivity with staphylococcal enterotoxin E (SEE). Several raw milk samples were evaluated for the presence of SEA with and without enrichment. Three samples were found to be positive for SEA after enrichment for 8h. Though IC-PCR-ELISA for SEA showed 100% correlation with PCR analysis for sea gene, the assay was unique in terms of sensitivity of detecting ~10pg/ml of SEA toxin from spiked milk samples. Result of IC-PCR-ELISA was further confirmed by conventional methods of isolation and characterization. The presented method can be very useful for rapid analysis of milk samples for SEA contamination and can be further extended for detection of multiple SE's in different wells of same PCR plate using common DNA substrate.

  7. Capture of farmed Nile crocodiles (Crocodylus niloticus): comparison of physiological parameters after manual capture and after capture with electrical stunning.

    Science.gov (United States)

    Pfitzer, S; Ganswindt, A; Fosgate, G T; Botha, P J; Myburgh, J G

    2014-09-27

    The electric stunner (e-stunner) is commonly used to handle Nile crocodiles (Crocodylus niloticus) on commercial farms in South Africa, but while it seems to improve handling and safety for the keepers, no information regarding physiological reactions to e-stunning is currently available. The aim of this study was therefore to compare various physiological parameters in farmed C niloticus captured either manually (noosing) or by using an e-stunner. A total of 45 crocodiles were captured at a South African farm by either e-stunning or noosing, and blood samples were taken immediately as well as four hours after capture. Parameters monitored were serum corticosterone, lactate, glucose, as well as alanine aminotransferase, alkaline phosphatase, aspartate aminotransferase and creatine kinase. Lactate concentrations were significantly higher in noosed compared with e-stunned animals (Pcrocodiles in a commercial setup because it is quicker, safer and did not cause a significant increase in any of the parameters measured.

  8. Linear independence measure of logarithms over affine groups

    OpenAIRE

    Huicochea, Mario

    2015-01-01

    Linear forms in logarithms over connected commutative algebraic groups over the algebraic numbers field have been studied widely. However, the theory of linear forms in logarithms over noncommutative algebraic groups have not been developed as the one of the commutative algebraic groups and in this paper we start studying linear forms in logarithms over affine groups.

  9. Electrochemical affinity biosensors for detection of mycotoxins: A review.

    Science.gov (United States)

    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.

  10. Self-Affine Sets with Positive Lebesgue Measure

    NARCIS (Netherlands)

    Dajani, Karma; Jiang, Kan; Kempton, Tom

    2014-01-01

    Using techniques introduced by C. G ̈unt ̈urk, we prove that the attractors of a family of overlapping self-affine iterated function systems contain a neighbourhood of zero for all parameters in a certain range. This corresponds to giving conditions under which a single sequence may serve as a ‘simu

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

    CERN Document Server

    Chou, Ching-Yi; Soo, Chopin

    2013-01-01

    Using the affine group formalism, we perform a nonperturbative quantization leading to the construction of elements of a physical Hilbert space for full, Lorentzian quantum gravity coupled to the Standard Model in four spacetime dimensions. This paper constitutes a first step toward understanding the phenomenology of quantum gravitational effects stemming from a consistent treatment of minimal couplings to matter.

  12. Several Affinity Tags Commonly Used in Chromatographic Purification

    Directory of Open Access Journals (Sweden)

    Xinyu Zhao

    2013-01-01

    Full Text Available Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP tag, calmodulin-binding peptide (CBP, glutathione S-transferase (GST, maltose-binding protein (MBP, S-tag, HA tag, and c-Myc tag. In some cases, a large-size affinity tag, such as GST or MBP, can significantly impact on the structure and biological activity of the fusion partner protein. So it is usually necessary to excise the tag by protease. The most commonly used endopeptidases are enterokinase, factor Xa, thrombin, tobacco etch virus, and human rhinovirus 3C protease. The proteolysis features of these proteases are described in order to provide a general guidance on the proteolytic removal of the affinity tags.

  13. On global asymptotic controllability of planar affine nonlinear systems

    Institute of Scientific and Technical Information of China (English)

    SUN Yimin; GUO Lei

    2005-01-01

    In this paper, we present a necessary and sufficient condition for globally asymptotic controllability of the general planar affine nonlinear systems with single-input.This result is obtained by introducing a new method in the analysis, which is based on the use of some basic results in planar topology and in the geometric theory of ordinary differential equations.

  14. Reconfigurable Control of Input Affine Nonlinear Systems under Actuator Fault

    DEFF Research Database (Denmark)

    Tabatabaeipour, Mojtaba; Galeazzi, Roberto

    2015-01-01

    This paper proposes a fault tolerant control method for input-affine nonlinear systems using a nonlinear reconfiguration block (RB). The basic idea of the method is to insert the RB between the plant and the nominal controller such that fault tolerance is achieved without re-designing the nominal...

  15. Demazure modules and vertex models the affine sl(2) case

    CERN Document Server

    Foda, O E; Okado, M; Foda, Omar; Misra, Kailash C; Okado, Masato

    1996-01-01

    We characterize, in the case of affine sl(2), the crystal base of the Demazure module E_w(\\La) in terms of extended Young diagrams or paths for any dominant integral weight \\La and Weyl group element w. Its character is evaluated via two expressions, 'bosonic' and 'fermionic'.

  16. "The Hunger Games": Literature, Literacy, and Online Affinity Spaces

    Science.gov (United States)

    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…

  17. T-Duality in Affine NA Toda Models

    CERN Document Server

    Gomes, J F; Zimerman, A H

    2004-01-01

    The construction of Non Abelian affine Toda models is discussed in terms of its underlying Lie algebraic structure. It is shown that a subclass of such non conformal two dimensional integrable models naturally leads to the construction of a pair of actions which share the same spectra and are related by canonical transformations.

  18. An invariant interest point detector under image affine transformation

    Institute of Scientific and Technical Information of China (English)

    林睿; 黄海波; 孙荣川; 孙立宁

    2015-01-01

    For vision-based mobile robot navigation, images of the same scene may undergo a general affine transformation in the case of significant viewpoint changes. So, a novel method for detecting affine invariant interest points is proposed to obtain the invariant local features, which is coined polynomial local orientation tensor (PLOT). The new detector is based on image local orientation tensor that is constructed from the polynomial expansion of image signal. Firstly, the properties of local orientation tensor of PLOT are analyzed, and a suitable tuning parameter of local orientation tensor is chosen so as to extract invariant features. The initial interest points are detected by local maxima search for the smaller eigenvalues of the orientation tensor. Then, an iterative procedure is used to allow the initial interest points to converge to affine invariant interest points and regions. The performances of this detector are evaluated on the repeatability criteria and recall versus 1-precision graphs, and then are compared with other existing approaches. Experimental results for PLOT show strong performance under affine transformation in the real-world conditions.

  19. An axially symmetric solution of metric-affine gravity

    CERN Document Server

    Vlachynsky, E J; Obukhov, Yu N; Hehl, F W

    1996-01-01

    We present an exact stationary {\\it axially symmetric} vacuum solution of metric-affine gravity (MAG) which generalises the recently reported spherically symmetric solution. Besides the metric, it carries nonmetricity and torsion as post-Riemannian geometrical structures. The parameters of the solution are interpreted as mass and angular momentum and as dilation, shear and spin charges.

  20. Smooth surfaces from bilinear patches: Discrete affine minimal surfaces

    KAUST Repository

    Käferböck, Florian

    2013-06-01

    Motivated by applications in freeform architecture, we study surfaces which are composed of smoothly joined bilinear patches. These surfaces turn out to be discrete versions of negatively curved affine minimal surfaces and share many properties with their classical smooth counterparts. We present computational design approaches and study special cases which should be interesting for the architectural application. 2013 Elsevier B.V.