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Sample records for reovirus fast proteins

  1. Reovirus FAST Protein Enhances Vesicular Stomatitis Virus Oncolytic Virotherapy in Primary and Metastatic Tumor Models

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    Fabrice Le Boeuf

    2017-09-01

    Full Text Available The reovirus fusion-associated small transmembrane (FAST proteins are the smallest known viral fusogens (∼100–150 amino acids and efficiently induce cell-cell fusion and syncytium formation in multiple cell types. Syncytium formation enhances cell-cell virus transmission and may also induce immunogenic cell death, a form of apoptosis that stimulates immune recognition of tumor cells. These properties suggest that FAST proteins might serve to enhance oncolytic virotherapy. The oncolytic activity of recombinant VSVΔM51 (an interferon-sensitive vesicular stomatitis virus [VSV] mutant encoding the p14 FAST protein (VSV-p14 was compared with a similar construct encoding GFP (VSV-GFP in cell culture and syngeneic BALB/c tumor models. Compared with VSV-GFP, VSV-p14 exhibited increased oncolytic activity against MCF-7 and 4T1 breast cancer spheroids in culture and reduced primary 4T1 breast tumor growth in vivo. VSV-p14 prolonged survival in both primary and metastatic 4T1 breast cancer models, and in a CT26 metastatic colon cancer model. As with VSV-GFP, VSV-p14 preferentially replicated in vivo in tumors and was cleared rapidly from other sites. Furthermore, VSV-p14 increased the numbers of activated splenic CD4, CD8, natural killer (NK, and natural killer T (NKT cells, and increased the number of activated CD4 and CD8 cells in tumors. FAST proteins may therefore provide a multi-pronged approach to improving oncolytic virotherapy via syncytium formation and enhanced immune stimulation.

  2. A compact, multifunctional fusion module directs cholesterol-dependent homomultimerization and syncytiogenic efficiency of reovirus p10 FAST proteins.

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    Tim Key

    2014-03-01

    Full Text Available The homologous p10 fusion-associated small transmembrane (FAST proteins of the avian (ARV and Nelson Bay (NBV reoviruses are the smallest known viral membrane fusion proteins, and are virulence determinants of the fusogenic reoviruses. The small size of FAST proteins is incompatible with the paradigmatic membrane fusion pathway proposed for enveloped viral fusion proteins. Understanding how these diminutive viral fusogens mediate the complex process of membrane fusion is therefore of considerable interest, from both the pathogenesis and mechanism-of-action perspectives. Using chimeric ARV/NBV p10 constructs, the 36-40-residue ectodomain was identified as the major determinant of the differing fusion efficiencies of these homologous p10 proteins. Extensive mutagenic analysis determined the ectodomain comprises two distinct, essential functional motifs. Syncytiogenesis assays, thiol-specific surface biotinylation, and liposome lipid mixing assays identified an ∼25-residue, N-terminal motif that dictates formation of a cystine loop fusion peptide in both ARV and NBV p10. Surface immunofluorescence staining, FRET analysis and cholesterol depletion/repletion studies determined the cystine loop motif is connected through a two-residue linker to a 13-residue membrane-proximal ectodomain region (MPER. The MPER constitutes a second, independent motif governing reversible, cholesterol-dependent assembly of p10 multimers in the plasma membrane. Results further indicate that: (1 ARV and NBV homomultimers segregate to distinct, cholesterol-dependent microdomains in the plasma membrane; (2 p10 homomultimerization and cholesterol-dependent microdomain localization are co-dependent; and (3 the four juxtamembrane MPER residues present in the multimerization motif dictate species-specific microdomain association and homomultimerization. The p10 ectodomain therefore constitutes a remarkably compact, multifunctional fusion module that directs syncytiogenic

  3. Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

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    Jolene Read

    2015-06-01

    Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

  4. Classification of Dutch and German avian reoviruses by sequencing the sigma-C protein.

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    Kant, A.; Balk, F.R.M.; Born, L.; Roozelaar, van D.; Heijmans, J.; Gielkens, A.; Huurne, ter A.A.H.M.

    2003-01-01

    We have amplified, cloned and sequenced (part of) the open reading frame of the S1 segment encoding the ¿ C protein of avian reoviruses isolated from chickens with different disease conditions in Germany and The Netherlands during 1980 up to 2000. These avian reoviruses were analysed

  5. Functional investigation of grass carp reovirus nonstructural protein NS80

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    Shao Ling

    2011-04-01

    Full Text Available Abstract Background Grass Carp Reovirus (GCRV, a highly virulent agent of aquatic animals, has an eleven segmented dsRNA genome encased in a multilayered capsid shell, which encodes twelve proteins including seven structural proteins (VP1-VP7, and five nonstructural proteins (NS80, NS38, NS31, NS26, and NS16. It has been suggested that the protein NS80 plays an important role in the viral replication cycle that is similar to that of its homologous protein μNS in the genus of Orthoreovirus. Results As a step to understanding the basis of the part played by NS80 in GCRV replication and particle assembly, we used the yeast two-hybrid (Y2H system to identify NS80 interactions with proteins NS38, VP4, and VP6 as well as NS80 and NS38 self-interactions, while no interactions appeared in the four protein pairs NS38-VP4, NS38-VP6, VP4-VP4, and VP4-VP6. Bioinformatic analyses of NS80 with its corresponding proteins were performed with all currently available homologous protein sequences in ARVs (avian reoviruses and MRVs (mammalian reoviruses to predict further potential functional domains of NS80 that are related to VFLS (viral factory-like structures formation and other roles in viral replication. Two conserved regions spanning from aa (amino acid residues of 388 to 433, and 562 to 580 were discovered in this study. The second conserved region with corresponding conserved residues Tyr565, His569, Cys571, Asn573, and Glu576 located between the two coiled-coils regions (aa ~513-550 and aa ~615-690 in carboxyl-proximal terminus were supposed to be essential to form VFLS, so that aa residues ranging from 513 to 742 of NS80 was inferred to be the smallest region that is necessary for forming VFLS. The function of the first conserved region including Ala395, Gly419, Asp421, Pro422, Leu438, and Leu443 residues is unclear, but one-third of the amino-terminal region might be species specific, dominating interactions with other viral components. Conclusions Our

  6. Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

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    Reiter, Dirk M; Frierson, Johnna M; Halvorson, Elizabeth E; Kobayashi, Takeshi; Dermody, Terence S; Stehle, Thilo

    2011-08-01

    Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

  7. Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

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    Dirk M Reiter

    2011-08-01

    Full Text Available Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

  8. Mutations in type 3 reovirus that determine binding to sialic acid are contained in the fibrous tail domain of viral attachment protein sigma1.

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    Chappell, J D; Gunn, V L; Wetzel, J D; Baer, G S; Dermody, T S

    1997-03-01

    The reovirus attachment protein, sigma1, determines numerous aspects of reovirus-induced disease, including viral virulence, pathways of spread, and tropism for certain types of cells in the central nervous system. The sigma1 protein projects from the virion surface and consists of two distinct morphologic domains, a virion-distal globular domain known as the head and an elongated fibrous domain, termed the tail, which is anchored into the virion capsid. To better understand structure-function relationships of sigma1 protein, we conducted experiments to identify sequences in sigma1 important for viral binding to sialic acid, a component of the receptor for type 3 reovirus. Three serotype 3 reovirus strains incapable of binding sialylated receptors were adapted to growth in murine erythroleukemia (MEL) cells, in which sialic acid is essential for reovirus infectivity. MEL-adapted (MA) mutant viruses isolated by serial passage in MEL cells acquired the capacity to bind sialic acid-containing receptors and demonstrated a dependence on sialic acid for infection of MEL cells. Analysis of reassortant viruses isolated from crosses of an MA mutant virus and a reovirus strain that does not bind sialic acid indicated that the sigma1 protein is solely responsible for efficient growth of MA mutant viruses in MEL cells. The deduced sigma1 amino acid sequences of the MA mutant viruses revealed that each strain contains a substitution within a short region of sequence in the sigma1 tail predicted to form beta-sheet. These studies identify specific sequences that determine the capacity of reovirus to bind sialylated receptors and suggest a location for a sialic acid-binding domain. Furthermore, the results support a model in which type 3 sigma1 protein contains discrete receptor binding domains, one in the head and another in the tail that binds sialic acid.

  9. Identification of carbohydrate-binding domains in the attachment proteins of type 1 and type 3 reoviruses.

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    Chappell, J D; Duong, J L; Wright, B W; Dermody, T S

    2000-09-01

    The reovirus attachment protein, sigma1, is responsible for strain-specific patterns of viral tropism in the murine central nervous system and receptor binding on cultured cells. The sigma1 protein consists of a fibrous tail domain proximal to the virion surface and a virion-distal globular head domain. To better understand mechanisms of reovirus attachment to cells, we conducted studies to identify the region of sigma1 that binds cell surface carbohydrate. Chimeric and truncated sigma1 proteins derived from prototype reovirus strains type 1 Lang (T1L) and type 3 Dearing (T3D) were expressed in insect cells by using a baculovirus vector. Assessment of expressed protein susceptibility to proteolytic cleavage, binding to anti-sigma1 antibodies, and oligomerization indicates that the chimeric and truncated sigma1 proteins are properly folded. To assess carbohydrate binding, recombinant sigma1 proteins were tested for the capacity to agglutinate mammalian erythrocytes and to bind sialic acid presented on glycophorin, the cell surface molecule bound by type 3 reovirus on human erythrocytes. Using a panel of two wild-type and ten chimeric and truncated sigma1 proteins, the sialic acid-binding domain of type 3 sigma1 was mapped to a region of sequence proposed to form the more amino terminal of two predicted beta-sheet structures in the tail. This unit corresponds to morphologic region T(iii) observed in computer-processed electron micrographs of sigma1 protein purified from virions. In contrast, the homologous region of T1L sigma1 sequence was not implicated in carbohydrate binding; rather, sequences in the distal portion of the tail known as the neck were required. Results of these studies demonstrate that a functional receptor-binding domain, which uses sialic acid as its ligand, is contained within morphologic region T(iii) of the type 3 sigma1 tail. Furthermore, our findings indicate that T1L and T3D sigma1 proteins contain different arrangements of receptor

  10. Conformational and functional analysis of the C-terminal globular head of the reovirus cell attachment protein.

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    Duncan, R; Horne, D; Strong, J E; Leone, G; Pon, R T; Yeung, M C; Lee, P W

    1991-06-01

    We have been investigating structure-function relationships in the reovirus cell attachment protein sigma 1 using various deletion mutants and protease analysis. In the present study, a series of deletion mutants were constructed which lacked 90, 44, 30, 12, or 4 amino acids from the C-terminus of the 455-amino acid-long reovirus type 3 (T3) sigma 1 protein. The full-length and truncated sigma 1 proteins were expressed in an in vitro transcription/translation system and assayed for L cell binding activity. It was found that the removal of as few as four amino acids from the C-terminus drastically affected the cell binding function of the sigma 1 protein. The C-terminal-truncated proteins were further characterized using trypsin, chymotrypsin, and monoclonal and polyclonal antibodies. Our results indicated that the C-terminal portions of the mutant proteins were misfolded, leading to a loss in cell binding function. The N-terminal fibrous tail of the proteins was unaffected by the deletions as was sigma 1 oligomerization, further illustrating the discrete structural and functional roles of the N- and C-terminal domains of sigma 1. In an attempt to identify smaller, functional peptides, full-length sigma 1 expressed in vitro was digested with trypsin and subsequently with chymotrypsin under various conditions. The results clearly demonstrated the highly stable nature of the C-terminal globular head of sigma 1, even when separated from the N-terminal fibrous tail. We concluded that: (1) the C-terminal globular head of sigma 1 exists as a compact, protease-resistant oligomeric structure; (2) an intact C-terminus is required for proper head folding and generation of the conformationally dependent cell binding domain.

  11. Reptilian reovirus: a new fusogenic orthoreovirus species

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    Duncan, Roy.; Corcoran, Jennifer; Shou Jingyun; Stoltz, Don

    2004-01-01

    The fusogenic subgroup of orthoreoviruses contains most of the few known examples of non-enveloped viruses capable of inducing syncytium formation. The only unclassified orthoreoviruses at the species level represent several fusogenic reptilian isolates. To clarify the relationship of reptilian reoviruses (RRV) to the existing fusogenic and nonfusogenic orthoreovirus species, we undertook a characterization of a python reovirus isolate. Biochemical, biophysical, and biological analyses confirmed the designation of this reptilian reovirus (RRV) isolate as an unclassified fusogenic orthoreovirus. Sequence analysis revealed that the RRV S1 and S3 genome segments contain a novel conserved 5'-terminal sequence not found in other orthoreovirus species. In addition, the gene arrangement and the coding potential of the bicistronic RRV S1 genome segment differ from that of established orthoreovirus species, encoding a predicted homologue of the reovirus cell attachment protein and a unique 125 residue p14 protein. The RRV S3 genome segment encodes a homologue of the reovirus sigma-class major outer capsid protein, although it is highly diverged from that of other orthoreovirus species (amino acid identities of only 16-25%). Based on sequence analysis, biological properties, and phylogenetic analysis, we propose this python reovirus be designated as the prototype strain of a fifth species of orthoreoviruses, the reptilian reoviruses

  12. Different intracellular distribution of avian reovirus core protein sigmaA in cells of avian and mammalian origin

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    Vázquez-Iglesias, Lorena; Lostalé-Seijo, Irene; Martínez-Costas, José; Benavente, Javier

    2012-01-01

    A comparative analysis of the intracellular distribution of avian reovirus (ARV) core protein sigmaA in cells of avian and mammalian origin revealed that, whereas the viral protein accumulates in the cytoplasm and nucleolus of avian cells, most sigmaA concentrates in the nucleoplasm of mammalian cells in tight association with the insoluble nuclear matrix fraction. Our results further showed that sigmaA becomes arrested in the nucleoplasm of mammalian cells via association with mammalian cell-specific factors and that this association prevents nucleolar targeting. Inhibition of RNA polymerase II activity, but not of RNA polymerase I activity, in infected mammalian cells induces nucleus-to-cytoplasm sigmaA translocation through a CRM1- and RanGTP-dependent mechanism, yet a heterokaryon assay suggests that sigmaA does not shuttle between the nucleus and cytoplasm. The scarcity of sigmaA in cytoplasmic viral factories of infected mammalian cells could be one of the factors contributing to limited ARV replication in mammalian cells.

  13. Different intracellular distribution of avian reovirus core protein sigmaA in cells of avian and mammalian origin

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    Vazquez-Iglesias, Lorena; Lostale-Seijo, Irene; Martinez-Costas, Jose [Departamento de Bioquimica y Biologia Molecular, Facultad de Farmacia, y Centro Singular de Investigacion en Quimica Biologica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782-Santiago de Compostela (Spain); Benavente, Javier, E-mail: franciscojavier.benavente@usc.es [Departamento de Bioquimica y Biologia Molecular, Facultad de Farmacia, y Centro Singular de Investigacion en Quimica Biologica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782-Santiago de Compostela (Spain)

    2012-10-25

    A comparative analysis of the intracellular distribution of avian reovirus (ARV) core protein sigmaA in cells of avian and mammalian origin revealed that, whereas the viral protein accumulates in the cytoplasm and nucleolus of avian cells, most sigmaA concentrates in the nucleoplasm of mammalian cells in tight association with the insoluble nuclear matrix fraction. Our results further showed that sigmaA becomes arrested in the nucleoplasm of mammalian cells via association with mammalian cell-specific factors and that this association prevents nucleolar targeting. Inhibition of RNA polymerase II activity, but not of RNA polymerase I activity, in infected mammalian cells induces nucleus-to-cytoplasm sigmaA translocation through a CRM1- and RanGTP-dependent mechanism, yet a heterokaryon assay suggests that sigmaA does not shuttle between the nucleus and cytoplasm. The scarcity of sigmaA in cytoplasmic viral factories of infected mammalian cells could be one of the factors contributing to limited ARV replication in mammalian cells.

  14. A strategy for genetic modification of the spike-encoding segment of human reovirus T3D for reovirus targeting.

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    van den Wollenberg, D J M; van den Hengel, S K; Dautzenberg, I J C; Cramer, S J; Kranenburg, O; Hoeben, R C

    2008-12-01

    Human Orthoreovirus Type 3 Dearing is not pathogenic to humans and has been evaluated clinically as an oncolytic agent. Its transduction efficiency and the tumor cell selectivity may be enhanced by incorporating ligands for alternative receptors. However, the genetic modification of reoviruses has been difficult, and genetic targeting of reoviruses has not been reported so far. Here we describe a technique for generating genetically targeted reoviruses. The propagation of wild-type reoviruses on cells expressing a modified sigma 1-encoding segment embedded in a conventional RNA polymerase II transcript leads to substitution of the wild-type genome segment by the modified version. This technique was used for generating reoviruses that are genetically targeted to an artificial receptor expressed on U118MG cells. These cells lack the junction adhesion molecule-1 and therefore resist infection by wild-type reoviruses. The targeted reoviruses were engineered to carry the ligand for this receptor at the C terminus of the sigma 1 spike protein. This demonstrates that the C terminus of the sigma 1 protein is a suitable locale for the insertion of oligopeptide ligands and that targeting of reoviruses is feasible. The genetically targeted viruses can be propagated using the modified U118MG cells as helper cells. This technique may be applicable for the improvement of human reoviruses as oncolytic agents.

  15. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

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    Xu Wanhong

    2008-12-01

    Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV

  16. Active participation of Hsp90 in the biogenesis of the trimeric reovirus cell attachment protein sigma1.

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    Gilmore, R; Coffey, M C; Lee, P W

    1998-06-12

    The reovirus cell attachment protein, sigma1, is a lollipop-shaped homotrimer with an N-terminal fibrous tail and a C-terminal globular head. Biogenesis of this protein involves two trimerization events: N-terminal trimerization, which occurs cotranslationally and is Hsp70/ATP-independent, and C-terminal trimerization, which occurs posttranslationally and is Hsp70/ATP-dependent. To determine if Hsp90 also plays a role in sigma1 biogenesis, we analyzed sigma1 synthesized in rabbit reticulocyte lysate. Coprecipitation experiments using anti-Hsp90 antibodies revealed that Hsp90 was associated with immature sigma1 trimers (hydra-like intermediates with assembled N termini and unassembled C termini) but not with mature trimers. The use of truncated sigma1 further demonstrated that only the C-terminal half of sigma1 associated with Hsp90. In the presence of the Hsp90 binding drug geldanamycin, N-terminal trimerization proceeded normally, but C-terminal trimerization was blocked. Geldanamycin did not inhibit the association of Hsp90 with sigma 1 but prevented the subsequent release of Hsp90 from the immature sigma1 complex. We also examined the status of p23, an Hsp90-associated cochaperone. Like Hsp90, p23 only associated with immature sigma1 trimers, and this association was mapped to the C-terminal half of sigma1. However, unlike Hsp90, p23 was released from the sigma1 complex upon the addition of geldanamycin. These results highlight an all-or-none concept of chaperone involvement in different oligomerization domains within a single protein and suggest a possible common usage of chaperones in the regulation of general protein folding and of steroid receptor activation.

  17. PUMA and NF-kB Are Cell Signaling Predictors of Reovirus Oncolysis of Breast Cancer.

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    Thirukkumaran, Chandini; Shi, Zhong-Qiao; Thirukkumaran, Ponnampalam; Luider, Joanne; Kopciuk, Karen; Spurrell, Jason; Elzinga, Kate; Morris, Don

    2017-01-01

    Reovirus is a ubiquitous RNA virus that exploits aberrant signaling pathways for its replication. The oncolytic potential of reovirus against numerous cancers under pre-clinical/clinical conditions has been documented by us and others. Despite its proven clinical activity, the underlying mechanisms of reovirus oncolysis is still not well elucidated. If reovirus therapy is to be optimized for cancer, including breast cancer patients, it is imperative to understand the mechanisms of reovirus oncolysis, especially in treatment of resistant tumour. In the present study global gene expression profiling was utilized as a preliminary roadmap to tease-out pivotal molecules involved in reovirus induced apoptosis in breast cancer. Reovirus treated HTB133 and MCF7 breast cancer cells revealed transcriptional alteration of a defined subset of apoptotic genes and members of the nuclear factor-kappa B (NF-kB) family and p53 upregulated modulator of apoptosis (PUMA) were prominent. Since NF-kB can paradoxically suppress or promote apoptosis in cancer, the significance of NF-kB in reovirus oncolysis of breast cancer was investigated. Real time PCR analysis indicated a 2.9-4.3 fold increase in NF-kB p65 message levels following reovirus infection of MCF7 and HTB133, respectively. Nuclear translocation of NF-kB p65 protein was also dramatically augmented post reovirus treatment and correlated with enhanced DNA binding. Pharmacologic inhibition of NF-kB lead to oncolytic protection and significant down regulation of PUMA message levels. PUMA down regulation using siRNA suppressed reovirus oncolysis via significantly repressed apoptosis in p53 mutant HTB133 cells. This study demonstrates for the first time that a prominent pathway of reovirus oncolysis of breast cancer is mediated through NF-kB and that PUMA upregulation is dependent on NF-kB activation. These findings represent potential therapeutic indicators of reovirus treatment in future clinical trials.

  18. The use of an in vitro microneutralization assay to evaluate the potential of recombinant VP5 protein as an antigen for vaccinating against Grass carp reovirus

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    Xu Dan

    2011-03-01

    Full Text Available Abstract Background Grass carp reovirus (GCRV is the causative pathogen of grass carp hemorrhagic disease, one of the major diseases damaging grass carp Ctenopharyngon idellus breeding industry in China. Prevention and control of the disease is impeded largely due to the lack of research in economic subunit vaccine development. This study aimed to evaluate the potential of viral outer shell protein VP5 as subunit vaccine. Methods The vp5 gene was isolated from the viral genome through RT-PCR and genetically engineered to express the recombinant VP5 protein in E coli. The viral origin of the recombinant protein was confirmed by Western blot analysis with a monoclonal antibody against viral VP5 protein. Polyclonal antibody against the recombinant VP5 protein was prepared from mice. A microneutralization assay was developed to test its neutralizing ability against GCRV infection in cell culture. Results The GST-VP5 fusion protein (rVP5 was produced from E. Coli with expected molecular weight of 90 kDa. The protein was purified and employed to prepare anti-VP5 polyclonal antibody from mice. The anti-VP5 antibody was found to neutralize GCRV through in vitro microneutralization assay and viral progeny quantification analysis. Conclusions The present study showed that the viral VP5 protein was involved in viral infection and bacterially-expressed VP5 could be suitable for developing subunit vaccine for the control of GCRV infection.

  19. Identification of mud crab reovirus VP12 and its interaction with the voltage-dependent anion-selective channel protein of mud crab Scylla paramamosain.

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    Xu, Hai-Dong; Su, Hong-Jun; Zou, Wei-Bin; Liu, Shan-Shan; Yan, Wen-Rui; Wang, Qian-Qian; Yuan, Li-Li; Chan, Siuming Francis; Yu, Xiao-Qiang; He, Jian-Guo; Weng, Shao-Ping

    2015-05-01

    Mud crab reovirus (MCRV) is the causative agent of a severe disease in cultured mud crab (Scylla paramamosain), which has caused huge economic losses in China. MCRV is a double-stranded RNA virus with 12 genomic segments. In this paper, SDS-PAGE, mass spectrometry and Western blot analyses revealed that the VP12 protein encoded by S12 gene is a structural protein of MCRV. Immune electron microscopy assay indicated that MCRV VP12 is a component of MCRV outer shell capsid. Yeast two hybrid cDNA library of mud crab was constructed and mud crab voltage-dependent anion-selective channel (mcVDAC) was obtained by MCRV VP12 screening. The full length of mcVDAC was 1180 bp with an open reading frame (ORF) of 849 bp encoding a 282 amino acid protein. The mcVDAC had a constitutive expression pattern in different tissues of mud crab. The interaction between MCRV VP12 and mcVDAC was determined by co-immunoprecipitation assay. The results of this study have provided an insight on the mechanisms of MCRV infection and the interactions between the virus and mud crab. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Non-biased enrichment does not improve quantitative proteomic delineation of reovirus T3D-infected HeLa cell protein alterations

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    Jieyuan eJiang

    2012-09-01

    Full Text Available Mass spectrometry-based methods have allowed elucidation of alterations in complex proteomes, such as eukaryotic cells. Such studies have identified and measured relative abundances of thousands of host proteins after cells are infected with a virus. One of the potential limitations in such studies is that generally only the most abundant proteins are identified, leaving the deep richness of the cellular proteome largely unexplored. We differentially labeled HeLa cells with light and heavy stable isotopic forms of lysine and arginine (SILAC and infected cells with reovirus strain T3D. Cells were harvested at 24 hours post-infection. Heavy-labeled infected and light-labeled mock-infected cells were mixed together 1:1. Cells were then divided into cytosol and nuclear fractions and each fraction analyzed, both by standard 2D-HPLC/MS, and also after each fraction had been reacted with a random hexapeptide library (Proteominer® beads to attempt to enrich for low-abundance cellular proteins. A total of 2736 proteins were identified by 2 or more peptides at >99% confidence, of which 66 were significantly up-regulated and 67 were significantly down-regulated. Up-regulated proteins included those involved in antimicrobial and antiviral responses, GTPase activity, nucleotide binding, interferon signaling, and enzymes associated with energy generation. Down-regulated proteins included those involved in cell and biological adhesion, regulation of cell proliferation, structural molecule activity, and numerous molecular binding activities. Comparisons of the r2 correlations, degree of dataset overlap, and numbers of peptides detected suggest that non-biased enrichment approaches may not provide additional data to allow deeper quantitative and comparative mining of complex proteomes.

  1. Independent regulation of reovirus membrane penetration and apoptosis by the mu1 phi domain.

    Science.gov (United States)

    Danthi, Pranav; Coffey, Caroline M; Parker, John S L; Abel, Ty W; Dermody, Terence S

    2008-12-01

    Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein mu1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of mu1 indicates that the mu1 phi domain is sufficient to elicit a cell death response. To evaluate the contribution of the mu1 phi domain to the induction of apoptosis following reovirus infection, phi mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in phi diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in phi affect the apoptotic potential of reovirus, suggesting that phi initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective phi mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the phi domain of mu1 plays an important regulatory role in reovirus-induced apoptosis and disease.

  2. Independent regulation of reovirus membrane penetration and apoptosis by the mu1 phi domain.

    Directory of Open Access Journals (Sweden)

    Pranav Danthi

    2008-12-01

    Full Text Available Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein mu1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of mu1 indicates that the mu1 phi domain is sufficient to elicit a cell death response. To evaluate the contribution of the mu1 phi domain to the induction of apoptosis following reovirus infection, phi mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in phi diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in phi affect the apoptotic potential of reovirus, suggesting that phi initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective phi mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the phi domain of mu1 plays an important regulatory role in reovirus-induced apoptosis and disease.

  3. Fidelity in the translation of reovirus mRNA in oocytes of Xenopus laevis

    International Nuclear Information System (INIS)

    Opperman, D.P.J.; Van der Walt, M.P.K.; Reinecke, C.J.

    1988-01-01

    The translation products formed from reovirus mRNA micro-injected into oocytes of Xenopus laevis were compared with authentic reovirus proteins by polyacrylamide gel electrophoresis, immunoprecipition, isolation of immune complexes by affinity chromatography and peptide mapping using proteolytic digestion with Staphylococcus aureus V8 protease. Products from the s-, m- and l-class mRNAs were detectable in quantities comparable to those synthesized in vivo, confirming that the differences in the translational efficiencies in the oocyte system resemble those found in vivo. The experimental procedures during this study, include the labelling of these translation products with [ 35 S]methionine. Protein μ1C was formed in the oocytes by post-translational cleavage of its precursor, protein μ1. The V8 protease peptide profile of the translation product with the same electrophoretic mobility as protein, σ3, is identical to that of the authentic reovirus protein. All these observations indicate a high degree of fidelity in the translation of reovirus mRNA in the oocyte system. The fidelity in translation, ratios of the various translation products, as well as post-translational modification suggest that the oocyte system might provide a means for studying the mechanism of reovirus morphogenesis

  4. Efficacy of reovirus against breast cancer

    International Nuclear Information System (INIS)

    Zhu Jingzhi; Chen Jue; Dong Shengxiang; Yan Weili; Wu Zhiyong

    2011-01-01

    To investigate the role of oncolytic reovirus in breast cancer, a tumor xenograft model of NOD/SCID mice was established using a biopsy sample of a primary infiltrating ductal carcinoma obtained from a breast cancer patient. The result of HE and TUNEL was analyzed after injecting the reovirus peritoneally for 3 days. The results showed that estrogen supplementation was required to establish appropriate human breast cancer xenograft model of NOD/SCID mice. 29.6% of these transplanted tumors grew with supplementation of Estrogen. Otherwise none grew (P<0.01). ER of the xenograft model was positive.After treatment with reovirus for 3 days, breast cancer cells were disrupted and disappeared which induced tissue looseness. The rate of apoptosis increased double than before. The biological characteristics of tumor xenograft model confirm with the primary breast cancer. The oncolytic reovirus can kill breast cancer in short time. (authors)

  5. 21 CFR 866.3470 - Reovirus serological reagents.

    Science.gov (United States)

    2010-04-01

    ... (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3470 Reovirus... and antisera used in serological tests to identify antibodies to reovirus in serum. The identification...

  6. Whole-Genome Analysis of a Novel Fish Reovirus (MsReV Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments

    Directory of Open Access Journals (Sweden)

    Zhong-Yuan Chen

    2015-08-01

    Full Text Available Aquareoviruses are serious pathogens of aquatic animals. Here, genome characterization and functional gene analysis of a novel aquareovirus, largemouth bass Micropterus salmoides reovirus (MsReV, was described. It comprises 11 dsRNA segments (S1–S11 covering 24,024 bp, and encodes 12 putative proteins including the inclusion forming-related protein NS87 and the fusion-associated small transmembrane (FAST protein NS22. The function of NS22 was confirmed by expression in fish cells. Subsequently, MsReV was compared with two representative aquareoviruses, saltwater fish turbot Scophthalmus maximus reovirus (SMReV and freshwater fish grass carp reovirus strain 109 (GCReV-109. MsReV NS87 and NS22 genes have the same structure and function with those of SMReV, whereas GCReV-109 is either missing the coiled-coil region in NS79 or the gene-encoding NS22. Significant similarities are also revealed among equivalent genome segments between MsReV and SMReV, but a difference is found between MsReV and GCReV-109. Furthermore, phylogenetic analysis showed that 13 aquareoviruses could be divided into freshwater and saline environments subgroups, and MsReV was closely related to SMReV in saline environments. Consequently, these viruses from hosts in saline environments have more genomic structural similarities than the viruses from hosts in freshwater. This is the first study of the relationships between aquareovirus genomic structure and their host environments.

  7. Avian Reovirus Protein p17 Functions as a Nucleoporin Tpr Suppressor Leading to Activation of p53, p21 and PTEN and Inactivation of PI3K/AKT/mTOR and ERK Signaling Pathways.

    Directory of Open Access Journals (Sweden)

    Wei-Ru Huang

    Full Text Available Avian reovirus (ARV protein p17 has been shown to regulate cell cycle and autophagy by activation of p53/PTEN pathway; nevertheless, it is still unclear how p53 and PTEN are activated by p17. Here, we report for the first time that p17 functions as a nucleoporin Tpr suppressor that leads to p53 nuclear accumulation and consequently activates p53, p21, and PTEN. The nuclear localization signal (119IAAKRGRQLD128 of p17 has been identified for Tpr binding. This study has shown that Tpr suppression occurs by p17 interacting with Tpr and by reducing the transcription level of Tpr, which together inhibit Tpr function. In addition to upregulation of PTEN by activation of p53 pathway, this study also suggests that ARV protein p17 acts as a positive regulator of PTEN. ARV p17 stabilizes PTEN by stimulating phosphorylation of cytoplasmic PTEN and by elevating Rak-PTEN association to prevent it from E3 ligase NEDD4-1 targeting. To activate PTEN, p17 is able to promote β-arrestin-mediated PTEN translocation from the cytoplasm to the plasma membrane via a Rock-1-dependent manner. The accumulation of p53 in the nucleus induces the PTEN- and p21-mediated downregulation of cyclin D1 and CDK4. Furthermore, Tpr and CDK4 knockdown increased virus production in contrast to depletion of p53, PTEN, and LC3 reducing virus yield. Taken together, our data suggest that p17-mediated Tpr suppression positively regulates p53, PTEN, and p21 and negatively regulates PI3K/AKT/mTOR and ERK signaling pathways, both of which are beneficial for virus replication.

  8. Mucosal vaccination by adenoviruses displaying reovirus sigma 1

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, Eric A. [Department of Internal Medicine, Division of Infectious Diseases, Translational Immunovirology and Biodefense Program, Mayo Clinic, Rochester, MN 55902 (United States); Camacho, Zenaido T. [Department of Cell Biology, Department of Natural Sciences, Western New Mexico University, Silver City, NM 88062 (United States); Hillestad, Matthew L. [Nephrology Training Program, Mayo Clinic, Rochester, MN 55902 (United States); Crosby, Catherine M.; Turner, Mallory A.; Guenzel, Adam J.; Fadel, Hind J. [Virology and Gene Therapy Graduate Program, Mayo Clinic, Rochester, MN 55902 (United States); Mercier, George T. [Department of Physics, University of Houston, Houston, TX 77004 (United States); Barry, Michael A., E-mail: mab@mayo.edu [Department of Internal Medicine, Division of Infectious Diseases, Translational Immunovirology and Biodefense Program, Mayo Clinic, Rochester, MN 55902 (United States); Department of Immunology and Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55902 (United States)

    2015-08-15

    We developed adenovirus serotype 5 (Ad5) vectors displaying the sigma 1 protein from reovirus as mucosal vaccines. Ad5-sigma retargets to JAM-1 and sialic acid, but has 40-fold reduced gene delivery when compared to Ad5. While weaker at transduction, Ad5-sigma generates stronger T cell responses than Ad5 when used for mucosal immunization. In this work, new Ad5-fiber-sigma vectors were generated by varying the number of fiber β-spiral shaft repeats (R) between the fiber tail and sigma. Increasing chimera length led to decreasing insertion of these proteinsAd5 virions. Ad-R3 and R14 vectors effectively targeted JAM-1 in vitro while R20 did not. When wereused to immunize mice by the intranasal route, Ad5-R3-sigma produced higher serum and vaginal antibody responses than Ad5. These data suggest optimized Ad-sigma vectors may be useful vectors for mucosal vaccination. - Highlights: • Constructed adenoviruses (Ads) displaying different reovirus sigma 1 fusion proteins. • Progressively longer chimeras were more poorly encapsidated onto Ad virions. • Ad5-R3-sigma mediated better systemic and mucosal immune responses than Ad5.

  9. Mucosal vaccination by adenoviruses displaying reovirus sigma 1

    International Nuclear Information System (INIS)

    Weaver, Eric A.; Camacho, Zenaido T.; Hillestad, Matthew L.; Crosby, Catherine M.; Turner, Mallory A.; Guenzel, Adam J.; Fadel, Hind J.; Mercier, George T.; Barry, Michael A.

    2015-01-01

    We developed adenovirus serotype 5 (Ad5) vectors displaying the sigma 1 protein from reovirus as mucosal vaccines. Ad5-sigma retargets to JAM-1 and sialic acid, but has 40-fold reduced gene delivery when compared to Ad5. While weaker at transduction, Ad5-sigma generates stronger T cell responses than Ad5 when used for mucosal immunization. In this work, new Ad5-fiber-sigma vectors were generated by varying the number of fiber β-spiral shaft repeats (R) between the fiber tail and sigma. Increasing chimera length led to decreasing insertion of these proteinsAd5 virions. Ad-R3 and R14 vectors effectively targeted JAM-1 in vitro while R20 did not. When wereused to immunize mice by the intranasal route, Ad5-R3-sigma produced higher serum and vaginal antibody responses than Ad5. These data suggest optimized Ad-sigma vectors may be useful vectors for mucosal vaccination. - Highlights: • Constructed adenoviruses (Ads) displaying different reovirus sigma 1 fusion proteins. • Progressively longer chimeras were more poorly encapsidated onto Ad virions. • Ad5-R3-sigma mediated better systemic and mucosal immune responses than Ad5

  10. Protamine precipitation of two reovirus particle types from polluted waters.

    OpenAIRE

    Adams, D J; Ridinger, D N; Spendlove, R S; Barnett, B B

    1982-01-01

    Two forms of virus particle are released from reovirus-infected cell cultures, infectious reovirus and potentially infectious reovirus (PIV). PIV particle forms have a complete outer coat and are not infectious until the outer coat is altered or removed. The PIV concentration in polluted waters, however, has not been determined. Protamine sulfate precipitation, using 0.25% fetal bovine serum and 0.005% protamine sulfate for the first precipitation of the sample and 0.0025% for the second, was...

  11. Isolation of reovirus T3D mutants capable of infecting human tumor cells independent of junction adhesion molecule-A.

    Directory of Open Access Journals (Sweden)

    Diana J M van den Wollenberg

    Full Text Available Mammalian Reovirus is a double-stranded RNA virus with a distinctive preference to replicate in and lyse transformed cells. On that account, Reovirus type 3 Dearing (T3D is clinically evaluated as oncolytic agent. The therapeutic efficacy of this approach depends in part on the accessibility of the reovirus receptor Junction Adhesion Molecule-A (JAM-A on the target cells. Here, we describe the isolation and characterization of reovirus T3D mutants that can infect human tumor cells independent of JAM-A. The JAM-A-independent (jin mutants were isolated on human U118MG glioblastoma cells, which do not express JAM-A. All jin mutants harbour mutations in the S1 segments close to the region that encodes the sialic acid-binding pocket in the shaft of the spike protein. In addition, two of the jin mutants encode spike proteins with a Q336R substitution in their head domain. The jin mutants can productively infect a wide range of cell lines that resist wt reovirus T3D infection, including chicken LMH cells, hamster CHO cells, murine endothelioma cells, human U2OS and STA-ET2.1 cells, but not primary human fibroblasts. The jin-mutants rely on the presence of sialic-acid residues on the cell surface for productive infection, as is evident from wheat germ agglutinin (WGA inhibition experiments, and from the jin-reovirus resistance of CHO-Lec2 cells, which have a deficiency of sialic-acids on their glycoproteins. The jin mutants may be useful as oncolytic agents for use in tumors in which JAM-A is absent or inaccessible.

  12. Reduction of virion-associated σ1 fibers on oncolytic reovirus variants promotes adaptation toward tumorigenic cells.

    Science.gov (United States)

    Mohamed, Adil; Teicher, Carmit; Haefliger, Sarah; Shmulevitz, Maya

    2015-04-01

    Wild-type mammalian orthoreovirus serotype 3 Dearing (T3wt) is nonpathogenic in humans but preferentially infects and kills cancer cells in culture and demonstrates promising antitumor activity in vivo. Using forward genetics, we previously isolated two variants of reovirus, T3v1 and T3v2, with increased infectivity toward a panel of cancer cell lines and improved in vivo oncolysis in a murine melanoma model relative to that of T3wt. Our current study explored how mutations in T3v1 and T3v2 promote infectivity. Reovirions contain trimers of σ1, the reovirus cell attachment protein, at icosahedral capsid vertices. Quantitative Western blot analysis showed that purified T3v1 and T3v2 virions had ∼ 2- and 4-fold-lower levels of σ1 fiber than did T3wt virions. Importantly, using RNA interference to reduce σ1 levels during T3wt production, we were able to generate wild-type reovirus with reduced levels of σ1 per virion. As σ1 levels were reduced, virion infectivity increased by 2- to 5-fold per cell-bound particle, demonstrating a causal relationship between virion σ1 levels and the infectivity of incoming virions. During infection of tumorigenic L929 cells, T3wt, T3v1, and T3v2 uncoated the outer capsid proteins σ3 and μ1C at similar rates. However, having started with fewer σ1 molecules, a complete loss of σ1 was achieved sooner for T3v1 and T3v2. Distinct from intracellular uncoating, chymotrypsin digestion, as a mimic of natural enteric infection, resulted in more rapid σ3 and μ1C removal, unique disassembly intermediates, and a rapid loss of infectivity for T3v1 and T3v2 compared to T3wt. Optimal infectivity toward natural versus therapeutic niches may therefore require distinct reovirus structures and σ1 levels. Wild-type reovirus is currently in clinical trials as a potential cancer therapy. Our molecular studies on variants of reovirus with enhanced oncolytic activity in vitro and in vivo now show that distinct reovirus structures promote

  13. Analyzing Protein Denaturation using Fast Differential Scanning Calorimetry

    NARCIS (Netherlands)

    Splinter, R.; Van Herwaarden, A.W.; Iervolino, E.; Vanden Poel, G.; Istrate, D.; Sarro, P.M.

    2012-01-01

    This paper investigates the possibility to measure protein denaturation with Fast Differential Scanning Calorimetry (FDSC). Cancer can be diagnosed by measuring protein denaturation in blood plasma using Differential Scanning Calorimetry (DSC). FDSC can reduce diagnosis time from hours to minutes,

  14. The Protein-Sparing Modified Fast Diet

    Directory of Open Access Journals (Sweden)

    Marwan Bakhach MD

    2016-01-01

    Full Text Available Objectives: The protein-sparing modified fast (PSMF is a rigorous way of rapidly losing a large amount of weight. Although adult studies have shown the PSMF to be effective, data in adolescents are lacking. The aim of this study was to determine the efficacy and safety of the PSMF in severely obese adolescents. Methods: 12 subjects who were evaluated in the Obesity Management Program at the Cleveland Clinic from 2011 to 2014 were included. The subjects were initiated on the PSMF after failing other conventional methods of weight loss. Once the goal weight was achieved, subjects were transitioned to the refeeding phase for weight maintenance. Results: Follow-up was scheduled at 3-month (11 patients and 6-month (6 patients intervals. At the 6-month follow-up visit, the average weight loss was 11.19 kg (95% confidence interval = -5.4, -27.8, P = .028, with average of 9.8% from baseline. Fifty percent of subjects had >5% weight loss and 20% had >10% weight loss. Four patients were lost to the follow-up (40%. An improvement was noted in total cholesterol and high-density lipoprotein. Due to a small sample size these results were not statistically significant. Side effects reported by subjects were mild dehydration due to nausea (2 patients, decreased energy (1 patient, and transient labile mood (1 patient. No life-threatening side effects were reported. Conclusion: Our results show that the PSMF diet can be used as an effective and safe method in the outpatient setting for rapid weight loss in adolescents with severe obesity.

  15. Growth performance of broilers in experimental Reovirus infections

    Directory of Open Access Journals (Sweden)

    Sudhakar P. Awandkar

    Full Text Available Background: The avian reoviruses have emerged to induce various manifestations in chickens. They are associated with disease conditions including malabsorption syndrome, tenosynovitis etc. Reoviruses are an important cause of suboptimum performance in broilers, resulting in poor growth performance. Poultry industry in India is facing a catastrophe due to such infections which go unnoticed in field due to masking of the symptoms by secondary infections and commonly observed nutritional disorders. Aim: To investigate the effect of reovirus infection on overall performance of broiler birds. Material and Methods: The broiler birds were challenged with homologous strains of malabsorption syndrome and tenosynovitis syndrome of reovirus. The growth performance was recorded. Results and conclusion: The growth performance and immune response to NDV did not differ in the birds challenged with tenosynovitis syndrome strain of reo virus as compared to un challenged birds. However, poor live body weight, feed intake, FCR, PE and BPEI and better serum NDV titres were found in chicks challenged with malabsorption syndrome strain of reovirus as compared to the chicks from control group. [Vet World 2012; 5(11.000: 685-689

  16. Asprosin, a fasting-induced glucogenic protein hormone

    Science.gov (United States)

    Hepatic glucose release into the circulation is vital for brain function and survival during periods of fasting and is modulated by an array of hormones that precisely regulate plasma glucose levels. We have identified a fasting-induced protein hormone that modulates hepatic glucose release. It is t...

  17. Fast loop modeling for protein structures

    Science.gov (United States)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  18. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  19. Differential Delivery of Genomic Double-Stranded RNA Causes Reovirus Strain-Specific Differences in Interferon Regulatory Factor 3 Activation.

    Science.gov (United States)

    Stuart, Johnasha D; Holm, Geoffrey H; Boehme, Karl W

    2018-05-01

    Serotype 3 (T3) reoviruses induce substantially more type 1 interferon (IFN-I) secretion than serotype 1 (T1) strains. However, the mechanisms underlying differences in IFN-I production between T1 and T3 reoviruses remain undefined. Here, we found that differences in IFN-I production between T1 and T3 reoviruses correlate with activation of interferon regulatory factor 3 (IRF3), a key transcription factor for the production of IFN-I. T3 strain rsT3D activated IRF3 more rapidly and to a greater extent than the T1 strain rsT1L, in simian virus 40 (SV40) immortalized endothelial cells (SVECs). Differences in IRF3 activation between rsT1L and rsT3D were observed in the first hours of infection and were independent of de novo viral RNA and protein synthesis. NF-κB activation mirrored IRF3 activation, with rsT3D inducing more NF-κB activity than rsT1L. We also found that IRF3 and NF-κB are activated in a mitochondrial antiviral-signaling protein (MAVS)-dependent manner. rsT1L does not suppress IRF3 activation, as IRF3 phosphorylation could be induced in rsT1L-infected cells. Transfected rsT1L and rsT3D RNA induced IRF3 phosphorylation, indicating that genomic RNA from both strains has the capacity to activate IRF3. Finally, bypassing the normal route of reovirus entry by transfecting in vitro -generated viral cores revealed that rsT1L and rsT3D core particles induced equivalent IRF3 activation. Taken together, our findings indicate that entry-related events that occur after outer capsid disassembly, but prior to deposition of viral cores into the cytoplasm, influence the efficiency of IFN-I responses to reovirus. This work provides further insight into mechanisms by which nonenveloped viruses activate innate immune responses. IMPORTANCE Detection of viral nucleic acids by the host cell triggers type 1 interferon (IFN-I) responses, which are critical for containing and clearing viral infections. Viral RNA is sensed in the cytoplasm by cellular receptors that initiate

  20. FastBLAST: homology relationships for millions of proteins.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    Full Text Available BACKGROUND: All-versus-all BLAST, which searches for homologous pairs of sequences in a database of proteins, is used to identify potential orthologs, to find new protein families, and to provide rapid access to these homology relationships. As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding. METHODOLOGY/PRINCIPAL FINDINGS: We present FastBLAST, a heuristic replacement for all-versus-all BLAST that relies on alignments of proteins to known families, obtained from tools such as PSI-BLAST and HMMer. FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences. FastBLAST runs in two stages: the first stage identifies additional families and aligns them, and the second stage quickly identifies the homologs of a query sequence, based on the alignments of the families, before generating pairwise alignments. On 6.53 million proteins from the non-redundant Genbank database ("NR", FastBLAST identifies new families 25 times faster than all-versus-all BLAST. Once the first stage is completed, FastBLAST identifies homologs for the average query in less than 5 seconds (8.6 times faster than BLAST and gives nearly identical results. For hits above 70 bits, FastBLAST identifies 98% of the top 3,250 hits per query. CONCLUSIONS/SIGNIFICANCE: FastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast.

  1. Respiratory reovirus 1/L induction of diffuse alveolar damage: pulmonary fibrosis is not modulated by corticosteroids in acute respiratory distress syndrome in mice.

    Science.gov (United States)

    London, Lucille; Majeski, Elizabeth I; Altman-Hamamdzic, Sanja; Enockson, Candace; Paintlia, Manjeet K; Harley, Russell A; London, Steven D

    2002-06-01

    Acute respiratory distress syndrome (ARDS) is a clinical syndrome characterized by diffuse alveolar damage (DAD) secondary to an intense host inflammatory response of the lung to a pulmonary or extrapulmonary infectious or noninfectious insult. We have previously described a unique animal model in which CBA/J mice infected with reovirus 1/L develop ARDS. This model recapitulates the histopathological changes observed in human ARDS, which consist of the overlapping phases of exudation, including the formation of hyaline membranes, regeneration, and healing via repair with fibrosis. In this report, we show that the development of DAD in the acute phase of the disease and intraalveolar fibrosis in the late phase of the disease was not modulated by treatment with methylprednisolone (MPS). In the presence or absence of MPS, the majority of cells infiltrating the lungs after reovirus 1/L infection were polymorphonuclear leukocytes and macrophages. A number of key proinflammatory and anti-inflammatory cytokines/chemokines that are observed in the BAL fluid of ARDS patients were also found in the lungs of mice after reovirus 1/L infection and were not modulated by MPS. These include interferon-gamma, interleukin-10, and monocyte chemoattractant protein. The histopathology, cytokine/chemokine expression, and response to corticosteroids in reovirus 1/L-induced ARDS are similar to what is observed in human patients, making this a clinically relevant model.

  2. American woodcock (Scolopax minor) mortality associated with a reovirus

    Science.gov (United States)

    Docherty, D.E.; Converse, K.A.; Hansen, W.R.; Norman, G.W.

    1994-01-01

    A virus isolate associated with a 1989-90 die-off in American woodcock (Scolopax minor) was identified as a reovirus. Emaciation was a consistent necropsy finding in the woodcock involved in this die-off. This reovirus infection appeared to be systemic, had the potential for fecal-oral virus transmission, and was associated with deterioration of body condition. To our knowledge this is the first report of a virus isolate from wild American woodcock. A survey conducted in 1990-92 indicated that this virus was not present at detectable levels in the woodcock breeding and wintering population. /// Un virus asociado con la mortalidad de becadas o perdices americanas (Scolopax minor) en 1989-1990-fue identificado como reovirus. La emaciaci??n fue un resultado com??n a la necropsia de las aves que murieron. Esta infecci??n por reovirus pareci?? ser sist??mica, ten?-a el potencial de transmisi??n fecal-oral y estuvo asociada con el deterioro del ave. Creemos que este sea el primer reporte de aislamiento viral a partir de becadas americanas. Una encuesta hecha entre 1990 y 1992 indic?? que este virus no estaba presente en los niveles detectables en los reproductores y en las aves invernales.

  3. Ramadan Fasting Decreases Body Fat but Not Protein Mass.

    Science.gov (United States)

    Fahrial Syam, Ari; Suryani Sobur, Cecep; Abdullah, Murdani; Makmun, Dadang

    2016-01-01

    Many studies have shown various results regarding the effects of Ramadan fasting on weight and body composition in healthy individuals. This study aimed to evaluate the effect of Ramadan fasting on body composition in healthy Indonesian medical staff. In this study, we examined the influence of Ramadan fasting on body composition in healthy medical staff. The longitudinal study was performed during and after Ramadan fasting in 2013 (August to October). Fourty-three medical staff members (physicians, nurses and nutritionists) at the Internal Medicine Ward of the Dr. Cipto Mangunkusumo General Hospital were measured to compare their calorie intake, weight, body mass index, waist-to-hip ratio (WHR), and body composition, including body fat, protein, minerals and water, on the first and 28(th) days of Ramadan and also 4-5 weeks after Ramadan fasting. Measurements were obtained for all 43 subjects on the 28(th) day of Ramadan, but they were obtained for only 25 subjects 4 - 5 weeks after Ramadan. By the 28(th) day of Ramadan, it was found that the body weight, BMI, body fat, water and mineral measures had decreased significantly (-0.874 ± 0.859 kg, P Ramadan, body weight and composition had returned to the same levels as on the first day of Ramadan. Ramadan fasting resulted in weight loss even it was only a temporary effect, as the weight was quickly regained within one month after fasting. The catabolism catabolic state, which is related to protein loss, was not triggered during Ramadan fasting. Further research is needed to evaluate the effects of weight loss during Ramadan fasting in healthy individuals.

  4. Adjustments of Protein Metabolism in Fasting Arctic Charr, Salvelinus alpinus.

    Directory of Open Access Journals (Sweden)

    Alicia A Cassidy

    Full Text Available Protein metabolism, including the interrelated processes of synthesis and degradation, mediates the growth of an animal. In ectothermic animals, protein metabolism is responsive to changes in both biotic and abiotic conditions. This study aimed to characterise responses of protein metabolism to food deprivation that occur in the coldwater salmonid, Arctic charr, Salvelinus alpinus. We compared two groups of Arctic charr: one fed continuously and the other deprived of food for 36 days. We measured the fractional rate of protein synthesis (KS in individuals from the fed and fasted groups using a flooding dose technique modified for the use of deuterium-labelled phenylalanine. The enzyme activities of the three major protein degradation pathways (ubiquitin proteasome, lysosomal cathepsins and the calpain systems were measured in the same fish. This study is the first to measure both KS and the enzymatic activity of protein degradation in the same fish, allowing us to examine the apparent contribution of different protein degradation pathways to protein turnover in various tissues (red and white muscle, liver, heart and gills. KS was lower in the white muscle and in liver of the fasted fish compared to the fed fish. There were no observable effects of food deprivation on the protease activities in any of the tissues with the exception of liver, where the ubiquitin proteasome pathway seemed to be activated during fasting conditions. Lysosomal proteolysis appears to be the primary degradation pathway for muscle protein, while the ubiquitin proteasome pathway seems to predominate in the liver. We speculate that Arctic charr regulate protein metabolism during food deprivation to conserve proteins.

  5. Concentration of Reovirus and Adenovirus from Sewage and Effluents by Protamine Sulfate (Salmine) Treatment 1

    Science.gov (United States)

    England, Beatrice

    1972-01-01

    Protamine sulfate was employed to recover reoviruses, adenoviruses, and certain enteroviruses from sewage and treated effluents; 50- to 400-fold concentration of viral content was achieved. PMID:4342842

  6. Postvaccinal reovirus infection with high mortality in breeder chicks.

    Science.gov (United States)

    Chénier, Sonia; Boulianne, Martine; Gagnon, Carl A

    2014-12-01

    A broiler breeder flock was subcutaneously vaccinated at the hatchery with a live avian orthoreovirus (ARV) vaccine against viral arthritis. Chicks began to die at 3 days of age and postmortem examination revealed massive subcutaneous hemorrhages and edema on the dorsal aspect of the neck at the site of vaccination, a severe necrotic hepatitis, and pulmonary edema. Microscopically, the main lesion was a multifocal vacuolar degeneration and necrosis of randomly distributed small groups of hepatocytes with presence of apoptotic and multinucleated syncytial cells. Necrotic foci were also found in the lungs as well as a hemorrhagic, granulomatous, and heterophilic cellulitis and myositis of the neck and a generalized depletion and lymphocytolysis of lymphoid organs. At 8 days of age, birds also began to show hock swelling histologically characterized by a fibrinoleucocytic inflammation of the articulation and tendon sheaths, with hyperplasia of the synovial membrane, and lymphoplasmocytic infiltration. PCR and viral culture of livers were positive for ARV. Partial sequencing of the S1 gene from the virus isolate showed 99.2% to 99.8% homology with three vaccinal strains (ARV S1133, 1733, and 2408). Viral particles compatible with reovirus virions were observed at transmission electron microscopy. Investigation at the hatchery revealed that chicks were inadvertently administered an S1133 reovirus vaccine labeled for water administration in 10- to 17-week-old chickens. This human error is most likely the reason for this unusually severe viremic reovirus infection that affected this flock at such an early age.

  7. Methodology for fast evaluation of Bacillus thuringiensis crystal protein content

    Directory of Open Access Journals (Sweden)

    Alves Lúcia M. Carareto

    2000-01-01

    Full Text Available The development of the production and use of Bacillus thuringiensis in Brazil at a commercial scale faces certain difficulties, among them the establishment of efficient methodologies for the quantitation of toxic products to be commercialized. Presently, the amount of toxin is given in percentage by analyzing the samples total protein content. Such methodology however, does not measure the actual amount of active protein present in the product, since most strains express different endotoxin genes and might even produce b-toxin. Since the various types of toxins exhibit different antigenic characteristics, this work has as objective the utilization of fast immunological techniques to quantify the level of crystal protein. Crystal protein produced by a subspecies of Bacillus thuringiensis var. israelensis was purified by ultracentrifugation and utilized to immunize rabbits and to produce hiperimmune sera. Such sera were latter used to evaluate the level of proteins on commercial bioinsecticide and on laboratory cultures of B. thuringiensis through the immunodot technique. The results were obtained by comparison of data obtained from reactions with known concentrations of crystal protein permitting to evaluate the level of such protein on various materials.

  8. Antitumour responses induced by a cell-based Reovirus vaccine in murine lung and melanoma models

    International Nuclear Information System (INIS)

    Campion, Ciorsdan A.; Soden, Declan; Forde, Patrick F.

    2016-01-01

    The ever increasing knowledge in the areas of cell biology, the immune system and the mechanisms of cancer are allowing a new phase of immunotherapy to develop. The aim of cancer vaccination is to activate the host immune system and some success has been observed particularly in the use of the BCG vaccine for bladder cancer as an immunostimulant. Reovirus, an orphan virus, has proven itself as an oncolytic virus in vitro and in vivo. Over 80 % of tumour cell lines have been found to be susceptible to Reovirus infection and it is currently in phase III clinical trials. It has been shown to induce immune responses to tumours with very low toxicities. In this study, Reovirus was examined in two main approaches in vivo, in mice, using the melanoma B16F10 and Lewis Lung Carcinoma (LLC) models. Initially, mice were treated intratumourally (IT) with Reovirus and the immune responses determined by cytokine analysis. Mice were also vaccinated using a cell-based Reovirus vaccine and subsequently exposed to a tumourigenic dose of cells (B16F10 or LLC). Using the same cell-based Reovirus vaccine, established tumours were treated and subsequent immune responses and virus retrieval investigated. Upregulation of several cytokines was observed following treatment and replication-competent virus was also retrieved from treated tumours. Varying levels of cytokine upregulation were observed and no replication-competent virus was retrieved in vaccine-treated mice. Prolongation of survival and delayed tumour growth were observed in all models and an immune response to Reovirus, either using Reovirus alone or a cell-based vaccine was also observed in all mice. This study provides evidence of immune response to tumours using a cell-based Reovirus vaccine in both tumour models investigated, B16F10 and LLC, cytokine induction was observed with prolongation of survival in almost all cases which may suggest a new method for using Reovirus in the clinic

  9. Developing Fast Fluorescent Protein Voltage Sensors by Optimizing FRET Interactions.

    Directory of Open Access Journals (Sweden)

    Uhna Sung

    Full Text Available FRET (Förster Resonance Energy Transfer-based protein voltage sensors can be useful for monitoring neuronal activity in vivo because the ratio of signals between the donor and acceptor pair reduces common sources of noise such as heart beat artifacts. We improved the performance of FRET based genetically encoded Fluorescent Protein (FP voltage sensors by optimizing the location of donor and acceptor FPs flanking the voltage sensitive domain of the Ciona intestinalis voltage sensitive phosphatase. First, we created 39 different "Nabi1" constructs by positioning the donor FP, UKG, at 8 different locations downstream of the voltage-sensing domain and the acceptor FP, mKO, at 6 positions upstream. Several of these combinations resulted in large voltage dependent signals and relatively fast kinetics. Nabi1 probes responded with signal size up to 11% ΔF/F for a 100 mV depolarization and fast response time constants both for signal activation (~2 ms and signal decay (~3 ms. We improved expression in neuronal cells by replacing the mKO and UKG FRET pair with Clover (donor FP and mRuby2 (acceptor FP to create Nabi2 probes. Nabi2 probes also had large signals and relatively fast time constants in HEK293 cells. In primary neuronal culture, a Nabi2 probe was able to differentiate individual action potentials at 45 Hz.

  10. Quantification of the host response proteome after mammalian reovirus T1L infection.

    Directory of Open Access Journals (Sweden)

    Alicia R Berard

    Full Text Available All viruses are dependent upon host cells for replication. Infection can induce profound changes within cells, including apoptosis, morphological changes, and activation of signaling pathways. Many of these alterations have been analyzed by gene arrays to measure the cellular "transcriptome." We used SILAC (stable isotope labeling by amino acids in cell culture, combined with high-throughput 2-D HPLC/mass spectrometry, to determine relative quantitative differences in host proteins at 6 and 24 hours after infecting HEK293 cells with reovirus serotype 1 Lang (T1L. 3,076 host proteins were detected at 6 hpi, of which 132 and 68 proteins were significantly up or down regulated, respectively. 2,992 cellular proteins, of which 104 and 49 were up or down regulated, respectively, were identified at 24 hpi. IPA and DAVID analyses indicated proteins involved in cell death, cell growth factors, oxygen transport, cell structure organization and inflammatory defense response to virus were up-regulated, whereas proteins involved in apoptosis, isomerase activity, and metabolism were down-regulated. These proteins and pathways may be suitable targets for intervention to either attenuate virus infection or enhance oncolytic potential.

  11. Synergistic effects of oncolytic reovirus and docetaxel chemotherapy in prostate cancer

    Directory of Open Access Journals (Sweden)

    Prestwich Robin

    2011-06-01

    Full Text Available Abstract Background Reovirus type 3 Dearing (T3D has demonstrated oncolytic activity in vitro, in in vivo murine models and in early clinical trials. However the true potential of oncolytic viruses may only be realized fully in combination with other modalities such as chemotherapy, targeted therapy and radiotherapy. In this study, we examine the oncolytic activity of reovirus T3D and chemotherapeutic agents against human prostate cancer cell lines, with particular focus on the highly metastatic cell line PC3 and the chemotherapeutic agent docetaxel. Docetaxel is the standard of care for metastatic prostate cancer and acts by disrupting the normal process of microtubule assembly and disassembly. Reoviruses have been shown to associate with microtubules and may require this association for efficient viral replication. Methods The effects of reovirus and chemotherapy on in vitro cytotoxicity were investigated in PC3 and Du 145 cells and the interactions between agents were assessed by combination index analysis. An Annexin V/propidium iodide fluorescence-activated cell sorting-based assay was used to determine mode of cell death. The effects of reovirus and docetaxel administered as single agent or combination therapy were tested in vivo in a murine model. The effects of docetaxel and reovirus, alone and together, on microtubule stabilisation were investigated by Western blot analysis. Results Variable degrees of synergistic cytotoxicity were observed in PC3 and Du 145 cells exposed to live reovirus and several chemotherapy agents. Combination of reovirus infection with docetaxel exposure led to increased late apoptotic/necrotic cell populations. Reovirus/docetaxel combined therapy led to reduced tumour growth and increased survival in a PC3 tumour bearing mouse model. Microtubule stabilization was enhanced in PC3 cells treated with reovirus/docetaxel combined therapy compared to other reovirus/chemotherapy combinations. Conclusions The co

  12. Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration

    Energy Technology Data Exchange (ETDEWEB)

    Simarro, Maria [Division of Rheumatology, Immunology and Allergy, Brigham and Women' s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Gimenez-Cassina, Alfredo [Department of Cancer Biology at Dana Farber Institute, Boston, MA 02115 (United States); Kedersha, Nancy [Division of Rheumatology, Immunology and Allergy, Brigham and Women' s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Lazaro, Jean-Bernard; Adelmant, Guillaume O.; Marto, Jarrod A. [Department of Cancer Biology at Dana Farber Institute, Boston, MA 02115 (United States); Rhee, Kirsten [Division of Rheumatology, Immunology and Allergy, Brigham and Women' s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Tisdale, Sarah; Danial, Nika [Department of Cancer Biology at Dana Farber Institute, Boston, MA 02115 (United States); Benarafa, Charaf [Theodor Kocher Institute, University of Bern, 3012 Bern (Switzerland); Orduna, Anonio [Unidad de Investigacion, Hospital Clinico Universitario de Valladolid, 47005 Valladolid (Spain); Anderson, Paul, E-mail: panderson@rics.bwh.harvard.edu [Division of Rheumatology, Immunology and Allergy, Brigham and Women' s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States)

    2010-10-22

    Research highlights: {yields} Five members of the FAST kinase domain-containing proteins are localized to mitochondria in mammalian cells. {yields} The FASTKD3 interactome includes proteins involved in various aspects of mitochondrial metabolism. {yields} Targeted knockdown of FASTKD3 significantly reduces basal and maximal mitochondrial oxygen consumption. -- Abstract: Fas-activated serine/threonine phosphoprotein (FAST) is the founding member of the FAST kinase domain-containing protein (FASTKD) family that includes FASTKD1-5. FAST is a sensor of mitochondrial stress that modulates protein translation to promote the survival of cells exposed to adverse conditions. Mutations in FASTKD2 have been linked to a mitochondrial encephalomyopathy that is associated with reduced cytochrome c oxidase activity, an essential component of the mitochondrial electron transport chain. We have confirmed the mitochondrial localization of FASTKD2 and shown that all FASTKD family members are found in mitochondria. Although human and mouse FASTKD1-5 genes are expressed ubiquitously, some of them are most abundantly expressed in mitochondria-enriched tissues. We have found that RNA interference-mediated knockdown of FASTKD3 severely blunts basal and stress-induced mitochondrial oxygen consumption without disrupting the assembly of respiratory chain complexes. Tandem affinity purification reveals that FASTKD3 interacts with components of mitochondrial respiratory and translation machineries. Our results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration.

  13. Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration

    International Nuclear Information System (INIS)

    Simarro, Maria; Gimenez-Cassina, Alfredo; Kedersha, Nancy; Lazaro, Jean-Bernard; Adelmant, Guillaume O.; Marto, Jarrod A.; Rhee, Kirsten; Tisdale, Sarah; Danial, Nika; Benarafa, Charaf; Orduna, Anonio; Anderson, Paul

    2010-01-01

    Research highlights: → Five members of the FAST kinase domain-containing proteins are localized to mitochondria in mammalian cells. → The FASTKD3 interactome includes proteins involved in various aspects of mitochondrial metabolism. → Targeted knockdown of FASTKD3 significantly reduces basal and maximal mitochondrial oxygen consumption. -- Abstract: Fas-activated serine/threonine phosphoprotein (FAST) is the founding member of the FAST kinase domain-containing protein (FASTKD) family that includes FASTKD1-5. FAST is a sensor of mitochondrial stress that modulates protein translation to promote the survival of cells exposed to adverse conditions. Mutations in FASTKD2 have been linked to a mitochondrial encephalomyopathy that is associated with reduced cytochrome c oxidase activity, an essential component of the mitochondrial electron transport chain. We have confirmed the mitochondrial localization of FASTKD2 and shown that all FASTKD family members are found in mitochondria. Although human and mouse FASTKD1-5 genes are expressed ubiquitously, some of them are most abundantly expressed in mitochondria-enriched tissues. We have found that RNA interference-mediated knockdown of FASTKD3 severely blunts basal and stress-induced mitochondrial oxygen consumption without disrupting the assembly of respiratory chain complexes. Tandem affinity purification reveals that FASTKD3 interacts with components of mitochondrial respiratory and translation machineries. Our results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration.

  14. Proteomics analysis of the DF-1 chicken fibroblasts infected with avian reovirus strain S1133.

    Directory of Open Access Journals (Sweden)

    Wen-Ting Chen

    Full Text Available BACKGROUND: Avian reovirus (ARV is a member of the Orthoreovirus genus in the Reoviridae family. It is the etiological agent of several diseases, among which viral arthritis and malabsorption syndrome are the most commercially important, causing considerable economic losses in the poultry industry. Although a small but increasing number of reports have characterized some aspects of ARV infection, global changes in protein expression in ARV-infected host cells have not been examined. The current study used a proteomics approach to obtain a comprehensive view of changes in protein levels in host cells upon infection by ARV. METHODOLOGY AND PRINCIPAL FINDINGS: The proteomics profiles of DF-1 chicken fibroblast cells infected with ARV strain S1133 were analyzed by two-dimensional differential-image gel electrophoresis. The majority of protein expression changes (≥ 1.5 fold, p<0.05 occurred at 72 h post-infection. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identified 51 proteins with differential expression levels, including 25 that were upregulated during ARV infection and 26 that were downregulated. These proteins were divided into eight groups according to biological function: signal transduction, stress response, RNA processing, the ubiquitin-proteasome pathway, lipid metabolism, carbohydrate metabolism, energy metabolism, and cytoskeleton organization. They were further examined by immunoblotting to validate the observed alterations in protein expression. CONCLUSION/SIGNIFICANCE: This is the first report of a time-course proteomic analysis of ARV-infected host cells. Notably, all identified proteins involved in signal transduction, RNA processing, and the ubiquitin-proteasome pathway were downregulated in infected cells, whereas proteins involved in DNA synthesis, apoptosis, and energy production pathways were upregulated. In addition, other differentially expressed proteins were linked with the cytoskeleton

  15. Fasting Lipoprotein Lipase Protein Levels Can Predict a Postmeal Increment of Triglyceride Levels in Fasting Normohypertriglyceridemic Subjects.

    Science.gov (United States)

    Tsuzaki, Kokoro; Kotani, Kazuhiko; Yamada, Kazunori; Sakane, Naoki

    2016-09-01

    Although a postprandial increment in triglyceride (TG) levels is considered to be a risk factor for atherogenesis, tests (e.g., fat load) to assess postprandial changes in TG levels cannot be easily applied to clinical practice. Therefore, fasting markers that predict postprandial TG states are needed to be developed. One current candidate is lipoprotein lipase (LPL) protein, a molecule that hydrides TGs. This study investigated whether fasting LPL levels could predict postprandial TG levels. A total of 17 subjects (11 men, 6 women, mean age 52 ± 11 years) with normotriglyceridemia during fasting underwent the meal test. Several fasting parameters, including LPL, were measured for the area under the curve of postprandial TGs (AUC-TG). The subjects' mean fasting TG level was 1.30 mmol/l, and their mean LPL level was 41.6 ng/ml. The subjects' TG levels increased after loading (they peaked after two postprandial hours). Stepwise multiple regression analysis demonstrated that fasting TG levels were a predictor of the AUC-TG. In addition, fasting LPL mass levels were found to be a predictor of the AUC-TG (β = 0.65, P fasting TG levels. Fasting LPL levels may be useful to predict postprandial TG increment in this population. © 2015 Wiley Periodicals, Inc.

  16. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

    Science.gov (United States)

    Muñoz, Victor; Cerminara, Michele

    2016-09-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. © 2016 The Author(s).

  17. Fasting-induced adipose factor/angiopoietin-like protein 4: a potential target for dyslipidemia?

    NARCIS (Netherlands)

    Zandbergen, F.J.; Dijk, van S.; Müller, M.R.; Kersten, A.H.

    2006-01-01

    Recently, several proteins with homology to angiopoietins have been discovered. Three members of this new group, designated angiopoietin-like proteins (ANGPTLs), have been linked to regulation of energy metabolism. This review will focus on the fasting-induced adipose factor (FIAF)/ANGPTL4 as an

  18. Protein determination in soya bean by fast neutron activation analysis

    International Nuclear Information System (INIS)

    Szegedi, S.; Mosbah, D.S.; Varadi, M.; Szaloki, I.

    1988-01-01

    For a non-destructive determination of the protein content in soya bean samples, 14-MeV neutron activation analysis was applied. To check the method, the results obtained by X-ray fluorescence analysis and the Kjeldahl procedure were compared. For pressed pellet samples of about 1 g with 15 min irradiation and 10 min measuring times the accuracy of the protein determination was found to be 15%. (author) 7 refs.; 4 figs.; 3 tabs

  19. Fast mapping of global protein folding states by multivariate NMR:

    DEFF Research Database (Denmark)

    Malmendal, Anders; Underhaug, Jarl; Otzen, Daniel

    2010-01-01

    To obtain insight into the functions of proteins and their specific roles, it is important to establish efficient procedures for exploring the states that encapsulate their conformational space. Global Protein folding State mapping by multivariate NMR (GPS NMR) is a powerful high-throughput method......-lactalbumin in the presence of the anionic surfactant sodium dodecyl sulfate, SDS, and compare these with other surfactants, acid, denaturants and heat....

  20. Fast Proton Titration Scheme for Multiscale Modeling of Protein Solutions.

    Science.gov (United States)

    Teixeira, Andre Azevedo Reis; Lund, Mikael; da Silva, Fernando Luís Barroso

    2010-10-12

    Proton exchange between titratable amino acid residues and the surrounding solution gives rise to exciting electric processes in proteins. We present a proton titration scheme for studying acid-base equilibria in Metropolis Monte Carlo simulations where salt is treated at the Debye-Hückel level. The method, rooted in the Kirkwood model of impenetrable spheres, is applied on the three milk proteins α-lactalbumin, β-lactoglobulin, and lactoferrin, for which we investigate the net-charge, molecular dipole moment, and charge capacitance. Over a wide range of pH and salt conditions, excellent agreement is found with more elaborate simulations where salt is explicitly included. The implicit salt scheme is orders of magnitude faster than the explicit analog and allows for transparent interpretation of physical mechanisms. It is shown how the method can be expanded to multiscale modeling of aqueous salt solutions of many biomolecules with nonstatic charge distributions. Important examples are protein-protein aggregation, protein-polyelectrolyte complexation, and protein-membrane association.

  1. Enteropathogenicity of Dutch and German avian reoviruses in SPF white leghorn chickens and broilers.

    NARCIS (Netherlands)

    Songserm, T.; Roozelaar, van D.; Kant-Eenbergen, H.C.M.; Pol, J.; Pijpers, A.; Huurne, ter A.A.H.M.

    2003-01-01

    The enteropathogenicity of avian reoviruses (ARVs), isolated from chickens affected with malabsorption syndrome (MAS) from The Netherlands and Germany was studied. In the first trial seven different ARVs isolated from MAS cases were inoculated in 1-day-old specific pathogenic free (SPF) white

  2. Astrovirus, reovirus and rotavirus concomitant infection causes decreased weight gain in broad-breasted white poults

    Science.gov (United States)

    Turkey astrovirus type-2 (TAstV-2), turkey rotavirus (TRotV) and turkey reovirus (TReoV) were evaluated for pathogenesis in 3 day-old turkey poults in all possible combinations of one, two or three viruses. Body-weights were recorded at 2, 4, 7, 10 and 14 days post inoculation (PI) and were decreas...

  3. Ultra-fast evaluation of protein energies directly from sequence.

    Directory of Open Access Journals (Sweden)

    Gevorg Grigoryan

    2006-06-01

    Full Text Available The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7 compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0. Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages

  4. FAST

    DEFF Research Database (Denmark)

    Zuidmeer-Jongejan, Laurian; Fernandez-Rivas, Montserrat; Poulsen, Lars K.

    2012-01-01

    ABSTRACT: The FAST project (Food Allergy Specific Immunotherapy) aims at the development of safe and effective treatment of food allergies, targeting prevalent, persistent and severe allergy to fish and peach. Classical allergen-specific immunotherapy (SIT), using subcutaneous injections with aqu...

  5. Visceral organ mass and hepatic protein synthetic capacity in fed and fasted rats

    International Nuclear Information System (INIS)

    Burrin, D.G.; Britton, R.A.; Ferrell, C.L.

    1986-01-01

    Forty-two male rats (avg wt. = 320 g) were used to assess the effect of severe nutrient restriction (72 h fast) on visceral organ mass and hepatic protein synthetic capacity as measured by in vitro incorporation of U- 14 -C-VALINE ( 14 C-VAL) into isolated hepatocytes. Organ weights expressed as a percent of empty body weight for fed vs. fasted rats were; liver (5.21 +/- .54 vs 3.82 +/- .46), kidney (.87 +/- 0.6 vs .89 +/- .05), stomach (.60 +/- .06 vs .61 +/- .06), intestines (3.70 +/- .44 vs 3.41 +/- .37). No differences were observed in in vitro oxygen consumption (15.7 +/- 3.1 vs 16.1 +/- 3.3, umole min -1 g -1 dry tissue) or 14 -C VAL incorporation (4.93 +/- 1.28 vs 4.31 +/- 1.48, dpm min -1 mg -1 dry tissue) for hepatocytes from fed vs. fasted rats. Analysis of perfused liver tissue indicated fed rats had higher protein (152.1 +/- 16.3 vs 136.6 +/- 29.6, mg/g tissue) and RNA (8.81 +/- 1.66 vs 5.97 +/- 1.87, mg/g tissue) with lower DNA (2.19 +/- .31 vs 3.19 +/- .54, mg/g tissue) compared to fasted rats. Protein-nucleic acid ratios suggest liver tissue from fed rats had a greater capacity for protein synthesis compared to fasted rats, however, this was not evident from in vitro hepatocyte 14 -C VAL incorporation estimates. These data indicate that severe nutrient restriction (72 h fast) affects visceral organ mass largely by reduced liver and gut size as well as decreased hepatic protein synthetic capacity

  6. Selecting for Fast Protein-Protein Association As Demonstrated on a Random TEM1 Yeast Library Binding BLIP.

    Science.gov (United States)

    Cohen-Khait, Ruth; Schreiber, Gideon

    2018-04-27

    Protein-protein interactions mediate the vast majority of cellular processes. Though protein interactions obey basic chemical principles also within the cell, the in vivo physiological environment may not allow for equilibrium to be reached. Thus, in vitro measured thermodynamic affinity may not provide a complete picture of protein interactions in the biological context. Binding kinetics composed of the association and dissociation rate constants are relevant and important in the cell. Therefore, changes in protein-protein interaction kinetics have a significant impact on the in vivo activity of the proteins. The common protocol for the selection of tighter binders from a mutant library selects for protein complexes with slower dissociation rate constants. Here we describe a method to specifically select for variants with faster association rate constants by using pre-equilibrium selection, starting from a large random library. Toward this end, we refine the selection conditions of a TEM1-β-lactamase library against its natural nanomolar affinity binder β-lactamase inhibitor protein (BLIP). The optimal selection conditions depend on the ligand concentration and on the incubation time. In addition, we show that a second sort of the library helps to separate signal from noise, resulting in a higher percent of faster binders in the selected library. Fast associating protein variants are of particular interest for drug development and other biotechnological applications.

  7. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

    Directory of Open Access Journals (Sweden)

    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  8. Avian reovirus S1133-induced apoptosis is associated with Bip/GRP79-mediated Bim translocation to the endoplasmic reticulum.

    Science.gov (United States)

    Lin, Ping-Yuan; Liu, Hung-Jen; Chang, Ching-Dong; Chen, Yo-Chia; Chang, Chi-I; Shih, Wen-Ling

    2015-04-01

    In this study the mechanism of avian reovirus (ARV) S1133-induced pathogenesis was investigated, with a focus on the contribution of ER stress to apoptosis. Our results showed that upregulation of the ER stress response protein, as well as caspase-3 activation, occurred in ARV S1133-infected cultured cells and in SPF White Leghorn chicks organs. Upon infection, Bim was translocated specifically to the ER, but not mitochondria, in the middle to late infectious stages. In addition, ARV S1133 induced JNK phosphorylation and promoted JNK-Bim complex formation, which correlated with the Bim translocation and apoptosis induction that was observed at the same time point. Knockdown of BiP/GRP78 by siRNA and inhibition of BiP/GRP78 using EGCG both abolished the formation of the JNK-Bim complex, caspase-3 activation, and subsequent apoptosis induction by ARV S1133 efficiently. These results suggest that BiP/GRP78 played critical roles and works upstream of JNK-Bim in response to the ARV S1133-mediated apoptosis process.

  9. Fast axonal transport of labeled proteins in motoneurons of exercise-trained rats

    International Nuclear Information System (INIS)

    Jasmin, B.J.; Lavoie, P.A.; Gardiner, P.F.

    1988-01-01

    In this study, the fast orthograde axonal transport of radiolabeled proteins was measured to determine the effects of endurance-running training on transport velocity and amounts of transported proteins in rat sciatic motoneurons. Female rats were subjected to a progressive running-training program for 10-12 wk. Twenty-four hours after the last training session, rats underwent right L4-L5 dorsal root ganglionectomy. The next day, 20 microCi of [3H]leucine was injected bilaterally in the vicinity of the motoneuronal cell bodies supplying the sciatic nerve, to study axonal transport parameters. Results showed that peak and average transport velocities of labeled proteins were significantly (P less than 0.05) increased by 22 and 29%, respectively, in the deafferented nerves of the runners as compared with controls. Moreover, the amount of total transported protein-bound radioactivity was increased in both left (40%) and right (37%) sciatic nerves of the runners. An exhaustive exercise session reduced (P less than 0.05) peak displacement (8%) and total transported protein-bound radioactivity (36%) in the sciatic nerves of control rats, whereas no changes were noticed in trained animals. The data suggest that chronic endurance running induces significant adaptations in the fast axonal transport of labeled proteins

  10. Fish protein intake induces fast-muscle hypertrophy and reduces liver lipids and serum glucose levels in rats.

    Science.gov (United States)

    Kawabata, Fuminori; Mizushige, Takafumi; Uozumi, Keisuke; Hayamizu, Kohsuke; Han, Li; Tsuji, Tomoko; Kishida, Taro

    2015-01-01

    In our previous study, fish protein was proven to reduce serum lipids and body fat accumulation by skeletal muscle hypertrophy and enhancing basal energy expenditure in rats. In the present study, we examined the precise effects of fish protein intake on different skeletal muscle fiber types and metabolic gene expression of the muscle. Fish protein increased fast-twitch muscle weight, reduced liver triglycerides and serum glucose levels, compared with the casein diet after 6 or 8 weeks of feeding. Furthermore, fish protein upregulated the gene expressions of a fast-twitch muscle-type marker and a glucose transporter in the muscle. These results suggest that fish protein induces fast-muscle hypertrophy, and the enhancement of basal energy expenditure by muscle hypertrophy and the increase in muscle glucose uptake reduced liver lipids and serum glucose levels. The present results also imply that fish protein intake causes a slow-to-fast shift in muscle fiber type.

  11. A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

    Science.gov (United States)

    Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

    2011-04-01

    Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

  12. Diet-induced obesity alters protein synthesis: Tissue-specific effects in fasted vs. fed mice

    OpenAIRE

    Anderson, Stephanie R.; Gilge, Danielle A.; Steiber, Alison L.; Previs, Stephen F.

    2008-01-01

    The influence of obesity on protein dynamics is not clearly understood. We have designed experiments to test the hypothesis that obesity impairs the stimulation of tissue-specific protein synthesis following nutrient ingestion. C57BL/6J mice were randomized into two groups: group 1 (control, n = 16) were fed a low-fat, high-carbohydrate diet and group 2 (experimental, n = 16) were fed a high-fat, low-carbohydrate diet ad libitum for 9 weeks. On the experiment day, all mice were fasted for 6 h...

  13. Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

    Science.gov (United States)

    Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A; Gordeliy, Valentin; Popov, Alexander

    2017-05-01

    We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.

  14. Differential regulation of lipid and protein metabolism in obese vs. lean subjects before and after a 72-h fast

    DEFF Research Database (Denmark)

    Bak, Ann Mosegaard; Møller, Andreas Buch; Vendelbo, Mikkel Holm

    2016-01-01

    release in obese subjects under basal and fasting conditions. We therefore studied nine lean and nine obese subjects twice, after 12 and 72 h of fasting, using measurements of mRNA and protein expression and phosphorylation of lipolytic and protein metabolic signaling molecules in fat and muscle together...... with whole body and forearm tracer techniques. Obese subjects displayed increased whole body lipolysis, decreased urea production rates, and decreased forearm muscle protein breakdown per 100 ml of forearm tissue, differences that persisted after 72 h of fasting. Lipolysis per fat mass unit was reduced...... in obese subjects and, correspondingly, adipose tissue hormone-sensitive lipase (HSL) phosphorylation and mRNA and protein levels of the adipose triglyceride lipase (ATGL) coactivator CGI58 were decreased. Fasting resulted in higher HSL phosphorylations and lower protein levels of the ATGL inhibitor G0S2...

  15. The role of proteins and metal ions in the protection of chromatin DNA at fast neutrons action

    International Nuclear Information System (INIS)

    Radu, L.; Preoteasa, V.; Radulescu, I.; Constantinescu, B.

    1997-01-01

    The role of chromatin proteins and of some ions on the fast neutrons actions on chromatin DNA from rat Walker tumors was analysed. The DNA in chromatin is effectively protected against fast neutrons actions by DNA bound proteins and specially by histones, because of the limited accessibility of the condensed chromatin DNA to hydroxyl radicals and of the scavenging of radicals by the chromatin proteins. The ions utilised protect chromatin DNA against the damage produced ed by fast neutrons, through the induction of structural DNA changes with a less accessibility to OH radicals. (authors)

  16. Fast and accurate protein substructure searching with simulated annealing and GPUs

    Directory of Open Access Journals (Sweden)

    Stivala Alex D

    2010-09-01

    Full Text Available Abstract Background Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif searching. Results We developed an improved heuristic for tableau-based protein structure and substructure searching using simulated annealing, that is as fast or faster and comparable in accuracy, with some widely used existing methods. Furthermore, we created a parallel implementation on a modern graphics processing unit (GPU. Conclusions The GPU implementation achieves up to 34 times speedup over the CPU implementation of tableau-based structure search with simulated annealing, making it one of the fastest available methods. To the best of our knowledge, this is the first application of a GPU to the protein structural search problem.

  17. Effects of toluene on protein synthesis and the interaction with ethanol in hepatocytes isolated from fed and fasted rats

    International Nuclear Information System (INIS)

    Smith-Kielland, A.; Ripel, Aa.; Gadeholt, G.

    1989-01-01

    The effects of three different concentrations (about 20, 100 and 1000 μM) of toluene on protein synthesis were studied in hepatocytes isolated from fed and fasted rats after 60 and 120 min. of incubation. The interaction between ethanol (60 mM) and the low and high toluene concentrations were also tested. To measure protein synthesis, 14 C-valine was used as the precursor amino acid. Total valine concentration was 2 mM to ensure near-constant specific radioactivity of precursor. Toluene concentrations were measured by head-space gas chromatography. Protein synthesis was unchanged in the presence of low toluene concentrations. Intermediate toluene concentration decreased protein synthesis by about 20% and high toluene concentration decreased protein synthesis by about 60%. Protein synthesis was similar in cells from fed and fasted rats. Ethanol alone inhibited protein synthesis by 20-30%, more in fasted than in fed rats. Toluene and ethanol in combination inhibited protein synthesis additively. The high toluene concentration with or without ethanol appeared to inhibit synthesis/secretion of export proteins in hepatocytes from fasted rats. In conclusion, our study indicates that toluene in relatively high concentrations inhibits general protein synthesis in isolated rat hepatocytes. Toluene and ethanol seems to inhibit protein synthesis additively. (author)

  18. Effects of toluene on protein synthesis and the interaction with ethanol in hepatocytes isolated from fed and fasted rats

    Energy Technology Data Exchange (ETDEWEB)

    Smith-Kielland, A.; Ripel, Aa.; Gadeholt, G.

    1989-01-01

    The effects of three different concentrations (about 20, 100 and 1000 ..mu..M) of toluene on protein synthesis were studied in hepatocytes isolated from fed and fasted rats after 60 and 120 min. of incubation. The interaction between ethanol (60 mM) and the low and high toluene concentrations were also tested. To measure protein synthesis, /sup 14/C-valine was used as the precursor amino acid. Total valine concentration was 2 mM to ensure near-constant specific radioactivity of precursor. Toluene concentrations were measured by head-space gas chromatography. Protein synthesis was unchanged in the presence of low toluene concentrations. Intermediate toluene concentration decreased protein synthesis by about 20% and high toluene concentration decreased protein synthesis by about 60%. Protein synthesis was similar in cells from fed and fasted rats. Ethanol alone inhibited protein synthesis by 20-30%, more in fasted than in fed rats. Toluene and ethanol in combination inhibited protein synthesis additively. The high toluene concentration with or without ethanol appeared to inhibit synthesis/secretion of export proteins in hepatocytes from fasted rats. In conclusion, our study indicates that toluene in relatively high concentrations inhibits general protein synthesis in isolated rat hepatocytes. Toluene and ethanol seems to inhibit protein synthesis additively.

  19. Artificial receptor-functionalized nanoshell: facile preparation, fast separation and specific protein recognition

    Science.gov (United States)

    Ouyang, Ruizhuo; Lei, Jianping; Ju, Huangxian

    2010-05-01

    This work combined molecular imprinting technology with superparamagnetic nanospheres as the core to prepare artificial receptor-functionalized magnetic nanoparticles for separation of homologous proteins. Using dopamine as a functional monomer, novel surface protein-imprinted superparamagnetic polydopamine (PDA) core-shell nanoparticles were successfully prepared in physiological conditions, which could maintain the natural structure of a protein template and achieved the development of molecularly imprinted polymers (MIPs) from one dimension to zero dimension for efficient recognition towards large biomolecules. The resultant nanoparticles could be used for convenient magnetic separation of homologous proteins with high specificity. The nanoparticles possessed good monodispersibility, uniform surface morphology and high saturation magnetization value. The bound amounts of template proteins measured by both indirect and direct methods were in good agreement. The maximum number of imprinted cavities on the surface of the bovine hemoglobin (Hb)-imprinted nanoshell was 2.21 × 1018 g - 1, which well matched their maximum binding capacity toward bovine Hb. Both the simple method for preparation of MIPs and the magnetic nanospheres showed good application potential in fast separation, effective concentration and selective biosensing of large protein molecules.

  20. Artificial receptor-functionalized nanoshell: facile preparation, fast separation and specific protein recognition

    Energy Technology Data Exchange (ETDEWEB)

    Ouyang, Ruizhuo; Lei Jianping; Ju Huangxian, E-mail: jpl@nju.edu.cn, E-mail: hxju@nju.edu.cn [Key Laboratory of Analytical Chemistry for Life Science (Education Ministry of China), Department of Chemistry, Nanjing University, Nanjing 210093 (China)

    2010-05-07

    This work combined molecular imprinting technology with superparamagnetic nanospheres as the core to prepare artificial receptor-functionalized magnetic nanoparticles for separation of homologous proteins. Using dopamine as a functional monomer, novel surface protein-imprinted superparamagnetic polydopamine (PDA) core-shell nanoparticles were successfully prepared in physiological conditions, which could maintain the natural structure of a protein template and achieved the development of molecularly imprinted polymers (MIPs) from one dimension to zero dimension for efficient recognition towards large biomolecules. The resultant nanoparticles could be used for convenient magnetic separation of homologous proteins with high specificity. The nanoparticles possessed good monodispersibility, uniform surface morphology and high saturation magnetization value. The bound amounts of template proteins measured by both indirect and direct methods were in good agreement. The maximum number of imprinted cavities on the surface of the bovine hemoglobin (Hb)-imprinted nanoshell was 2.21 x 10{sup 18} g{sup -1}, which well matched their maximum binding capacity toward bovine Hb. Both the simple method for preparation of MIPs and the magnetic nanospheres showed good application potential in fast separation, effective concentration and selective biosensing of large protein molecules.

  1. Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Opron, Kristopher [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States)

    2014-06-21

    Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely

  2. Differential regulation of lipid and protein metabolism in obese vs. lean subjects before and after a 72-h fast.

    Science.gov (United States)

    Bak, Ann Mosegaard; Møller, Andreas Buch; Vendelbo, Mikkel Holm; Nielsen, Thomas Svava; Viggers, Rikke; Rungby, Jørgen; Pedersen, Steen Bønløkke; Jørgensen, Jens Otto Lunde; Jessen, Niels; Møller, Niels

    2016-07-01

    Increased availability of lipids may conserve muscle protein during catabolic stress. Our study was designed to define 1) intracellular mechanisms leading to increased lipolysis and 2) whether this scenario is associated with decreased amino acid and urea fluxes, and decreased muscle amino acid release in obese subjects under basal and fasting conditions. We therefore studied nine lean and nine obese subjects twice, after 12 and 72 h of fasting, using measurements of mRNA and protein expression and phosphorylation of lipolytic and protein metabolic signaling molecules in fat and muscle together with whole body and forearm tracer techniques. Obese subjects displayed increased whole body lipolysis, decreased urea production rates, and decreased forearm muscle protein breakdown per 100 ml of forearm tissue, differences that persisted after 72 h of fasting. Lipolysis per fat mass unit was reduced in obese subjects and, correspondingly, adipose tissue hormone-sensitive lipase (HSL) phosphorylation and mRNA and protein levels of the adipose triglyceride lipase (ATGL) coactivator CGI58 were decreased. Fasting resulted in higher HSL phosphorylations and lower protein levels of the ATGL inhibitor G0S2. Muscle protein expressions of mammalian target of rapamycin (mTOR) and 4EBP1 were lower in obese subjects, and MuRf1 mRNA was higher with fasting in lean but not obese subjects. Phosphorylation and signaling of mTOR decreased with fasting in both groups, whereas ULK1 protein and mRNA levels increased. In summary, obese subjects exhibit increased lipolysis due to a large fat mass with blunted prolipolytic signaling, together with decreased urea and amino acid fluxes both in the basal and 72-h fasted state; this is compatible with preservation of muscle and whole body protein. Copyright © 2016 the American Physiological Society.

  3. Fast high-pressure freezing of protein crystals in their mother liquor

    International Nuclear Information System (INIS)

    Burkhardt, Anja; Warmer, Martin; Panneerselvam, Saravanan; Wagner, Armin; Zouni, Athina; Glöckner, Carina; Reimer, Rudolph; Hohenberg, Heinrich; Meents, Alke

    2012-01-01

    Protein crystals were vitrified using high-pressure freezing in their mother liquor at 210 MPa and 77 K without cryoprotectants or oil coating. The method was successfully applied to photosystem II, which is representative of a membrane protein with a large unit cell and weak crystal contacts. High-pressure freezing (HPF) is a method which allows sample vitrification without cryoprotectants. In the present work, protein crystals were cooled to cryogenic temperatures at a pressure of 210 MPa. In contrast to other HPF methods published to date in the field of cryocrystallography, this protocol involves rapid sample cooling using a standard HPF device. The fast cooling rates allow HPF of protein crystals directly in their mother liquor without the need for cryoprotectants or external reagents. HPF was first attempted with hen egg-white lysozyme and cubic insulin crystals, yielding good to excellent diffraction quality. Non-cryoprotected crystals of the membrane protein photosystem II have been successfully cryocooled for the first time. This indicates that the presented HPF method is well suited to the vitrification of challenging systems with large unit cells and weak crystal contacts

  4. Postprandial lipemia detects the effect of soy protein on cardiovascular disease risk compared with the fasting lipid profile.

    Science.gov (United States)

    Santo, Antonio S; Santo, Ariana M; Browne, Richard W; Burton, Harold; Leddy, John J; Horvath, Steven M; Horvath, Peter J

    2010-12-01

    Studies examining the effect of soy protein on cardiovascular disease (CVD) risk factors have not taken advantage of the postprandial state as an adjunct to the fasting lipid profile. The American Heart Association has acknowledged the efficacy of soy protein in reducing CVD risk factors to be limited. We hypothesized that the postprandial state would be more sensitive to any favorable changes associated with consuming soy protein compared with the fasting lipid profile. Furthermore, the presence of isoflavones in soy would enhance this effect. Thirty sedentary males aged 18-30 years were randomly assigned to milk protein (Milk), isoflavone-poor soy (Soy-), or isoflavone-rich soy (Soy+). Usual diets were supplemented with 25 g/day of protein for 28 days. Serum samples were collected before and after supplementation in a fasted state and postprandially at 30, 60, 120, 240, and 360 min after a high-fat, 1,000 kcal shake. Triacylglycerol (TAG), total cholesterol, non-esterified fatty acids, apolipoproteins B-100 and A-I and glucose concentrations were quantified. Fasting concentrations were not different after any protein supplementation. Postprandial TAG and TAG AUC increased after Soy-consumption supporting the postprandial state as a more sensitive indicator of soy ingestion effects on CVD risk factors compared with the fasting lipid profile. Furthermore, the absence of isoflavones in soy protein may have deleterious consequences on purported cardio-protective effects.

  5. T-2 toxin impairment of enteric reovirus clearance in the mouse associated with suppressed immunoglobulin and IFN-γ responses

    International Nuclear Information System (INIS)

    Li Maoxiang; Cuff, Christopher F.; Pestka, James J.

    2006-01-01

    Trichothecenes are exquisitely toxic to the gastrointestinal (GI) tract and leukocytes and thus are likely to impair gut immunity. The purpose of this research was to test the hypothesis that the Type A trichothecene T-2 toxin interferes with the gut mucosal immune response to enteric reovirus infection. Mice were exposed i.p. first to 1.75 mg/kg bw T-2 and then 2 h later with 3 x 10 7 plaque-forming units of reovirus serotype 1, strain Lang (T1/L). As compared to vehicle-treated control, T-2-treated mice had dramatically elevated intestinal plaque-forming viral titers after 5 days and failed to completely clear the virus from intestine by 10 days. Levels of reovirus λ2 core spike (L2 gene) RNA in feces in T-2-treated mice were significantly higher at 1, 3, 5, and 7 days than controls. T-2 potentiated L2 mRNA expression in a dose-dependent manner with as little as 50 μg/kg of the toxin having a potentiative effect. T-2 exposure transiently suppressed induction of reovirus-specific IgA in feces (6 and 8 days) as well as specific IgA and IgG 2a in serum (5 days). This suppression corresponded to decreased secretion of reovirus-specific IgA and IgG 2a in Peyer's patch (PP) and lamina propria fragment cultures prepared 5 days after infection. T-2 suppressed IFN-γ responses in PP to reovirus at 3 and 7 days as compared to infected controls whereas IL-2 mRNA concentrations were unaffected. PP IL-6 mRNA levels were increased 2-fold 2 h after T-2 treatment, but no differences between infected T-2-exposed and infected vehicle-treated mice were detectable over the next 7 days. Overall, the results suggest that T-2 toxin increased both the extent of GI tract reovirus infection and fecal shedding which corresponded to both suppressed immunoglobulin and IFN-γ responses

  6. Preparation and properties of fast temperature-responsive soy protein/PNIPAAm IPN hydrogels

    Directory of Open Access Journals (Sweden)

    Liu Yong

    2014-01-01

    Full Text Available The interpenetrating polymer network of fast temperature-responsive hydrogels based on soy protein and poly(N-isopropylacrylamide were successfully prepared using the sodium bicarbonate (NaHCO3 solutions as the reaction medium. The structure and properties of the hydrogels were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, differential scanning calorimetry and thermal gravimetric analysis. The swelling and deswelling kinetics were also investigated in detail. The results have shown that the proposed hydrogels had high porous structure, good miscibility and thermal stability, and fast temperature responsivity. The presence of NaHCO3 had little effect on the volume phase transition temperature (VPTT of the hydrogels, and the VPTTs were at about 32°C. Compared with the traditional hydrogels, the proposed hydrogels had much faster swelling and deswelling rate. The swelling mechanism of the hydrogels was the non-Fickian diffusion. This fast temperature-responsive hydrogels may have potential applications in the field of biomedical materials.

  7. Fast hydrogen exchange affects 15N relaxation measurements in intrinsically disordered proteins

    International Nuclear Information System (INIS)

    Kim, Seho; Wu, Kuen-Phon; Baum, Jean

    2013-01-01

    Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, 1 H– 15 N HSQC, is used to measure the 15 N transverse relaxation rate (R 2 ), the measured R 2 rate is convoluted with the HX rate (k HX ) and has higher apparent R 2 values. Since the 15 N R 2 measurement is important for analyzing protein backbone dynamics, the HX effect on the R 2 measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing 15 N R 2 CPMG experiments on α-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R 2 CPMG can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D 2 O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R 2 CPMG values be obtained by methods described herein.

  8. Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Rasia, Rodolfo M. [Jean-Pierre Ebel CNRS/CEA/UJF, Institut de Biologie Structurale (France); Lescop, Ewen [CNRS, Institut de Chimie des Substances Naturelles (France); Palatnik, Javier F. [Universidad Nacional de Rosario, Instituto de Biologia Molecular y Celular de Rosario, Facultad de Ciencias Bioquimicas y Farmaceuticas (Argentina); Boisbouvier, Jerome, E-mail: jerome.boisbouvier@ibs.fr; Brutscher, Bernhard, E-mail: Bernhard.brutscher@ibs.fr [Jean-Pierre Ebel CNRS/CEA/UJF, Institut de Biologie Structurale (France)

    2011-11-15

    It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less than 24 h on a single aligned protein sample, greatly improves convergence of the Rosetta-NMR protocol, allowing for overnight fold calculation of small proteins. We demonstrate the performance of our fast fold calculation approach for ubiquitin as a test case, and for two RNA-binding domains of the plant protein HYL1. Structure calculations based on simulated RDC data highlight the importance of an accurate and precise set of several complementary RDCs as additional input restraints for high-quality de novo structure determination.

  9. Direct infusion-SIM as fast and robust method for absolute protein quantification in complex samples

    Directory of Open Access Journals (Sweden)

    Christina Looße

    2015-06-01

    Full Text Available Relative and absolute quantification of proteins in biological and clinical samples are common approaches in proteomics. Until now, targeted protein quantification is mainly performed using a combination of HPLC-based peptide separation and selected reaction monitoring on triple quadrupole mass spectrometers. Here, we show for the first time the potential of absolute quantification using a direct infusion strategy combined with single ion monitoring (SIM on a Q Exactive mass spectrometer. By using complex membrane fractions of Escherichia coli, we absolutely quantified the recombinant expressed heterologous human cytochrome P450 monooxygenase 3A4 (CYP3A4 comparing direct infusion-SIM with conventional HPLC-SIM. Direct-infusion SIM revealed only 14.7% (±4.1 (s.e.m. deviation on average, compared to HPLC-SIM and a decreased processing and analysis time of 4.5 min (that could be further decreased to 30 s for a single sample in contrast to 65 min by the LC–MS method. Summarized, our simplified workflow using direct infusion-SIM provides a fast and robust method for quantification of proteins in complex protein mixtures.

  10. Proteolytic Digestion and TiO2 Phosphopeptide Enrichment Microreactor for Fast MS Identification of Proteins

    Science.gov (United States)

    Deng, Jingren; Lazar, Iulia M.

    2016-04-01

    The characterization of phosphorylation state(s) of a protein is best accomplished by using isolated or enriched phosphoprotein samples or their corresponding phosphopeptides. The process is typically time-consuming as, often, a combination of analytical approaches must be used. To facilitate throughput in the study of phosphoproteins, a microreactor that enables a novel strategy for performing fast proteolytic digestion and selective phosphopeptide enrichment was developed. The microreactor was fabricated using 100 μm i.d. fused-silica capillaries packed with 1-2 mm beds of C18 and/or TiO2 particles. Proteolytic digestion-only, phosphopeptide enrichment-only, and sequential proteolytic digestion/phosphopeptide enrichment microreactors were developed and tested with standard protein mixtures. The protein samples were adsorbed on the C18 particles, quickly digested with a proteolytic enzyme infused over the adsorbed proteins, and further eluted onto the TiO2 microreactor for enrichment in phosphopeptides. A number of parameters were optimized to speed up the digestion and enrichments processes, including microreactor dimensions, sample concentrations, digestion time, flow rates, buffer compositions, and pH. The effective time for the steps of proteolytic digestion and enrichment was less than 5 min. For simple samples, such as standard protein mixtures, this approach provided equivalent or better results than conventional bench-top methods, in terms of both enzymatic digestion and selectivity. Analysis times and reagent costs were reduced ~10- to 15-fold. Preliminary analysis of cell extracts and recombinant proteins indicated the feasibility of integration of these microreactors in more advanced workflows amenable for handling real-world biological samples.

  11. FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

    Science.gov (United States)

    Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

    2016-07-01

    Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. chengji@missouri.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

    Directory of Open Access Journals (Sweden)

    Oliver C Redfern

    2007-11-01

    Full Text Available We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure-based method (using graph theory to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these

  13. (3,2)D GFT-NMR experiments for fast data collection from proteins

    International Nuclear Information System (INIS)

    Xia Youlin; Zhu Guang; Veeraraghavan, Sudha; Gao Xiaolian

    2004-01-01

    High throughput structure determination of proteins will contribute to the success of proteomics investigations. The G-Matrix Fourier Transformation NMR (GFT-NMR) method significantly shortens experimental time by reducing the number of the dimensions of data acquisition for isotopically labeled proteins (Kim, S. and Szyperski, T. (2003) J. Am. Chem. Soc.125, 1385). We demonstrate herein a suite of ten 3D → 2D or (3,2)D GFT-NMR experiments using 13 C/ 15 N-labeled ubiquitin. These experiments were completed within 18 hours, representing a 4- to 18-fold reduction in data acquisition time compared to the corresponding conventional 3D experiments. A subset of the GFT-NMR experiments, (3,2)D HNCO, HNCACB, HN(CO)CACB, and 2D 1 H- 15 N HSQC, which are necessary for backbone assignments, were carried out within 6 hours. To facilitate the analysis of the GFT-NMR spectra, we developed automated procedures for viewing and analyzing the GFT-NMR spectra. Our overall strategy allows (3,2)D GFT-NMR experiments to be readily performed and analyzed. Nevertheless, the increase in spectral overlap and the reduction in signal sensitivity in these fast NMR experiments presently limit their application to relatively small proteins

  14. FreeContact: fast and free software for protein contact prediction from residue co-evolution.

    Science.gov (United States)

    Kaján, László; Hopf, Thomas A; Kalaš, Matúš; Marks, Debora S; Rost, Burkhard

    2014-03-26

    20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct Coupling Analysis (EVfold-mfDCA); the method PSICOV applied a related concept by estimating a sparse inverse covariance matrix. Both methods (EVfold-mfDCA and PSICOV) are publicly available, but both require too much CPU time for interactive applications. On top, EVfold-mfDCA depends on proprietary software. Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability. FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud).

  15. Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae

    Science.gov (United States)

    McIsaac, R. Scott; Silverman, Sanford J.; McClean, Megan N.; Gibney, Patrick A.; Macinskas, Joanna; Hickman, Mark J.; Petti, Allegra A.; Botstein, David

    2011-01-01

    We describe the development and characterization of a system that allows the rapid and specific induction of individual genes in the yeast Saccharomyces cerevisiae without changes in nutrients or temperature. The system is based on the chimeric transcriptional activator Gal4dbd.ER.VP16 (GEV). Upon addition of the hormone β-estradiol, cytoplasmic GEV localizes to the nucleus and binds to promoters containing Gal4p consensus binding sequences to activate transcription. With galactokinase Gal1p and transcriptional activator Gal4p absent, the system is fast-acting, resulting in readily detectable transcription within 5 min after addition of the inducer. β-Estradiol is nearly a gratuitous inducer, as indicated by genome-wide profiling that shows unintended induction (by GEV) of only a few dozen genes. Response to inducer is graded: intermediate concentrations of inducer result in production of intermediate levels of product protein in all cells. We present data illustrating several applications of this system, including a modification of the regulated degron method, which allows rapid and specific degradation of a specific protein upon addition of β-estradiol. These gene induction and protein degradation systems provide important tools for studying the dynamics and functional relationships of genes and their respective regulatory networks. PMID:21965290

  16. Effect of Ramadan fasting on serum heat shock protein 70 and serum lipid profile.

    Science.gov (United States)

    Zare, A; Hajhashemi, M; Hassan, Z M; Zarrin, S; Pourpak, Z; Moin, M; Salarilak, S; Masudi, S; Shahabi, S

    2011-07-01

    Ramadan, the holy month for the Islamic world, is a period every year when food and fluid intake is restricted to the pre-sunrise and post-sunset hours. The aim of this study was to evaluate the effect of Ramadan fasting on the serum concentration of heat shock protein 70 (HSP70) and serum lipid profile in healthy men. A total of 32 male volunteers with a mean age of 28.5 (range 23-37) years were selected for the study. Blood samples were obtained one day prior to Ramadan and on the 3rd and 25th days of fasting. Serum HSP70, triglyceride (TG), cholesterol (Chol), low-density lipoprotein (LDL) and high-density lipoprotein (HDL), LDL/HDL and Chol/HDL ratios were investigated. It was observed that the mean concentrations of serum HSP70 and HDL on the 25th day of Ramadan were significantly higher than those recorded one day before Ramadan and on the 3rd day of Ramadan, and the levels on the 3rd day of Ramadan was significantly higher than those recorded one day before Ramadan. Mean concentrations of serum TG, Chol, LDL, and LDL/HDL and Chol/HDL ratios on the 25th day of Ramadan were significantly lower than those recorded one day before Ramadan and on the 3rd day of Ramadan, and the levels found on the 3rd day of Ramadan were also significantly lower than those recorded one day before Ramadan. Ramadan fasting increases serum HSP70 and improves serum lipid profile.

  17. Network single-walled carbon nanotube biosensors for fast and highly sensitive detection of proteins

    International Nuclear Information System (INIS)

    Hu Pingan; Zhang Jia; Wen Zhenzhong; Zhang Can

    2011-01-01

    Detection of proteins is powerfully assayed in the diagnosis of diseases. A strategy for the development of an ultrahigh sensitivity biosensor based on a network single-walled carbon nanotube (SWNT) field-effect transistor (FET) has been demonstrated. Metallic SWNTs (m-SWNTs) in the network nanotube FET were selectively removed or cut via a carefully controlled procedure of electrical break-down (BD), and left non-conducting m-SWNTs which magnified the Schottky barrier (SB) area. This nanotube FET exhibited ultrahigh sensitivity and fast response to biomolecules. The lowest detection limit of 0.5 pM was achieved by exploiting streptavidin (SA) or a biotin/SA pair as the research model, and BD-treated nanotube biosensors had a 2 x 10 4 -fold lower minimum detectable concentration than the device without BD treatment. The response time is in the range of 0.3-3 min.

  18. Fast hydrogen exchange affects {sup 15}N relaxation measurements in intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seho; Wu, Kuen-Phon; Baum, Jean, E-mail: jean.baum@rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology (United States)

    2013-03-15

    Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, {sup 1}H-{sup 15}N HSQC, is used to measure the {sup 15}N transverse relaxation rate (R{sub 2}), the measured R{sub 2} rate is convoluted with the HX rate (k{sub HX}) and has higher apparent R{sub 2} values. Since the {sup 15}N R{sub 2} measurement is important for analyzing protein backbone dynamics, the HX effect on the R{sub 2} measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing {sup 15}N R{sub 2}{sup CPMG} experiments on {alpha}-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R{sub 2}{sup CPMG} can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D{sub 2}O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R{sub 2}{sup CPMG} values be obtained by methods described herein.

  19. Fast automated placement of polar hydrogen atoms in protein-ligand complexes

    Directory of Open Access Journals (Sweden)

    Lippert Tobias

    2009-08-01

    Full Text Available Abstract Background Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

  20. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.

    Science.gov (United States)

    Meinicke, Peter

    2009-09-02

    Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time. For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.

  1. Analysis of Low Frequency Protein Truncating Stop-Codon Variants and Fasting Concentration of Growth Hormone.

    Directory of Open Access Journals (Sweden)

    Erik Hallengren

    Full Text Available The genetic background of Growth Hormone (GH secretion is not well understood. Mutations giving rise to a stop codon have a high likelihood of affecting protein function.To analyze likely functional stop codon mutations that are associated with fasting plasma concentration of Growth Hormone.We analyzed stop codon mutations in 5451 individuals in the Malmö Diet and Cancer study by genotyping the Illumina Exome Chip. To enrich for stop codon mutations with likely functional effects on protein function, we focused on those disrupting >80% of the predicted amino acid sequence, which were carried by ≥ 10 individuals. Such mutations were related to GH concentration, measured with a high sensitivity assay (hs-GH and, if nominally significant, to GH related phenotypes, using linear regression analysis.Two stop codon mutations were associated with the fasting concentration of hs-GH. rs121909305 (NP_005370.1:p.R93* [Minor Allele Frequency (MAF = 0.8%] in the Myosin 1A gene (MYO1A was associated with a 0.36 (95%CI, 0.04 to 0.54; p=0.02 increment of the standardized value of the natural logarithm of hs-GH per 1 minor allele and rs35699176 (NP_067040.1:p.Q100* in the Zink Finger protein 77 gene (ZNF77 (MAF = 4.8% was associated with a 0.12 (95%CI, 0.02 to 0.22; p = 0.02 increase of hs-GH. The mutated high hs-GH associated allele of MYO1A was related to lower BMI (β-coefficient, -0.22; p = 0.05, waist (β-coefficient, -0.22; p = 0.04, body fat percentage (β-coefficient, -0.23; p = 0.03 and with higher HDL (β-coefficient, 0.23; p = 0.04. The ZNF77 stop codon was associated with height (β-coefficient, 0.11; p = 0.02 but not with cardiometabolic risk factors.We here suggest that a stop codon of MYO1A, disrupting 91% of the predicted amino acid sequence, is associated with higher hs-GH and GH-related traits suggesting that MYO1A is involved in GH metabolism and possibly body fat distribution. However, our results are preliminary and need replication in

  2. GOSSIP: a method for fast and accurate global alignment of protein structures.

    Science.gov (United States)

    Kifer, I; Nussinov, R; Wolfson, H J

    2011-04-01

    The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

  3. Ultra-fast optical manipulation of single proteins binding to the actin cytoskeleton

    Science.gov (United States)

    Capitanio, Marco; Gardini, Lucia; Pavone, Francesco Saverio

    2014-02-01

    In the last decade, forces and mechanical stresses acting on biological systems are emerging as regulatory factors essential for cell life. Emerging evidences indicate that factors such as applied forces or the rigidity of the extracellular matrix (ECM) determine the shape and function of cells and organisms1. Classically, the regulation of biological systems is described through a series of biochemical signals and enzymatic reactions, which direct the processes and cell fate. However, mechanotransduction, i.e. the conversion of mechanical forces into biochemical and biomolecular signals, is at the basis of many biological processes fundamental for the development and differentiation of cells, for their correct function and for the development of pathologies. We recently developed an in vitro system that allows the investigation of force-dependence of the interaction of proteins binding the actin cytoskeleton, at the single molecule level. Our system displays a delay of only ~10 μs between formation of the molecular bond and application of the force and is capable of detecting interactions as short as 100 μs. Our assay allows direct measurements of load-dependence of lifetimes of single molecular bonds and conformational changes of single proteins and molecular motors. We demonstrate our technique on molecular motors, using myosin II from fast skeletal muscle and on protein-DNA interaction, specifically on Lactose repressor (LacI). The apparatus is stabilized to less than 1 nm with both passive and active stabilization, allowing resolving specific binding regions along the actin filament and DNA molecule. Our technique extends single-molecule force-clamp spectroscopy to molecular complexes that have been inaccessible up to now, opening new perspectives for the investigation of the effects of forces on biological processes.

  4. Protein and lipid metabolism adjustments in silver catfish (Rhamdia quelen during different periods of fasting and refeeding

    Directory of Open Access Journals (Sweden)

    A. Marqueze

    2017-10-01

    Full Text Available Abstract The fish may experience periods of food deprivation or starvation which produce metabolic changes. In this study, adult Rhamdia quelen males were subjected to fasting periods of 1, 7, 14, and 21 days and of refeeding 2, 4, 6, and 12 days. The results demonstrated that liver protein was depleted after 1 day of fasting, but recovered after 6 days of refeeding. After 14 days of fasting, mobilization in the lipids of the muscular tissue took place, and these reserves began to re-establish themselves after 4 days of refeeding. Plasmatic triglycerides increased after 1 day of fasting, and decreased following 2 days of refeeding. The glycerol in the plasma oscillated constantly during the different periods of fasting and refeeding. Changes in the metabolism of both protein and lipids during these periods can be considered as survival strategies used by R. quelen. The difference in the metabolic profile of the tissues, the influence of the period of fasting, and the type of reserves mobilized were all in evidence.

  5. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

    Science.gov (United States)

    Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

    2018-05-14

    Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

  6. Refeeding with a high-protein diet after a 48 h fast causes acute hepatocellular injury in mice.

    Science.gov (United States)

    Oarada, Motoko; Tsuzuki, Tsuyoshi; Nikawa, Takeshi; Kohno, Shohei; Hirasaka, Katsuya; Gonoi, Tohru

    2012-05-01

    Elucidating the effects of refeeding a high-protein diet after fasting on disease development is of interest in relation to excessive protein ingestion and irregular eating habits in developed countries. The objective of the present study was to address the hepatic effects of refeeding a high-protein diet after fasting. Mice were fasted for 48 h and then refed with a test diet containing 3, 15, 35, 40, 45 or 50 % casein. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities and liver immediate-early gene expression levels were sequentially measured for the first 24 h after initiation of refeeding. Refeeding with a 50 % casein diet after 48 h of fasting led to a rapid (within 2-3 h) and abnormal elevation in serum ALT (P = 0·006) and AST (P = 0·001) activities and a marked increase in liver Finkel-Biskis-Jinkins (FBJ) osteosarcoma oncogene (P = 0·007) and nuclear receptor subfamily 4, group A, member 1 (P = 0·002) mRNA levels. In contrast, refeeding of the 3, 15 or 35 % casein diets produced no substantial increases in serum ALT and AST activities in mice. Refeeding of 40, 45 or 50 % casein increased serum ALT and AST activities in proportion to this dietary casein content. In mice refed the 3, 15 or 35, but not 50 %, casein diets, liver heat shock protein 72 transcript levels greatly increased. We conclude from these data that the consumption of a high-protein diet after fasting causes acute hepatocellular injury in healthy animals, and propose that careful attention should be paid to the use of such diets.

  7. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences

    Directory of Open Access Journals (Sweden)

    Meinicke Peter

    2009-09-01

    Full Text Available Abstract Background Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Description Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time. Conclusion For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.

  8. Reovirus exerts potent oncolytic effects in head and neck cancer cell lines that are independent of signalling in the EGFR pathway

    International Nuclear Information System (INIS)

    Twigger, Katie; Coffey, Matt; Thompson, Brad; Jebar, Adel; Errington, Fiona; Melcher, Alan A; Vile, Richard G; Pandha, Hardev S; Harrington, Kevin J; Roulstone, Victoria; Kyula, Joan; Karapanagiotou, Eleni M; Syrigos, Konstantinos N; Morgan, Richard; White, Christine; Bhide, Shreerang; Nuovo, Gerard

    2012-01-01

    Reovirus exploits aberrant signalling downstream of Ras to mediate tumor-specific oncolysis. Since ~90% squamous cell carcinomas of the head and neck (SCCHN) over-express EGFR and SCCHN cell lines are sensitive to oncolytic reovirus, we conducted a detailed analysis of the effects of reovirus in 15 head and neck cancer cell lines. Both pre- and post-entry events were studied in an attempt to define biomarkers predictive of sensitivity/resistance to reovirus. In particular, we analysed the role of EGFR/Ras signalling in determining virus-mediated cytotoxicity in SCCHN. To test whether EGFR pathway activity was predictive of increased sensitivity to reovirus, correlative analyses between reoviral IC50 by MTT assay and EGFR levels by western blot and FACS were conducted. Inhibition or stimulation of EGFR signalling were analysed for their effect on reoviral oncolysis by MTT assay, and viral growth by TCID50 assay. We next analysed the effects of inhibiting signalling downstream of Ras, by specific inhibitors of p38MAPK, PI3-K or MEK, on reoviral killing examined by MTT assay. The role of PKR in reoviral killing was also determined by blockade of PKR using 2-aminopurine and assaying for cell survival by MTT assay. The apoptotic response of SCCHN to reovirus was examined by western blot analysis of caspase 3 cleavage. Correlative analyses between reoviral sensitivity and EGFR levels revealed no association. Intermediate sub-viral and core particles showed the same infectivity/cytotoxicity as intact reovirus. Therefore, sensitivity was not determined by cell entry. In 4 cell lines, oncolysis and viral growth were both unaffected by inhibition or stimulation of EGFR signalling. Inhibition of signalling downstream of Ras did not abrogate reoviral oncolysis and, in addition, modulation of PKR using 2-aminopurine did not alter reovirus sensitivity in resistant cell lines. Caspase 3 cleavage was not detected in infected cells and oncolysis was observed in pan

  9. Fasting and Systemic Insulin Signaling Regulate Phosphorylation of Brain Proteins That Modulate Cell Morphology and Link to Neurological Disorders*

    Science.gov (United States)

    Li, Min; Quan, Chao; Toth, Rachel; Campbell, David G.; MacKintosh, Carol; Wang, Hong Yu; Chen, Shuai

    2015-01-01

    Diabetes is strongly associated with cognitive decline, but the molecular reasons are unknown. We found that fasting and peripheral insulin promote phosphorylation and dephosphorylation, respectively, of specific residues on brain proteins including cytoskeletal regulators such as slit-robo GTPase-activating protein 3 (srGAP3) and microtubule affinity-regulating protein kinases (MARKs), in which deficiency or dysregulation is linked to neurological disorders. Fasting activates protein kinase A (PKA) but not PKB/Akt signaling in the brain, and PKA can phosphorylate the purified srGAP3. The phosphorylation of srGAP3 and MARKs were increased when PKA signaling was activated in primary neurons. Knockdown of PKA decreased the phosphorylation of srGAP3. Furthermore, WAVE1, a protein kinase A-anchoring protein, formed a complex with srGAP3 and PKA in the brain of fasted mice to facilitate the phosphorylation of srGAP3 by PKA. Although brain cells have insulin receptors, our findings are inconsistent with the down-regulation of phosphorylation of target proteins being mediated by insulin signaling within the brain. Rather, our findings infer that systemic insulin, through a yet unknown mechanism, inhibits PKA or protein kinase(s) with similar specificity and/or activates an unknown phosphatase in the brain. Ser858 of srGAP3 was identified as a key regulatory residue in which phosphorylation by PKA enhanced the GAP activity of srGAP3 toward its substrate, Rac1, in cells, thereby inhibiting the action of this GTPase in cytoskeletal regulation. Our findings reveal novel mechanisms linking peripheral insulin sensitivity with cytoskeletal remodeling in neurons, which may help to explain the association of diabetes with neurological disorders such as Alzheimer disease. PMID:26499801

  10. Fasting and Systemic Insulin Signaling Regulate Phosphorylation of Brain Proteins That Modulate Cell Morphology and Link to Neurological Disorders.

    Science.gov (United States)

    Li, Min; Quan, Chao; Toth, Rachel; Campbell, David G; MacKintosh, Carol; Wang, Hong Yu; Chen, Shuai

    2015-12-11

    Diabetes is strongly associated with cognitive decline, but the molecular reasons are unknown. We found that fasting and peripheral insulin promote phosphorylation and dephosphorylation, respectively, of specific residues on brain proteins including cytoskeletal regulators such as slit-robo GTPase-activating protein 3 (srGAP3) and microtubule affinity-regulating protein kinases (MARKs), in which deficiency or dysregulation is linked to neurological disorders. Fasting activates protein kinase A (PKA) but not PKB/Akt signaling in the brain, and PKA can phosphorylate the purified srGAP3. The phosphorylation of srGAP3 and MARKs were increased when PKA signaling was activated in primary neurons. Knockdown of PKA decreased the phosphorylation of srGAP3. Furthermore, WAVE1, a protein kinase A-anchoring protein, formed a complex with srGAP3 and PKA in the brain of fasted mice to facilitate the phosphorylation of srGAP3 by PKA. Although brain cells have insulin receptors, our findings are inconsistent with the down-regulation of phosphorylation of target proteins being mediated by insulin signaling within the brain. Rather, our findings infer that systemic insulin, through a yet unknown mechanism, inhibits PKA or protein kinase(s) with similar specificity and/or activates an unknown phosphatase in the brain. Ser(858) of srGAP3 was identified as a key regulatory residue in which phosphorylation by PKA enhanced the GAP activity of srGAP3 toward its substrate, Rac1, in cells, thereby inhibiting the action of this GTPase in cytoskeletal regulation. Our findings reveal novel mechanisms linking peripheral insulin sensitivity with cytoskeletal remodeling in neurons, which may help to explain the association of diabetes with neurological disorders such as Alzheimer disease. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Concentration of total protein and degree of acidity (pH of saliva when fasting and after breakfasting

    Directory of Open Access Journals (Sweden)

    Gemella Nur Illahi

    2016-04-01

    Full Text Available Background: While fasting, the mouth does not work to eat and drink so that the salivary glands become less active so saliva production decreased and there was a change in eating timewhich is relation to the mastication process that impact on changes in the degree of acidity (pH Objectives: To determine the concentration of total protein and the degree of acidity (pH of saliva when fasting and after breakfasting. Materials and Methods: The study was observational analytic design with longitudinal (follow up study conducted in the Hj. Halima Dg. Sikati Dental Hospital inKandea in July 2015, the sampling method was purposive sampling. Population was 35 clinical students at the Department of Dental Public Health, Faculty of Dentistry Hasanuddin University with a total sample of 16 students who fit the criteria of the study subjects. To calculate the total protein of saliva concentration using Kyltecautoanalyzerand pH meter to measure the acidity of saliva. Data was analyzed was using SPSS version 17.0 (paired t-test, p <0.05. Results: The mean of total protein (% while fasting by 0135% ± 0.026 and the mean total protein (% after breakfasting at 0.179% ± 0.035, while the average degree of acidity (pH during fasting at 7.26 ± 0:24 and the average degree of acidity (pH after breakfasting at 7.66 ± 0.23 with p-value (0.000. Conclusions: An increase in the total protein concentration and acidity (pH after breakfasting.

  12. A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS).

    Science.gov (United States)

    Løvoll, Marie; Wiik-Nielsen, Jannicke; Grove, Søren; Wiik-Nielsen, Christer R; Kristoffersen, Anja B; Faller, Randi; Poppe, Trygve; Jung, Joonil; Pedamallu, Chandra S; Nederbragt, Alexander J; Meyerson, Matthew; Rimstad, Espen; Tengs, Torstein

    2010-11-10

    Cardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly prior to slaughter. We recently reported the finding and the complete genomic sequence of a novel piscine reovirus (PRV), which is associated with another cardiac disease in Atlantic salmon; heart and skeletal muscle inflammation (HSMI). In the present work we have studied whether PRV or other infectious agents may be involved in the etiology of CMS. Using high throughput sequencing on heart samples from natural outbreaks of CMS and from fish experimentally challenged with material from fish diagnosed with CMS a high number of sequence reads identical to the PRV genome were identified. In addition, a sequence contig from a novel totivirus could also be constructed. Using RT-qPCR, levels of PRV in tissue samples were quantified and the totivirus was detected in all samples tested from CMS fish but not in controls. In situ hybridization supported this pattern indicating a possible association between CMS and the novel piscine totivirus. Although causality for CMS in Atlantic salmon could not be proven for either of the two viruses, our results are compatible with a hypothesis where, in the experimental challenge studied, PRV behaves as an opportunist whereas the totivirus might be more directly linked with the development of CMS.

  13. In vitro antiviral activity of chestnut and quebracho woods extracts against avian reovirus and metapneumovirus.

    Science.gov (United States)

    Lupini, C; Cecchinato, M; Scagliarini, A; Graziani, R; Catelli, E

    2009-12-01

    Field evidences have suggested that a natural extract, containing tannins, could be effective against poultry enteric viral infections. Moreover previous studies have shown that vegetable tannins can have antiviral activity against human viruses. Based on this knowledge three different Chestnut (Castanea spp.) wood extracts and one Quebracho (Schinopsis spp.) wood extract, all containing tannins and currently used in the animal feed industry, were tested for in vitro antiviral activity against avian reovirus (ARV) and avian metapneumovirus (AMPV). The MTT assay was used to evaluate the 50% cytotoxic compounds concentration (CC(50)) on Vero cells. The antiviral properties were tested before and after the adsorption of the viruses to Vero cells. Antiviral activities were expressed as IC(50) (concentration required to inhibit 50% of viral cytopathic effect). CC(50)s of tested compounds were > 200 microg/ml. All compounds had an extracellular antiviral effect against both ARV and AMPV with IC(50) values ranging from 25 to 66 microg/ml. Quebracho extract had also evident intracellular anti-ARV activity (IC(50) 24 microg/ml). These preliminary results suggest that the examined vegetable extracts might be good candidates in the control of some avian virus infections. Nevertheless further in vivo experiments are required to confirm these findings.

  14. A randomized trial of protein supplementation compared with extra fast food on the effects of resistance training to increase metabolism.

    Science.gov (United States)

    Hambre, David; Vergara, Marta; Lood, Yvonne; Bachrach-Lindström, Margareta; Lindström, Torbjörn; Nystrom, Fredrik H

    2012-10-01

    To prospectively evaluate the effects of resistance training combined with increased energy intake or protein-supplementation on lean body-mass, resting metabolic-rate (RMR) and cardiovascular risk factors. Twenty-four healthy males (aged 19-32 years) performed resistance exercise for 12 weeks aiming for at least 1 hour training-sessions 3 times a week. The participants were randomized to consume extra protein (33 g whey protein/day) or a meal of fast-food/day (1350 kcal, 41 g protein). Body-composition was measured with Dual-Energy X-ray Absorptiometry (DEXA) and RMR by indirect calorimetry. Fasting blood samples were drawn before and after the 3-month training period and after 12 months. The body weight increased from 75.1 ± 6.9 kg to 78.7 ± 7.2 kg (p < 0.0001), without differences between the groups. RMR increased from 1787 ± 143 kcal/24 h to 1954 ± 187 kcal/24 h (p < 0.0001, N = 24), which was more than expected from the increase in lean body-mass (increase from 59.7 ± 4.3 kg to 61.8 ± 4.1 kg p = 0.004). Fasting serum-insulin levels increased in the fast-food group compared with the extra-protein group (p = 0.03). ApoB increased from 0.691 ± 0.14 g/L to 0.768 ± 0.17 g/L, p = 0.004, in the fast-food group only. Long-term follow up after 12 months showed that RMR, body weight, total fat and lean body-masses did not differ from baseline (n = 19). Resistance training for 12 weeks increased RMR and lean body-mass similarly when based on either an increased energy-intake or protein supplement. However, the increase in RMR was higher than expected from the increase in lean body-mass. Thus resistance training could potentially decrease the risk of obesity by induction of increased RMR.

  15. Fast computational methods for predicting protein structure from primary amino acid sequence

    Science.gov (United States)

    Agarwal, Pratul Kumar [Knoxville, TN

    2011-07-19

    The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

  16. Fast electron transfer through a single molecule natively structured redox protein

    DEFF Research Database (Denmark)

    Della Pia, Eduardo Antonio; Chi, Qijin; Macdonald, J. Emyr

    2012-01-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conduc...

  17. Protein biomarker discovery and fast monitoring for the identification and detection of Anisakids by parallel reaction monitoring (PRM) mass spectrometry.

    Science.gov (United States)

    Carrera, Mónica; Gallardo, José M; Pascual, Santiago; González, Ángel F; Medina, Isabel

    2016-06-16

    Anisakids are fish-borne parasites that are responsible for a large number of human infections and allergic reactions around the world. World health organizations and food safety authorities aim to control and prevent this emerging health problem. In the present work, a new method for the fast monitoring of these parasites is described. The strategy is divided in three steps: (i) purification of thermostable proteins from fish-borne parasites (Anisakids), (ii) in-solution HIFU trypsin digestion and (iii) monitoring of several peptide markers by parallel reaction monitoring (PRM) mass spectrometry. This methodology allows the fast detection of Anisakids in Biomarker Discovery and the Fast Monitoring for the identification and detection of Anisakids in fishery products. The strategy is based on the purification of thermostable proteins, the use of accelerated in-solution trypsin digestions under an ultrasonic field provided by High-Intensity Focused Ultrasound (HIFU) and the monitoring of several peptide biomarkers by Parallel Reaction Monitoring (PRM) Mass Spectrometry in a linear ion trap mass spectrometer. The workflow allows the unequivocal detection of Anisakids, in <2h. The present strategy constitutes the fastest method for Anisakids detection, whose application in the food quality control area, could provide to the authorities an effective and rapid method to guarantee the safety to the consumers. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Katja E. Menger

    2015-06-01

    Full Text Available Altering the redox state of cysteine residues on protein surfaces is an important response to environmental challenges. Although aging and fasting alter many redox processes, the role of cysteine residues is uncertain. To address this, we used a redox proteomic technique, oxidative isotope-coded affinity tags (OxICAT, to assess cysteine-residue redox changes in Drosophila melanogaster during aging and fasting. This approach enabled us to simultaneously identify and quantify the redox state of several hundred cysteine residues in vivo. Cysteine residues within young flies had a bimodal distribution with peaks at ∼10% and ∼85% reversibly oxidized. Surprisingly, these cysteine residues did not become more oxidized with age. In contrast, 24 hr of fasting dramatically oxidized cysteine residues that were reduced under fed conditions while also reducing cysteine residues that were initially oxidized. We conclude that fasting, but not aging, dramatically alters cysteine-residue redox status in D. melanogaster.

  19. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  20. Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages

    International Nuclear Information System (INIS)

    Liu, Hung J.; Lee, Long H.; Hsu, Hsiao W.; Kuo, Liam C.; Liao, Ming H.

    2003-01-01

    Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The σC-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the σC-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the σC-encoding gene and σC protein was higher than for the other S-class genes and other family of viruses. With the exception of the σC-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses

  1. Effects of Supplementation of Branched-Chain Amino Acids to Reduced-Protein Diet on Skeletal Muscle Protein Synthesis and Degradation in the Fed and Fasted States in a Piglet Model

    Directory of Open Access Journals (Sweden)

    Liufeng Zheng

    2016-12-01

    Full Text Available Supplementation of branched-chain amino acids (BCAA has been demonstrated to promote skeletal muscle mass gain, but the mechanisms underlying this observation are still unknown. Since the regulation of muscle mass depends on a dynamic equilibrium (fasted losses–fed gains in protein turnover, the aim of this study was to investigate the effects of BCAA supplementation on muscle protein synthesis and degradation in fed/fasted states and the related mechanisms. Fourteen 26- (Experiment 1 and 28-day-old (Experiment 2 piglets were fed reduced-protein diets without or with supplemental BCAA. After a four-week acclimation period, skeletal muscle mass and components of anabolic and catabolic signaling in muscle samples after overnight fasting were determined in Experiment 1. Pigs in Experiment 2 were implanted with carotid arterial, jugular venous, femoral arterial and venous catheters, and fed once hourly along with the intravenous infusion of NaH13CO3 for 2 h, followed by a 6-h infusion of [1-13C]leucine. Muscle leucine kinetics were measured using arteriovenous difference technique. The mass of most muscles was increased by BCAA supplementation. During feeding, BCAA supplementation increased leucine uptake, protein synthesis, protein degradation and net transamination. The greater increase in protein synthesis than in protein degradation resulted in elevated protein deposition. Protein synthesis was strongly and positively correlated with the intramuscular net production of α-ketoisocaproate (KIC and protein degradation. Moreover, BCAA supplementation enhanced the fasted-state phosphorylation of protein translation initiation factors and inhibited the protein-degradation signaling of ubiquitin-proteasome and autophagy-lysosome systems. In conclusion, supplementation of BCAA to reduced-protein diet increases fed-state protein synthesis and inhibits fasted-state protein degradation, both of which could contribute to the elevation of skeletal muscle

  2. Intermittent fasting does not affect whole-body glucose, lipid, or protein metabolism

    NARCIS (Netherlands)

    Soeters, Maarten R.; Lammers, Nicolette M.; Dubbelhuis, Peter F.; Ackermans, Mariëtte T.; Jonkers-Schuitema, Cora F.; Fliers, Eric; Sauerwein, Hans P.; Aerts, Johannes M.; Serlie, Mireille J.

    2009-01-01

    Background: Intermittent fasting (IF) was shown to increase whole-body insulin sensitivity, but it is uncertain whether IF selectively influences intermediary metabolism. Such selectivity might be advantageous when adapting to periods of food abundance and food shortage. Objective: The objective was

  3. Anabolic effects of leucine-rich whey protein, carbohydrate, and soy protein with and without β-hydroxy-β-methylbutyrate (HMB) during fasting-induced catabolism: A human randomized crossover trial.

    Science.gov (United States)

    Rittig, Nikolaj; Bach, Ermina; Thomsen, Henrik H; Møller, Andreas B; Hansen, Jakob; Johannsen, Mogens; Jensen, Erik; Serena, Anja; Jørgensen, Jens O; Richelsen, Bjørn; Jessen, Niels; Møller, Niels

    2017-06-01

    Protein-rich beverages are widely used clinically to preserve muscle protein and improve physical performance. Beverages with high contents of leucine or its keto-metabolite β-hydroxy-β-methylbutyrate (HMB) are especially anabolic in muscle, but it is uncertain whether this also applies to catabolic conditions such as fasting and whether common or separate intracellular signaling cascades are involved. To compare a specific leucine-rich whey protein beverage (LWH) with isocaloric carbohydrate- (CHO), soy protein (SOY), and soy protein +3 g HMB (HMB) during fasting-induced catabolic conditions. Eight healthy lean male subjects underwent four interventions (LWH, CHO, SOY, and HMB) using a randomized crossover design. Each trial included a 36 h fast and consisted of a 3 h basal fasting period and a 4 h 'sipping' period. Forearm net balances of phenylalanine (NB phe , measure of net protein loss) improved for all groups (p HMB compared with SOY (p HMB have superior anabolic effects on muscle protein kinetics after 36 h of fasting, and LWH distinctly activates the mTOR pathway. These novel findings suggest that leucine-rich whey protein and/or HMB are specifically beneficial during fasting-induced catabolic conditions. Copyright © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  4. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

    Science.gov (United States)

    Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

    2016-02-01

    The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Fast protein tertiary structure retrieval based on global surface shape similarity.

    Science.gov (United States)

    Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

    2008-09-01

    Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

  6. Fast axonal transport of 3H-leucin-labelled proteins in the unhurt and isolated optical nerve of rats

    International Nuclear Information System (INIS)

    Wagner, H.E.

    1981-01-01

    The distribution of radioactivity of amino acid molecules incorporated in protein after injection of 3 H-Leucin into the right bulb was investigated and determined along optical nerve after 1, 2, and 4 h. A slightly increased radioactivity at the point of entrance of the optical nerves into the optical duct was found. A slightly reduced axon diameter was discussed as a possible cause. The radioactivity brought into the optical nerve via the vascular system was determined by measuring the contralateral optical nerve. In relation to the axonally transported activity, it was low. The speed of the fast axonal transport is 168 mm/d. If the processes ruling the amino acids in the perikaryon are taken into consideration, the transport speed is 240 mm/d. The application of the protein synthesis prohibitor, Cycloheximide, 5 minutes after the injection of Leucinin completely prevented the appearance of axonally transported labelled proteins. When cycloheximide was administered 2 h after Leucin, a significantly loner radioactivity than in the nerve could be determined after another 2 h; i.e. the incorporation of Leucin was not completed yet after 2 h. The profile of active compounds was the same as in the control group. In other experiments, the axonal transport of labelled proteins in isolated optical nerve fibres was tested. If the separation was carried out 2 h after the injection of Leucin an extreme reduction in activity could be determined after 1 or 2 h. The continued distribution of activity after cycloheximide treatment and removal of perikarya in comparison with the control indicate the continuation of the transport, also after separation of the axon from the perikaryon. This means that, during the time of the experiment, the mechanism of the fast axonal transport functions independently of the perikaryon. (orig./MG) [de

  7. GLUCOSE AND TOTAL PROTEIN LEVEL IN LABORATORY RATS UNDER CONDITIONS OF SHORT-TERM FASTING

    Directory of Open Access Journals (Sweden)

    Damir Suljević

    2013-09-01

    Full Text Available Glucose level (UV enzymatic method and total protein level (Biuret method were measured in the blood samples of the rats exposed to short-term starvation. We found a statistically significant increase in the glucose level in experimental animals during starvation, which is also evident in males and females in the experimental group (p <0.05, while decrease in the total protein level was not statistically significant. During starvation, more significant weight loss was observed in females compared to males.Key words: glucose, total protein, serum, Rattus

  8. A method for fast energy estimation and visualization of protein-ligand interaction

    Science.gov (United States)

    Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

    1987-10-01

    A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

  9. Fast and Selective Modification of Thiol Proteins/Peptides by N-(Phenylseleno)phthalimide

    Science.gov (United States)

    Wang, Zhengfang; Zhang, Yun; Zhang, Hao; Harrington, Peter B.; Chen, Hao

    2012-03-01

    We previously reported that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used to selectively derivatize thiols for mass spectrometric analysis, and the introduced selenium tags are useful as they could survive or removed with collision-induced dissociation (CID). Described herein is the further study of the reactivity of various protein/peptide thiols toward NPSP and its application to derivatize thiol peptides in protein digests. With a modified protocol (i.e., dissolving NPSP in acetonitrile instead of aqueous solvent), we found that quantitative conversion of thiols can be obtained in seconds, using NPSP in a slight excess amount (NPSP:thiol of 1.1-2:1). Further investigation shows that the thiol reactivity toward NPSP reflects its chemical environment and accessibility in proteins/peptides. For instance, adjacent basic amino acid residues increase the thiol reactivity, probably because they could stabilize the thiolate form to facilitate the nucleophilic attack of thiol on NPSP. In the case of creatine phosphokinase, the native protein predominately has one thiol reacted with NPSP while all of four thiol groups of the denatured protein can be derivatized, in accordance with the corresponding protein conformation. In addition, thiol peptides in protein/peptide enzymatic digests can be quickly and effectively tagged by NPSP following tri- n-butylphosphine (TBP) reduction. Notably, all three thiols of the peptide QCCASVCSL in the insulin peptic digest can be modified simultaneously by NPSP. These results suggest a novel and selective method for protecting thiols in the bottom-up approach for protein structure analysis.

  10. Analysis of Protein Content in Rices Using Fast Neutron Reaction 14N(n,2 n) N13

    International Nuclear Information System (INIS)

    Sri-Sulamdari; Elin-Nuraini; Chotimah

    2000-01-01

    Protein content in rices such as IR 33 , Cisadane, and Rojolele has beendetermined using fast neutron activation analysis (FNAA). The existence ofprotein is characterized using E γ = 0.511 MeV from nuclear reaction 14 N (n,2 n) N 13 . Two methods of FNAA for quantification were used. Inabsolute method, the protein content was determined by measuring the neutronflux using Al foil, and in comparative additive method it was determined bycomparing to the known N standard which was additive to the samples. Theexperimental results show that the protein content in those rices ranges from(6.33 ± 0.05) % to (6.9 ± 0.11) % in weight. From the reference, thegrained rices contained 6.8 % in weight of protein. The value of the proteinstandard from the reference was in range of the experimental result. Howeverthere were still differences due to nuclear data stability of flux neutron,flux sample composition and the utilization of detector. (author)

  11. Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water.

    Directory of Open Access Journals (Sweden)

    Ignacio Gutiérrez-Del-Río

    Full Text Available Drinking water can be exposed to different biological contaminants from the source, through the pipelines, until reaching the final consumer or industry. Some of these are pathogenic bacteria and viruses which may cause important gastrointestinal or systemic diseases. The microbiological quality of drinking water relies mainly in monitoring three indicator bacteria of faecal origin, Escherichia coli, Enterococcus faecalis and Clostridium perfringens, which serve as early sentinels of potential health hazards for the population. Here we describe the analysis of three chimeric fluorescent protein bullets as biosensor candidates for fast detection of E. coli in drinking water. Two of the chimeric proteins (based on GFP-hadrurin and GFP-pb5 chimera proteins failed with respect to specificity and/or sensitivity, but the GFP-colS4 chimera protein was able to carry out specific detection of E. coli in drinking water samples in a procedure encompassing about 8 min for final result and this biosensor protein was able to detect in a linear way between 20 and 103 CFU of this bacterium. Below 20 CFU, the system cannot differentiate presence or absence of the target bacterium. The fluorescence in this biosensor system is provided by the GFP subunit of the chimeric protein, which, in the case of the better performing sensor bullet, GFP-colS4 chimera, is covalently bound to a flexible peptide bridge and to a bacteriocin binding specifically to E. coli cells. Once bound to the target bacteria, the excitation step with 395 nm LED light causes emission of fluorescence from the GFP domain, which is amplified in a photomultiplier tube, and finally this signal is converted into an output voltage which can be associated with a CFU value and these data distributed along mobile phone networks, for example. This method, and the portable fluorimeter which has been developed for it, may contribute to reduce the analysis time for detecting E. coli presence in drinking

  12. High-throughput fractionation of human plasma for fast enrichment of low- and high-abundance proteins.

    Science.gov (United States)

    Breen, Lucas; Cao, Lulu; Eom, Kirsten; Srajer Gajdosik, Martina; Camara, Lila; Giacometti, Jasminka; Dupuy, Damian E; Josic, Djuro

    2012-05-01

    Fast, cost-effective and reproducible isolation of IgM from plasma is invaluable to the study of IgM and subsequent understanding of the human immune system. Additionally, vast amounts of information regarding human physiology and disease can be derived from analysis of the low abundance proteome of the plasma. In this study, methods were optimized for both the high-throughput isolation of IgM from human plasma, and the high-throughput isolation and fractionation of low abundance plasma proteins. To optimize the chromatographic isolation of IgM from human plasma, many variables were examined including chromatography resin, mobile phases, and order of chromatographic separations. Purification of IgM was achieved most successfully through isolation of immunoglobulin from human plasma using Protein A chromatography with a specific resin followed by subsequent fractionation using QA strong anion exchange chromatography. Through these optimization experiments, an additional method was established to prepare plasma for analysis of low abundance proteins. This method involved chromatographic depletion of high-abundance plasma proteins and reduction of plasma proteome complexity through further chromatographic fractionation. Purification of IgM was achieved with high purity as confirmed by SDS-PAGE and IgM-specific immunoblot. Isolation and fractionation of low abundance protein was also performed successfully, as confirmed by SDS-PAGE and mass spectrometry analysis followed by label-free quantitative spectral analysis. The level of purity of the isolated IgM allows for further IgM-specific analysis of plasma samples. The developed fractionation scheme can be used for high throughput screening of human plasma in order to identify low and high abundance proteins as potential prognostic and diagnostic disease biomarkers.

  13. Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water.

    Science.gov (United States)

    Gutiérrez-Del-Río, Ignacio; Marín, Laura; Fernández, Javier; Álvarez San Millán, María; Ferrero, Francisco Javier; Valledor, Marta; Campo, Juan Carlos; Cobián, Natalia; Méndez, Ignacio; Lombó, Felipe

    2018-01-01

    Drinking water can be exposed to different biological contaminants from the source, through the pipelines, until reaching the final consumer or industry. Some of these are pathogenic bacteria and viruses which may cause important gastrointestinal or systemic diseases. The microbiological quality of drinking water relies mainly in monitoring three indicator bacteria of faecal origin, Escherichia coli, Enterococcus faecalis and Clostridium perfringens, which serve as early sentinels of potential health hazards for the population. Here we describe the analysis of three chimeric fluorescent protein bullets as biosensor candidates for fast detection of E. coli in drinking water. Two of the chimeric proteins (based on GFP-hadrurin and GFP-pb5 chimera proteins) failed with respect to specificity and/or sensitivity, but the GFP-colS4 chimera protein was able to carry out specific detection of E. coli in drinking water samples in a procedure encompassing about 8 min for final result and this biosensor protein was able to detect in a linear way between 20 and 103 CFU of this bacterium. Below 20 CFU, the system cannot differentiate presence or absence of the target bacterium. The fluorescence in this biosensor system is provided by the GFP subunit of the chimeric protein, which, in the case of the better performing sensor bullet, GFP-colS4 chimera, is covalently bound to a flexible peptide bridge and to a bacteriocin binding specifically to E. coli cells. Once bound to the target bacteria, the excitation step with 395 nm LED light causes emission of fluorescence from the GFP domain, which is amplified in a photomultiplier tube, and finally this signal is converted into an output voltage which can be associated with a CFU value and these data distributed along mobile phone networks, for example. This method, and the portable fluorimeter which has been developed for it, may contribute to reduce the analysis time for detecting E. coli presence in drinking water.

  14. Protein metabolism in slow- and fast-twitch skeletal muscle during turpentine-induced inflammation.

    Science.gov (United States)

    Muthny, Tomas; Kovarik, Miroslav; Sispera, Ludek; Tilser, Ivan; Holecek, Milan

    2008-02-01

    The aim of our study was to evaluate the differences in protein and amino acid metabolism after subcutaneous turpentine administration in the soleus muscle (SOL), predominantly composed of red fibres, and the extensor digitorum longus muscle (EDL) composed of white fibres. Young rats (40-60 g) were injected subcutaneously with 0.2 ml of turpentine oil/100 g body weight (inflammation) or with the same volume of saline solution (control). Twenty-four hours later SOL and EDL were dissected and incubated in modified Krebs-Heinseleit buffer to estimate total and myofibrillar proteolysis, chymotrypsin-like activity of proteasome (CHTLA), leucine oxidation, protein synthesis and amino acid release into the medium. The data obtained demonstrate that in intact rats, all parameters measured except protein synthesis are significantly higher in SOL than in EDL. In turpentine treated animals, CHTLA increased and protein synthesis decreased significantly more in EDL. Release of leucine was inhibited significantly more in SOL. We conclude that turpentine-induced inflammation affects more CHTLA, protein synthesis and leucine release in EDL compared to SOL.

  15. A new method for protein estimation in large seeds using fast-neutron-activation analysis

    International Nuclear Information System (INIS)

    Gupta, U.C.; Misra, S.C.; Rao, U.S.

    1974-01-01

    A new method was developed for the determination of protein content of large seeds, using powders of different N content. The powders were obtained by mixing glucose with amino acids in different proportions and were irradiated with and without the seeds in the MeV neutron flux. The irradiated samples were counted under identical conditions and their activities were used to calculate the protein content of the seeds. The results were compared with those obtained by conventional activation technique and were found to be in good agreement. This new method has the advantage of being non-destructive. (author)

  16. Intermittent fasting reduces body fat but exacerbates hepatic insulin resistance in young rats regardless of high protein and fat diets.

    Science.gov (United States)

    Park, Sunmin; Yoo, Kyung Min; Hyun, Joo Suk; Kang, Suna

    2017-02-01

    Intermittent fasting (IMF) is a relatively new dietary approach to weight management, although the efficacy and adverse effects have not been full elucidated and the optimal diets for IMF are unknown. We tested the hypothesis that a one-meal-per-day intermittent fasting with high fat (HF) or protein (HP) diets can modify energy, lipid, and glucose metabolism in normal young male Sprague-Dawley rats with diet-induced obesity or overweight. Male rats aged 5 weeks received either HF (40% fat) or HP (26% protein) diets ad libitum (AL) or for 3 h at the beginning of the dark cycle (IMF) for 5 weeks. Epidydimal fat pads and fat deposits in the leg and abdomen were lower with HP and IMF. Energy expenditure at the beginning of the dark cycle, especially from fat oxidation, was higher with IMF than AL, possibly due to greater activity levels. Brown fat content was higher with IMF. Serum ghrelin levels were higher in HP-IMF than other groups, and accordingly, cumulative food intake was also higher in HP-IMF than HF-IMF. HF-IMF exhibited higher area under the curve (AUC) of serum glucose at the first part (0-40 min) during oral glucose tolerance test, whereas AUC of serum insulin levels in both parts were higher in IMF and HF. During intraperitoneal insulin tolerance test, serum glucose levels were higher with IMF than AL. Consistently, hepatic insulin signaling (GLUT2, pAkt) was attenuated and PEPCK expression was higher with IMF and HF than other groups, and HOMA-IR revealed significantly impaired attenuated insulin sensitivity in the IMF groups. However, surprisingly, hepatic and skeletal muscle glycogen storage was higher in IMF groups than AL. The higher glycogen storage in the IMF groups was associated with the lower expression of glycogen phosphorylase than the AL groups. In conclusion, IMF especially with HF increased insulin resistance, possibly by attenuating hepatic insulin signaling, and lowered glycogen phosphorylase expression despite decreased fat mass in young

  17. Fast and efficient detection of tuberculosis antigens using liposome encapsulated secretory proteins of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Dileep Tiwari

    2017-04-01

    Conclusion: Our study demonstrated that the newly developed liposome tuberculosis antigen card test detected antigens in our study population with approximately 97.48% sensitivity and 95.79% specificity. This is the first study to report the liposomal encapsulation of culture filtrate proteins from M. tuberculosis for diagnostic application.

  18. FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

    Science.gov (United States)

    Huang, Yi-Fei; Golding, G Brian

    2015-02-15

    A number of statistical phylogenetic methods have been developed to infer conserved functional sites or regions in proteins. Many methods, e.g. Rate4Site, apply the standard phylogenetic models to infer site-specific substitution rates and totally ignore the spatial correlation of substitution rates in protein tertiary structures, which may reduce their power to identify conserved functional patches in protein tertiary structures when the sequences used in the analysis are highly similar. The 3D sliding window method has been proposed to infer conserved functional patches in protein tertiary structures, but the window size, which reflects the strength of the spatial correlation, must be predefined and is not inferred from data. We recently developed GP4Rate to solve these problems under the Bayesian framework. Unfortunately, GP4Rate is computationally slow. Here, we present an intuitive web server, FuncPatch, to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site. The functional patches predicted by FuncPatch in the four case studies are supported by experimental evidence, which corroborates the usefulness of FuncPatch. The software FuncPatch is freely available at the web site, http://info.mcmaster.ca/yifei/FuncPatch golding@mcmaster.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

    OpenAIRE

    Soichiro Tsujino; Takashi Tomizaki

    2016-01-01

    Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinn...

  20. Flavodiiron Proteins Promote Fast and Transient O2 Photoreduction in Chlamydomonas.

    Science.gov (United States)

    Chaux, Frédéric; Burlacot, Adrien; Mekhalfi, Malika; Auroy, Pascaline; Blangy, Stéphanie; Richaud, Pierre; Peltier, Gilles

    2017-07-01

    During oxygenic photosynthesis, the reducing power generated by light energy conversion is mainly used to reduce carbon dioxide. In bacteria and archae, flavodiiron (Flv) proteins catalyze O 2 or NO reduction, thus protecting cells against oxidative or nitrosative stress. These proteins are found in cyanobacteria, mosses, and microalgae, but have been lost in angiosperms. Here, we used chlorophyll fluorescence and oxygen exchange measurement using [ 18 O]-labeled O 2 and a membrane inlet mass spectrometer to characterize Chlamydomonas reinhardtii flvB insertion mutants devoid of both FlvB and FlvA proteins. We show that Flv proteins are involved in a photo-dependent electron flow to oxygen, which drives most of the photosynthetic electron flow during the induction of photosynthesis. As a consequence, the chlorophyll fluorescence patterns are strongly affected in flvB mutants during a light transient, showing a lower PSII operating yield and a slower nonphotochemical quenching induction. Photoautotrophic growth of flvB mutants was indistinguishable from the wild type under constant light, but severely impaired under fluctuating light due to PSI photo damage. Remarkably, net photosynthesis of flv mutants was higher than in the wild type during the initial hour of a fluctuating light regime, but this advantage vanished under long-term exposure, and turned into PSI photo damage, thus explaining the marked growth retardation observed in these conditions. We conclude that the C. reinhardtii Flv participates in a Mehler-like reduction of O 2 , which drives a large part of the photosynthetic electron flow during a light transient and is thus critical for growth under fluctuating light regimes. © 2017 American Society of Plant Biologists. All Rights Reserved.

  1. Divergent flow isoelectric focusing: fast and efficient method for protein sample preparation for mass spectrometry

    Czech Academy of Sciences Publication Activity Database

    Mazanec, Karel; Bobálová, Janette; Šlais, Karel

    2009-01-01

    Roč. 393, 6-7 (2009), s. 1769-1778 ISSN 1618-2642 R&D Projects: GA MŠk 1M0570; GA AV ČR IAAX00310701 Institutional research plan: CEZ:AV0Z40310501 Keywords : Isoelectric focusing * proteins * MALDI-TOF/TOF MS Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.480, year: 2009

  2. fLPS: Fast discovery of compositional biases for the protein universe.

    Science.gov (United States)

    Harrison, Paul M

    2017-11-13

    Proteins often contain regions that are compositionally biased (CB), i.e., they are made from a small subset of amino-acid residue types. These CB regions can be functionally important, e.g., the prion-forming and prion-like regions that are rich in asparagine and glutamine residues. Here I report a new program fLPS that can rapidly annotate CB regions. It discovers both single-residue and multiple-residue biases. It works through a process of probability minimization. First, contigs are constructed for each amino-acid type out of sequence windows with a low degree of bias; second, these contigs are searched exhaustively for low-probability subsequences (LPSs); third, such LPSs are iteratively assessed for merger into possible multiple-residue biases. At each of these stages, efficiency measures are taken to avoid or delay probability calculations unless/until they are necessary. On a current desktop workstation, the fLPS algorithm can annotate the biased regions of the yeast proteome (>5700 sequences) in 65 million sequences) in as little as ~1 h, which is >2 times faster than the commonly used program SEG, using default parameters. fLPS discovers both shorter CB regions (of the sort that are often termed 'low-complexity sequence'), and milder biases that may only be detectable over long tracts of sequence. fLPS can readily handle very large protein data sets, such as might come from metagenomics projects. It is useful in searching for proteins with similar CB regions, and for making functional inferences about CB regions for a protein of interest. The fLPS package is available from: http://biology.mcgill.ca/faculty/harrison/flps.html , or https://github.com/pmharrison/flps , or is a supplement to this article.

  3. Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    Science.gov (United States)

    Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan

    2017-01-25

    Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.

  4. A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics.

    Science.gov (United States)

    Burke, Kelly S; Parul, Dzmitry; Reddish, Michael J; Dyer, R Brian

    2013-08-07

    We present a simple, yet flexible microfluidic mixer with a demonstrated mixing time as short as 80 μs that is widely accessible because it is made of commercially available parts. To simplify the study of fast protein dynamics, we have developed an inexpensive continuous-flow microfluidic mixer, requiring no specialized equipment or techniques. The mixer uses three-dimensional, hydrodynamic focusing of a protein sample stream by a surrounding sheath solution to achieve rapid diffusional mixing between the sample and sheath. Mixing initiates the reaction of interest. Reactions can be spatially observed by fluorescence or absorbance spectroscopy. We characterized the pixel-to-time calibration and diffusional mixing experimentally. We achieved a mixing time as short as 80 μs. We studied the kinetics of horse apomyoglobin (apoMb) unfolding from the intermediate (I) state to its completely unfolded (U) state, induced by a pH jump from the initial pH of 4.5 in the sample stream to a final pH of 2.0 in the sheath solution. The reaction time was probed using the fluorescence of 1-anilinonaphthalene-8-sulfonate (1,8-ANS) bound to the folded protein. We observed unfolding of apoMb within 760 μs, without populating additional intermediate states under these conditions. We also studied the reaction kinetics of the conversion of pyruvate to lactate catalyzed by lactate dehydrogenase using the intrinsic tryptophan emission of the enzyme. We observe sub-millisecond kinetics that we attribute to Michaelis complex formation and loop domain closure. These results demonstrate the utility of the three-dimensional focusing mixer for biophysical studies of protein dynamics.

  5. Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

    Directory of Open Access Journals (Sweden)

    Yoojin Hong

    2010-10-01

    Full Text Available A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.. Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity. Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low

  6. Fast large-scale clustering of protein structures using Gauss integrals

    DEFF Research Database (Denmark)

    Harder, Tim; Borg, Mikael; Boomsma, Wouter

    2011-01-01

    trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by rst mapping structures to Gauss integral vectors – which were introduced by Røgen and co......-workers – and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a signicantly larger number of structures, while providing state-ofthe- art results. The number of low energy structures generated...

  7. Integrated Solid-Phase Extraction-Capillary Liquid Chromatography (speLC) Interfaced to ESI-MS/MS for Fast Characterization and Quantification of Protein and Proteomes

    DEFF Research Database (Denmark)

    Falkenby, Lasse Gaarde; Such-Sanmartín, Gerard; Larsen, Martin Røssel

    2014-01-01

    min speLC-MS/MS experiment. Analysis by selected reaction monitoring by speLC-SRM-MS/MS of distinct peptides derived from the blood proteins IGF1, IGF2, IBP2, and IBP3 demonstrated protein quantification with CV values below 10% across 96 replicates. The speLC-MS/MS system is ideally suited for fast......The high peptide sequencing speed provided by modern hybrid tandem mass spectrometers enables the utilization of fast liquid chromatographic (LC) separation techniques. We present a robust solid-phase extraction/capillary LC system (speLC) for 5-10 min separation of semicomplex peptide mixtures...

  8. Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

    Science.gov (United States)

    Tsujino, Soichiro; Tomizaki, Takashi

    2016-05-01

    Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

  9. Fast evaluation of protein dynamics from deficient 15N relaxation data

    KAUST Repository

    Jaremko, Łukasz

    2018-03-28

    Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S and R, can be elucidated. The generalized order parameter, S, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.

  10. Fast evaluation of protein dynamics from deficient 15N relaxation data

    KAUST Repository

    Jaremko, Łukasz; Jaremko, Mariusz; Ejchart, Andrzej; Nowakowski, Michał

    2018-01-01

    Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S and R, can be elucidated. The generalized order parameter, S, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.

  11. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.

    Science.gov (United States)

    Sehnal, David; Pravda, Lukáš; Svobodová Vařeková, Radka; Ionescu, Crina-Maria; Koča, Jaroslav

    2015-07-01

    Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Quasi-isoelectric buffers for protein analysis in a fast alternative to conventional capillary zone electrophoresis.

    Science.gov (United States)

    Antonioli, Paolo; Mendieta, Martha E; Sebastiano, Roberto; Citterio, Attilio; Peltre, Gabriel; Busnel, Jean-Marc; Descroix, Stephanie; Candiano, Giovanni; Righetti, Pier Giorgio

    2006-03-20

    Two different approaches are here reported for obtaining ultra-narrow pI cuts from 2-pH unit wide carrier ampholyte ranges, as commercially available, for use as quasi-isoelectric buffers in capillary electrophoresis separations of proteins. One of them uses multicompartment electrolyzers endowed with isoelectric membranes (Immobiline technology); the other employs the Rotofor equipment. Although the first approach results in more precise pI cuts, the latter technique is much faster, easier to handle and permits the immediate collection of 20 fractions in a single run. This results in ultra-narrow, ca. 0.1-pH unit intervals, uniformly spaced apart along the original wider gradient utilized for the fractionation. It is here shown that such quasi-isoelectric buffers, especially those in the pH 8-9 interval, have the unique property of coating the silica wall, thus preventing interaction of the proteins with the silica surface, that would otherwise totally disrupt the separation. On the contrary, such a shielding is not obtained in control, non isoelectric buffers (such as phosphate), that give very poor separations in uncoated capillaries. It is hypothesized that such a unique shielding effect is due to the oligo-amino backbone of the carrier ampholytes, typically composed (in the Vesterberg's synthetic approach) of 4-6 nitrogens spaced apart by ethylene moieties. Although such oligoprotic buffers should bear, in the isoelectric state, just one positive and one negative charge, they might be transiently ionized upon contact with the silanols, thus inducing a cooperative binding to the silica wall.

  13. A Critical Role of Fatty Acid Binding Protein 4 and 5 (FABP4/5) in the Systemic Response to Fasting

    Science.gov (United States)

    Syamsunarno, Mas Rizky A. A.; Iso, Tatsuya; Hanaoka, Hirofumi; Yamaguchi, Aiko; Obokata, Masaru; Koitabashi, Norimichi; Goto, Kosaku; Hishiki, Takako; Nagahata, Yoshiko; Matsui, Hiroki; Sano, Motoaki; Kobayashi, Masaki; Kikuchi, Osamu; Sasaki, Tsutomu; Maeda, Kazuhisa; Murakami, Masami; Kitamura, Tadahiro; Suematsu, Makoto; YoshitoTsushima; Endo, Keigo; Hotamisligil, Gökhan S.; Kurabayashi, Masahiko

    2013-01-01

    During prolonged fasting, fatty acid (FA) released from adipose tissue is a major energy source for peripheral tissues, including the heart, skeletal muscle and liver. We recently showed that FA binding protein 4 (FABP4) and FABP5, which are abundantly expressed in adipocytes and macrophages, are prominently expressed in capillary endothelial cells in the heart and skeletal muscle. In addition, mice deficient for both FABP4 and FABP5 (FABP4/5 DKO mice) exhibited defective uptake of FA with compensatory up-regulation of glucose consumption in these tissues during fasting. Here we showed that deletion of FABP4/5 resulted in a marked perturbation of metabolism in response to prolonged fasting, including hyperketotic hypoglycemia and hepatic steatosis. Blood glucose levels were reduced, whereas the levels of non-esterified FA (NEFA) and ketone bodies were markedly increased during fasting. In addition, the uptake of the 125I-BMIPP FA analogue in the DKO livers was markedly increased after fasting. Consistent with an increased influx of NEFA into the liver, DKO mice showed marked hepatic steatosis after a 48-hr fast. Although gluconeogenesis was observed shortly after fasting, the substrates for gluconeogenesis were reduced during prolonged fasting, resulting in insufficient gluconeogenesis and enhanced hypoglycemia. These metabolic responses to prolonged fasting in DKO mice were readily reversed by re-feeding. Taken together, these data strongly suggested that a maladaptive response to fasting in DKO mice occurred as a result of an increased influx of NEFA into the liver and pronounced hypoglycemia. Together with our previous study, the metabolic consequence found in the present study is likely to be attributed to an impairment of FA uptake in the heart and skeletal muscle. Thus, our data provided evidence that peripheral uptake of FA via capillary endothelial FABP4/5 is crucial for systemic metabolism and may establish FABP4/5 as potentially novel targets for the

  14. Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins

    Science.gov (United States)

    Ishii, Yoshitaka; Wickramasinghe, Ayesha; Matsuda, Isamu; Endo, Yuki; Ishii, Yuji; Nishiyama, Yusuke; Nemoto, Takahiro; Kamihara, Takayuki

    2018-01-01

    Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (νR) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at νR of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR. A 1H-detected 2D 1H-15N correlation SSNMR spectrum for ∼27 nmol of a uniformly 13C- and 15N-labeled GB1 protein sample in microcrystalline form was acquired in only 9 s with 50% non-uniform sampling and short recycle delays of 100 ms. Additional data suggests that it is now feasible to detect as little as 1 nmol of the protein in 5.9 h by 1H-detected 2D 1H-15N SSNMR at a nominal signal-to-noise ratio of five. The demonstrated sensitivity is comparable to that of modern solution protein NMR. Moreover, this article summarizes the influence of ultra-fast MAS and 1H-detection on the spectral resolution and sensitivity of protein SSNMR. Recent progress in signal assignment and structural elucidation by 1H-detected protein SSNMR is outlined with both theoretical and experimental aspects.

  15. Comparison of High-Protein, Intermittent Fasting Low-Calorie Diet and Heart Healthy Diet for Vascular Health of the Obese.

    Science.gov (United States)

    Zuo, Li; He, Feng; Tinsley, Grant M; Pannell, Benjamin K; Ward, Emery; Arciero, Paul J

    2016-01-01

    It has been debated whether different diets are more or less effective in long-term weight loss success and cardiovascular disease prevention among men and women. To further explore these questions, the present study evaluated the combined effects of a high-protein, intermittent fasting, low-calorie diet plan compared with a heart healthy diet plan during weight loss, and weight loss maintenance on blood lipids and vascular compliance of obese individuals. The experiment involved 40 obese adults (men, n = 21; women, n = 19) and was divided into two phases: (a) 12-week high-protein, intermittent fasting, low-calorie weight loss diet comparing men and women (Phase 1) and (b) a 1-year weight maintenance phase comparing high-protein, intermittent fasting with a heart healthy diet (Phase 2). Body weight, body mass index (BMI), blood lipids, and arterial compliance outcomes were assessed at weeks 1 (baseline control), 12 (weight loss), and 64 (12 + 52 week; weight loss maintenance). At the end of weight loss intervention, concomitant reductions in body weight, BMI and blood lipids were observed, as well as enhanced arterial compliance. No sex-specific differences in responses were observed. During phase 2, the high-protein, intermittent fasting group demonstrated a trend for less regain in BMI, low-density lipoprotein (LDL), and aortic pulse wave velocity than the heart healthy group. Our results suggest that a high-protein, intermittent fasting and low-calorie diet is associated with similar reductions in BMI and blood lipids in obese men and women. This diet also demonstrated an advantage in minimizing weight regain as well as enhancing arterial compliance as compared to a heart healthy diet after 1 year.

  16. Comparison of High-Protein, Intermittent-Fasting Low-Calorie Diet and Heart Healthy Diet for Vascular Health of the Obese

    Directory of Open Access Journals (Sweden)

    Li Zuo

    2016-08-01

    Full Text Available Aim: It has been debated whether different diets are more or less effective in long-term weight loss success and cardiovascular diseases among men and women. Thus, the present study evaluated the combined effects of a high-protein, intermittent-fasting, low-calorie diet plan compared with heart healthy diet plan during weight loss maintenance on blood lipids and vascular compliance of individuals with obesity. Methods: The experiment involved 40 adults with obesity (men, n = 21; women, n = 19 and was divided into two phases: (a 12-week high-protein, intermittent-fasting, low-calorie weight loss diet comparing men and women (Phase 1 and (b a 1-year (52-week weight loss maintenance comparing high-protein, intermittent-fasting with a heart healthy diet (Phase 2. Body weight, body mass index, blood lipids, and arterial compliance outcomes were assessed at weeks 1 (baseline control, 12 (weight loss, and 64 (12+52 week; weight loss maintenance.Results: At the end of weight loss intervention, concomitant with reductions in body weight, body mass index, blood lipids, and arterial compliance was enhanced (p < 0.05. No sex-specific differences were observed. During phase 2, high-protein, intermittent-fasting, low-calorie group demonstrated less weight regain and percentage change in aortic pulse wave velocity than heart healthy group (p < 0.05. Conclusion: Our results suggest that high-protein, intermittent-fasting and low-calorie diet is associated with body weight loss and reduction in blood lipids. This diet also demonstrated a potential advantage in minimizing weight gain relapse as well as enhancing arterial compliance compared to the heart healthy diet in the long term.

  17. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

    Directory of Open Access Journals (Sweden)

    Raiker Witter

    2015-01-01

    Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

  18. Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein.

    Science.gov (United States)

    Chung, Hoi Sung; Gopich, Irina V; McHale, Kevin; Cellmer, Troy; Louis, John M; Eaton, William A

    2011-04-28

    Recently developed statistical methods by Gopich and Szabo were used to extract folding and unfolding rate coefficients from single-molecule Förster resonance energy transfer (FRET) data for proteins with kinetics too fast to measure waiting time distributions. Two types of experiments and two different analyses were performed. In one experiment bursts of photons were collected from donor and acceptor fluorophores attached to a 73-residue protein, α(3)D, freely diffusing through the illuminated volume of a confocal microscope system. In the second, the protein was immobilized by linkage to a surface, and photons were collected until one of the fluorophores bleached. Folding and unfolding rate coefficients and mean FRET efficiencies for the folded and unfolded subpopulations were obtained from a photon by photon analysis of the trajectories using a maximum likelihood method. The ability of the method to describe the data in terms of a two-state model was checked by recoloring the photon trajectories with the extracted parameters and comparing the calculated FRET efficiency histograms with the measured histograms. The sum of the rate coefficients for the two-state model agreed to within 30% with the relaxation rate obtained from the decay of the donor-acceptor cross-correlation function, confirming the high accuracy of the method. Interestingly, apparently reliable rate coefficients could be extracted using the maximum likelihood method, even at low (rate coefficients and mean FRET efficiencies were also obtained in an approximate procedure by simply fitting the FRET efficiency histograms, calculated by binning the donor and acceptor photons, with a sum of three-Gaussian functions. The kinetics are exposed in these histograms by the growth of a FRET efficiency peak at values intermediate between the folded and unfolded peaks as the bin size increases, a phenomenon with similarities to NMR exchange broadening. When comparable populations of folded and unfolded

  19. Pro-inflammatory cytokine/chemokine production by reovirus treated melanoma cells is PKR/NF-κB mediated and supports innate and adaptive anti-tumour immune priming

    Directory of Open Access Journals (Sweden)

    Coffey Matt

    2011-02-01

    Full Text Available Abstract Background As well as inducing direct oncolysis, reovirus treatment of melanoma is associated with activation of innate and adaptive anti-tumour immune responses. Results Here we characterise the effects of conditioned media from reovirus-infected, dying human melanoma cells (reoTCM, in the absence of live virus, to address the immune bystander potential of reovirus therapy. In addition to RANTES, IL-8, MIP-1α and MIP-1β, reovirus-infected melanoma cells secreted eotaxin, IP-10 and the type 1 interferon IFN-β. To address the mechanisms responsible for the inflammatory composition of reoTCM, we show that IL-8 and IFN-β secretion by reovirus-infected melanoma cells was associated with activation of NF-κB and decreased by pre-treatment with small molecule inhibitors of NF-κB and PKR; specific siRNA-mediated knockdown further confirmed a role for PKR. This pro-inflammatory milieu induced a chemotactic response in isolated natural killer (NK cells, dendritic cells (DC and anti-melanoma cytotoxic T cells (CTL. Following culture in reoTCM, NK cells upregulated CD69 expression and acquired greater lytic potential against tumour targets. Furthermore, melanoma cell-loaded DC cultured in reoTCM were more effective at priming adaptive anti-tumour immunity. Conclusions These data demonstrate that the PKR- and NF-κB-dependent induction of pro-inflammatory molecules that accompanies reovirus-mediated killing can recruit and activate innate and adaptive effector cells, thus potentially altering the tumour microenvironment to support bystander immune-mediated therapy as well as direct viral oncolysis.

  20. Differential Role of the Fas/Fas Ligand Apoptotic Pathway in Inflammation and Lung Fibrosis Associated with Reovirus 1/L-Induced Bronchiolitis Obliterans Organizing Pneumonia and Acute Respiratory Distress Syndrome1

    Science.gov (United States)

    Lopez, Andrea D.; Avasarala, Sreedevi; Grewal, Suman; Murali, Anuradha K.; London, Lucille

    2010-01-01

    Bronchiolitis obliterans organizing pneumonia (BOOP) and acute respiratory distress syndrome (ARDS) are two clinically and histologically distinct syndromes sharing the presence of an inflammatory and fibrotic component. Apoptosis via the Fas/Fas ligand (FasL) pathway plays an important role in the development of acute lung injury and fibrosis characteristic of these and other pulmonary inflammatory and fibrotic syndromes. We evaluated the role of apoptosis via the Fas/FasL pathway in the development of pulmonary inflammation and fibrosis in reovirus 1/L-induced BOOP and ARDS. CBA/J mice were intranasally inoculated with saline, 1 × 106 (BOOP), or 1 × 107 (ARDS) PFU reovirus 1/L, and evaluated at various days postinoculation for in situ apoptosis by TUNEL analysis and Fas/FasL expression. Our results demonstrate the presence of apoptotic cells and up-regulation of Fas/FasL expression in alveolar epithelium and in infiltrating cells during the inflammatory and fibrotic stages of both reovirus 1/L-induced ARDS and BOOP. Treatment of mice with the caspase 8 inhibitor, zIETD-fmk, inhibited apoptosis, inflammation, and fibrotic lesion development in reovirus 1/L-induced BOOP and ARDS. However, CBA/KlJms-Faslpr-cg/J mice, which carry a point mutation in the Fas cytoplasmic region that abolishes the ability of Fas to transduce an apoptotic signal, do not develop pulmonary inflammation and fibrotic lesions associated with reovirus 1/L-induced BOOP, but still develop inflammation and fibrotic lesions associated with reovirus 1/L-induced ARDS. These results suggest a differential role for the Fas/FasL apoptotic pathway in the development of inflammation and fibrotic lesions associated with BOOP and ARDS. PMID:20007588

  1. Differential role of the Fas/Fas ligand apoptotic pathway in inflammation and lung fibrosis associated with reovirus 1/L-induced bronchiolitis obliterans organizing pneumonia and acute respiratory distress syndrome.

    Science.gov (United States)

    Lopez, Andrea D; Avasarala, Sreedevi; Grewal, Suman; Murali, Anuradha K; London, Lucille

    2009-12-15

    Bronchiolitis obliterans organizing pneumonia (BOOP) and acute respiratory distress syndrome (ARDS) are two clinically and histologically distinct syndromes sharing the presence of an inflammatory and fibrotic component. Apoptosis via the Fas/Fas ligand (FasL) pathway plays an important role in the development of acute lung injury and fibrosis characteristic of these and other pulmonary inflammatory and fibrotic syndromes. We evaluated the role of apoptosis via the Fas/FasL pathway in the development of pulmonary inflammation and fibrosis in reovirus 1/L-induced BOOP and ARDS. CBA/J mice were intranasally inoculated with saline, 1 x 10(6) (BOOP), or 1 x 10(7) (ARDS) PFU reovirus 1/L, and evaluated at various days postinoculation for in situ apoptosis by TUNEL analysis and Fas/FasL expression. Our results demonstrate the presence of apoptotic cells and up-regulation of Fas/FasL expression in alveolar epithelium and in infiltrating cells during the inflammatory and fibrotic stages of both reovirus 1/L-induced ARDS and BOOP. Treatment of mice with the caspase 8 inhibitor, zIETD-fmk, inhibited apoptosis, inflammation, and fibrotic lesion development in reovirus 1/L-induced BOOP and ARDS. However, CBA/KlJms-Fas(lpr-cg)/J mice, which carry a point mutation in the Fas cytoplasmic region that abolishes the ability of Fas to transduce an apoptotic signal, do not develop pulmonary inflammation and fibrotic lesions associated with reovirus 1/L-induced BOOP, but still develop inflammation and fibrotic lesions associated with reovirus 1/L-induced ARDS. These results suggest a differential role for the Fas/FasL apoptotic pathway in the development of inflammation and fibrotic lesions associated with BOOP and ARDS.

  2. Piscine reovirus: Genomic and molecular phylogenetic analysis from farmed and wild salmonids collected on the Canada/US Pacific Coast

    Science.gov (United States)

    Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul S.; Richmond, Zina; Purcell, Maureen K.; Johns, Robert; Johnson, Stewart C.; Sakasida, Sonja M.

    2015-01-01

    Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

  3. Associations between piscine reovirus infection and life history traits in wild-caught Atlantic salmon Salmo salar L. in Norway.

    Science.gov (United States)

    Garseth, Ase Helen; Biering, Eirik; Aunsmo, Arnfinn

    2013-10-01

    Piscine Reovirus (PRV), the putative causative agent of heart and skeletal muscle inflammation (HSMI), is widely distributed in both farmed and wild Atlantic salmon (Salmo salar L.) in Norway. While HSMI is a common and commercially important disease in farmed Atlantic salmon, the presence of PRV has so far not been associated with HSMI related lesions in wild salmon. Factors associated with PRV-infection were investigated in returning Atlantic salmon captured in Norwegian rivers. A multilevel mixed-effect logistic regression model confirmed clustering within rivers and demonstrated that PRV-infection is associated with life-history, sex, catch-year and body length as a proxy for sea-age. Escaped farmed salmon (odds ratio/OR: 7.32, p<0.001) and hatchery-reared salmon (OR: 1.69 p=0.073) have higher odds of being PRV-infected than wild Atlantic salmon. Male salmon have double odds of being PRV infected compared to female salmon (OR: 2.11, p<0.001). Odds of being PRV-infected increased with body-length measured as decimetres (OR: 1.20, p=0.004). Since body length and sea-age are correlated (r=0.85 p<0.001), body length serves as a proxy for sea-age, meaning that spending more years in sea increases the odds of being PRV-infected. Copyright © 2013 The Author. Published by Elsevier B.V. All rights reserved.

  4. Hericium erinaceus polysaccharide facilitates restoration of injured intestinal mucosal immunity in Muscovy duck reovirus-infected Muscovy ducklings.

    Science.gov (United States)

    Wu, Yijian; Jiang, Huihui; Zhu, Erpeng; Li, Jian; Wang, Quanxi; Zhou, Wuduo; Qin, Tao; Wu, Xiaoping; Wu, Baocheng; Huang, Yifan

    2018-02-01

    To elucidate the effect of Hericium erinaceus polysaccharide (HEP) on the intestinal mucosal immunity in normal and Muscovy duck reovirus (MDRV)-infected Muscovy ducklings, 1-day-old healthy Muscovy ducklings were pretreated with 0.2g/L HEP and/or following by MDRV infection in this study, duodenal samples were respectively collected at 1, 3, 6, 10, 15 and 21day post-infection, tissue sections were prepared for observation of morphological structure and determination of intestinal parameters (villus height/crypt depth ratio, villus surface area) as well as counts of intraepithelial lymphocytes (IELs), goblet cells, mast cells. Additionally, dynamics of secretory immunoglobin A (sIgA), interferon-γ (IFN-γ) and interleukin-4 (IL-4) productions in intestinal mucosa were measured with radioimmunoassay. Results showed that HEP significantly improved intestinal morphological structure and related indexes, and significantly inhibited the reduction of intestinal mucosal IELs, goblet cells and mast cells caused by MDRV infection. Furthermore, HEP significantly increased the secretion of sIgA, IFN-γ and IL-4 to enhance intestinal mucosal immune functions. Our findings indicate that HEP treatment can effectively repair MDRV-caused injures of small intestinal mucosal immune barrier, and improve mucosal immune function in sick Muscovy ducklings, which will provide valuable help for further application of HEP in prevention and treatment of MDRV infection. Copyright © 2017. Published by Elsevier B.V.

  5. Sorting protein lists with nwCompare: a simple and fast algorithm for n-way comparison of proteomic data files.

    Science.gov (United States)

    Pont, Frédéric; Fournié, Jean Jacques

    2010-03-01

    MS, the reference technology for proteomics, routinely produces large numbers of protein lists whose fast comparison would prove very useful. Unfortunately, most softwares only allow comparisons of two to three lists at once. We introduce here nwCompare, a simple tool for n-way comparison of several protein lists without any query language, and exemplify its use with differential and shared cancer cell proteomes. As the software compares character strings, it can be applied to any type of data mining, such as genomic or metabolomic datalists.

  6. Fasting Induces Nuclear Factor E2-Related Factor 2 and ATP-Binding Cassette Transporters via Protein Kinase A and Sirtuin-1 in Mouse and Human

    Science.gov (United States)

    Kulkarni, Supriya R.; Donepudi, Ajay C.; Xu, Jialin; Wei, Wei; Cheng, Qiuqiong C.; Driscoll, Maureen V.; Johnson, Delinda A.; Johnson, Jeffrey A.; Li, Xiaoling

    2014-01-01

    Abstract Aims: The purpose of this study was to determine whether 3′-5′-cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) and Sirtuin-1 (SIRT1) dependent mechanisms modulate ATP-binding Cassette (ABC) transport protein expression. ABC transport proteins (ABCC2–4) are essential for chemical elimination from hepatocytes and biliary excretion. Nuclear factor-E2 related-factor 2 (NRF2) is a transcription factor that mediates ABCC induction in response to chemical inducers and liver injury. However, a role for NRF2 in the regulation of transporter expression in nonchemical models of liver perturbation is largely undescribed. Results: Here we show that fasting increased NRF2 target gene expression through NRF2- and SIRT1–dependent mechanisms. In intact mouse liver, fasting induces NRF2 target gene expression by at least 1.5 to 5-fold. In mouse and human hepatocytes, treatment with 8-Bromoadenosine-cAMP, a cAMP analogue, increased NRF2 target gene expression and antioxidant response element activity, which was decreased by the PKA inhibitor, H-89. Moreover, fasting induced NRF2 target gene expression was decreased in liver and hepatocytes of SIRT1 liver-specific null mice and NRF2-null mice. Lastly, NRF2 and SIRT1 were recruited to MAREs and Antioxidant Response Elements (AREs) in the human ABCC2 promoter. Innovation: Oxidative stress mediated NRF2 activation is well described, yet the influence of basic metabolic processes on NRF2 activation is just emerging. Conclusion: The current data point toward a novel role of nutrient status in regulation of NRF2 activity and the antioxidant response, and indicates that cAMP/PKA and SIRT1 are upstream regulators for fasting-induced activation of the NRF2-ARE pathway. Antioxid. Redox Signal. 20, 15–30. PMID:23725046

  7. A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

    Science.gov (United States)

    2015-01-01

    Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

  8. One and two-dimensional electrophoresis of fast axonally-transported proteins in rat nerves following acrylamide and 2,5-hexanedione exposure

    International Nuclear Information System (INIS)

    Sickles, D.W.

    1990-01-01

    Transient and repeated deficiencies in protein delivery to the axon are observed following injections of acrylamide (ACR) and 2,5-hexanedione (2,5-HD) (Sickles DW, Neurotoxicology 10: 91;103, 1989; Neurosci Abstr 14:1219, 1988). We have furthered these studies by measuring the effects of single 50 mg/kg ACR and 4 nmole/kg 2,5-HD injections on the quantity of select fast-transported proteins. Proteins were radiolabelled with 3H-leucine injections of the DRG; 1 and 2 dimensional gels were used for separation of the sciatic nerve (9-45mm distal to the ganglion) homogenates. Scintillation counting demonstrated that transport of all proteins studied were affected by both toxicants. Some variation in effect was observed; a direct correlation between molecular weight (r=0.71) and original quantity of radiolabel (r=0.80) with the percent reduction in transport was observed. Some apparent increases in transport of certain proteins were observed on the 2D gels; but this may indicate a change in the isoelectric points of these transported proteins

  9. S-Nitrosylation and uncompetitive/fast off-rate (UFO) drug therapy in neurodegenerative disorders of protein misfolding.

    Science.gov (United States)

    Nakamura, T; Lipton, S A

    2007-07-01

    Although activation of glutamate receptors is essential for normal brain function, excessive activity leads to a form of neurotoxicity known as excitotoxicity. Key mediators of excitotoxic damage include overactivation of N-methyl-D-aspartate (NMDA) receptors, resulting in excessive Ca(2+) influx with production of free radicals and other injurious pathways. Overproduction of free radical nitric oxide (NO) contributes to acute and chronic neurodegenerative disorders. NO can react with cysteine thiol groups to form S-nitrosothiols and thus change protein function. S-nitrosylation can result in neuroprotective or neurodestructive consequences depending on the protein involved. Many neurodegenerative diseases manifest conformational changes in proteins that result in misfolding and aggregation. Our recent studies have linked nitrosative stress to protein misfolding and neuronal cell death. Molecular chaperones - such as protein-disulfide isomerase, glucose-regulated protein 78, and heat-shock proteins - can provide neuroprotection by facilitating proper protein folding. Here, we review the effect of S-nitrosylation on protein function under excitotoxic conditions, and present evidence that NO contributes to degenerative conditions by S-nitrosylating-specific chaperones that would otherwise prevent accumulation of misfolded proteins and neuronal cell death. In contrast, we also review therapeutics that can abrogate excitotoxic damage by preventing excessive NMDA receptor activity, in part via S-nitrosylation of this receptor to curtail excessive activity.

  10. Dietary changes in fasting levels of factor VII coagulant activity (FVII:C) are accompanied by changes in factor VII protein and other vitamin K-dependent proteins

    DEFF Research Database (Denmark)

    Bladbjerg, Else-Marie; Tholstrup, T; Marckmann, P

    1995-01-01

    The mechanisms behind dietary effects on fasting coagulant activity of factor VII (FVII:C) are not clarified. In the present study of 15 young volunteers, two experimental diets differing in composition of saturated fatty acids (C18:0 [diet S] or C12:0 + C14:0 [diet ML]) were served for 3 weeks...

  11. A new approach to protein enzymatic digestion for fast protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

    Czech Academy of Sciences Publication Activity Database

    Dyčka, Filip; Laštovičková, Markéta; Bobálová, Janette

    2008-01-01

    Roč. 102, č. 15 (2008), s967-s968 ISSN 1803-2389. [Meeting on Chemistry and Life /4./. Brno, 09.09.2008-11.09.2008] R&D Projects: GA AV ČR IAA600040701 Institutional research plan: CEZ:AV0Z40310501 Keywords : enzymatic digest ion * fast approach Subject RIV: CB - Analytical Chemistry, Separation

  12. Nonsynonymous substitution rate (Ka is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes

    Directory of Open Access Journals (Sweden)

    Wang Lei

    2011-02-01

    Full Text Available Abstract Background Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics. Results We chose human and eleven other high-coverage mammalian genome data–as well as an avian genome as an outgroup–to analyze orthologous protein-coding genes using nonsynonymous (Ka and synonymous (Ks substitution rates. After evaluating eight commonly-used methods of Ka and Ks calculation, we observed that these methods yielded a nearly uniform result when estimating Ka, but not Ks (or Ka/Ks. When sorting genes based on Ka, we noticed that fast-evolving and slow-evolving genes often belonged to different functional classes, with respect to species-specificity and lineage-specificity. In particular, we identified two functional classes of genes in the acquired immune system. Fast-evolving genes coded for signal-transducing proteins, such as receptors, ligands, cytokines, and CDs (cluster of differentiation, mostly surface proteins, whereas the slow-evolving genes were for function-modulating proteins, such as kinases and adaptor proteins. In addition, among slow-evolving genes that had functions related to the central nervous system, neurodegenerative disease-related pathways were enriched significantly in most mammalian species. We also confirmed that gene expression was negatively correlated with evolution rate, i.e. slow-evolving genes were expressed at higher levels than fast-evolving genes. Our results indicated that the functional specializations of the three major mammalian clades were: sensory perception and oncogenesis in primates, reproduction and hormone regulation in large mammals, and immunity and angiotensin in rodents. Conclusion Our study suggests that Ka calculation, which is less biased compared to Ks and Ka

  13. Hepatic protein phosphatase 1 regulatory subunit 3B (Ppp1r3b) promotes hepatic glycogen synthesis and thereby regulates fasting energy homeostasis.

    Science.gov (United States)

    Mehta, Minal B; Shewale, Swapnil V; Sequeira, Raymond N; Millar, John S; Hand, Nicholas J; Rader, Daniel J

    2017-06-23

    Maintenance of whole-body glucose homeostasis is critical to glycemic function. Genetic variants mapping to chromosome 8p23.1 in genome-wide association studies have been linked to glycemic traits in humans. The gene of known function closest to the mapped region, PPP1R3B (protein phosphatase 1 regulatory subunit 3B), encodes a protein (G L ) that regulates glycogen metabolism in the liver. We therefore sought to test the hypothesis that hepatic PPP1R3B is associated with glycemic traits. We generated mice with either liver-specific deletion ( Ppp1r3b Δ hep ) or liver-specific overexpression of Ppp1r3b The Ppp1r3b deletion significantly reduced glycogen synthase protein abundance, and the remaining protein was predominantly phosphorylated and inactive. As a consequence, glucose incorporation into hepatic glycogen was significantly impaired, total hepatic glycogen content was substantially decreased, and mice lacking hepatic Ppp1r3b had lower fasting plasma glucose than controls. The concomitant loss of liver glycogen impaired whole-body glucose homeostasis and increased hepatic expression of glycolytic enzymes in Ppp1r3b Δ hep mice relative to controls in the postprandial state. Eight hours of fasting significantly increased the expression of two critical gluconeogenic enzymes, phosphoenolpyruvate carboxykinase and glucose-6-phosphatase, above the levels in control livers. Conversely, the liver-specific overexpression of Ppp1r3b enhanced hepatic glycogen storage above that of controls and, as a result, delayed the onset of fasting-induced hypoglycemia. Moreover, mice overexpressing hepatic Ppp1r3b upon long-term fasting (12-36 h) were protected from blood ketone-body accumulation, unlike control and Ppp1r3b Δ hep mice. These findings indicate a major role for Ppp1r3b in regulating hepatic glycogen stores and whole-body glucose/energy homeostasis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Low-molecular weight protein profiling of genetically modified maize using fast liquid chromatography electrospray ionization and time-of-flight mass spectrometry.

    Science.gov (United States)

    Koc, Anna; Cañuelo, Ana; Garcia-Reyes, Juan F; Molina-Diaz, Antonio; Trojanowicz, Marek

    2012-06-01

    In this work, the use of liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC-TOFMS) has been evaluated for the profiling of relatively low-molecular weight protein species in both genetically modified (GM) and non-GM maize. The proposed approach consisted of a straightforward sample fractionation with different water and ethanol-based buffer solutions followed by separation and detection of the protein species using liquid chromatography with a small particle size (1.8 μm) C(18) column and electrospray-time-of-flight mass spectrometry detection in the positive ionization mode. The fractionation of maize reference material containing different content of transgenic material (from 0 to 5% GM) led to five different fractions (albumins, globulins, zeins, zein-like glutelins, and glutelins), all of them containing different protein species (from 2 to 52 different species in each fraction). Some relevant differences in the quantity and types of protein species were observed in the different fractions of the reference material (with different GM contents) tested, thus revealing the potential use of the proposed approach for fast protein profiling and to detect tentative GMO markers in maize. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Synergistic antitumor activity of oncolytic reovirus and chemotherapeutic agents in non-small cell lung cancer cells

    Directory of Open Access Journals (Sweden)

    Coffey Matthew C

    2009-07-01

    Full Text Available Abstract Background Reovirus type 3 Dearing strain (ReoT3D has an inherent propensity to preferentially infect and destroy cancer cells. The oncolytic activity of ReoT3D as a single agent has been demonstrated in vitro and in vivo against various cancers, including colon, pancreatic, ovarian and breast cancers. Its human safety and potential efficacy are currently being investigated in early clinical trials. In this study, we investigated the in vitro combination effects of ReoT3D and chemotherapeutic agents against human non-small cell lung cancer (NSCLC. Results ReoT3D alone exerted significant cytolytic activity in 7 of 9 NSCLC cell lines examined, with the 50% effective dose, defined as the initial virus dose to achieve 50% cell killing after 48 hours of infection, ranging from 1.46 ± 0.12 ~2.68 ± 0.25 (mean ± SD log10 pfu/cell. Chou-Talalay analysis of the combination of ReoT3D with cisplatin, gemcitabine, or vinblastine demonstrated strong synergistic effects on cell killing, but only in cell lines that were sensitive to these compounds. In contrast, the combination of ReoT3D and paclitaxel was invariably synergistic in all cell lines tested, regardless of their levels of sensitivity to either agent. Treatment of NSCLC cell lines with the ReoT3D-paclitaxel combination resulted in increased poly (ADP-ribose polymerase cleavage and caspase activity compared to single therapy, indicating enhanced apoptosis induction in dually treated NSCLC cells. NSCLC cells treated with the ReoT3D-paclitaxel combination showed increased proportions of mitotic and apoptotic cells, and a more pronounced level of caspase-3 activation was demonstrated in mitotically arrested cells. Conclusion These data suggest that the oncolytic activity of ReoT3D can be potentiated by taxanes and other chemotherapeutic agents, and that the ReoT3D-taxane combination most effectively achieves synergy through accelerated apoptosis triggered by prolonged mitotic arrest.

  16. Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Songlin; Matsuda, Isamu; Long, Fei; Ishii, Yoshitaka, E-mail: yishii@uic.edu [University of Illinois at Chicago, Department of Chemistry (United States)

    2016-02-15

    This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40–80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055–15058, 2015) combines the reverse {sup 13}C, {sup 15}N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of “highlighted” labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching {sup 13}CO or {sup 15}N signals for a pair of consecutively labeled residues by recoupling {sup 13}CO–{sup 15}N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ∼15 % loss of signals for the highlighted residues while quenching as much as ∼90 % of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D {sup 15}N/{sup 13}C{sub α} correlation and 2D {sup 13}C{sub α}/{sup 13}CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and {sup 1}H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using {sup 13}C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (∼300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable

  17. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Science.gov (United States)

    Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

    2015-01-01

    The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  18. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Directory of Open Access Journals (Sweden)

    Markus Niklasson

    2015-01-01

    Full Text Available The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  19. Using guanidine-hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry

    DEFF Research Database (Denmark)

    Poulsen, Jon Wriedt; Madsen, Christian Toft; Young, Clifford

    2013-01-01

    be optimally completed within 30 min with endoprotease Lys-C. No chemical artifacts were introduced when samples were incubated in Gnd-HCl at 95 °C, making Gnd-HCl an appropriate digestion buffer for shotgun proteomics. Current methodologies for investigating protein-protein interactions (PPIs) often require......Protein digestion is an integral part of the "shotgun" proteomics approach and commonly requires overnight incubation prior to mass spectrometry analysis. Quadruplicate "shotgun" proteomic analysis of whole yeast lysate demonstrated that Guanidine-Hydrochloride (Gnd-HCl) protein digestion can....... To validate the Gnd-HCl approach, label-free PPI analysis of several GFP-tagged yeast deubiquitinating enzymes was performed. The identification of known interaction partners demonstrates the utility of the optimized Gnd-HCl protocol that is also scalable to the 96 well-plate format....

  20. Fast and selective determination of total protein in milk powder via titration of moving reaction boundary electrophoresis.

    Science.gov (United States)

    Guo, Cheng-ye; Wang, Hou-yu; Liu, Xiao-ping; Fan, Liu-yin; Zhang, Lei; Cao, Cheng-xi

    2013-05-01

    In this paper, moving reaction boundary titration (MRBT) was developed for rapid and accurate quantification of total protein in infant milk powder, from the concept of moving reaction boundary (MRB) electrophoresis. In the method, the MRB was formed by the hydroxide ions and the acidic residues of milk proteins immobilized via cross-linked polyacrylamide gel (PAG), an acid-base indicator was used to denote the boundary motion. As a proof of concept, we chose five brands of infant milk powders to study the feasibility of MRBT method. The calibration curve of MRB velocity versus logarithmic total protein content of infant milk powder sample was established based on the visual signal of MRB motion as a function of logarithmic milk protein content. Weak influence of nonprotein nitrogen (NPN) reagents (e.g., melamine and urea) on MRBT method was observed, due to the fact that MRB was formed with hydroxide ions and the acidic residues of captured milk proteins, rather than the alkaline residues or the NPN reagents added. The total protein contents in infant milk powder samples detected via the MRBT method were in good agreement with those achieved by the classic Kjeldahl method. In addition, the developed method had much faster measuring speed compared with the Kjeldahl method. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate

    Directory of Open Access Journals (Sweden)

    Shane D. Trask

    2010-06-01

    Full Text Available A recently solved structure of the aquareovirus virion (Zhang, X; Jin, L.; Fang, Q; Hui, W.H.; Zhou Z.H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell 2010, 141, 472-482 [1] provides new insights into the order of entry events, as well as confirming and refining several aspects of the entry mechanism, for aquareovirus and the related orthoreovirus. In particular, the structure provides evidence of a defined order for the progressive proteolytic cleavages of myristoylated penetration protein VP5 that prime the virion for membrane penetration. These observations reinforce the concept that, much like enveloped viruses, nonenveloped virions often undergo priming events that lead to a meta-stable state, preparing the virus for membrane penetration under the appropriate circumstances. In addition, this and other recent studies highlight the increasing power of electron cryomicroscopy to analyze large, geometrically regular structures, such as icosahedral viruses, at atomic resolution.

  2. SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

    Directory of Open Access Journals (Sweden)

    Paccanaro Alberto

    2010-03-01

    Full Text Available Abstract Background An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. Results SCPS (Spectral Clustering of Protein Sequences is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences and the complete genome of the yeast Saccharomyces cerevisiae (6,690 sequences. Conclusions Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein

  3. SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

    Science.gov (United States)

    Nepusz, Tamás; Sasidharan, Rajkumar; Paccanaro, Alberto

    2010-03-09

    An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences) and the complete genome of the yeast Saccharomyces cerevisiae (6,690 sequences). Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with

  4. Optimization of photoactive protein Z for fast and efficient site-specific conjugation of native IgG.

    Science.gov (United States)

    Hui, James Z; Tsourkas, Andrew

    2014-09-17

    Antibody conjugates have been used in a variety of applications from immunoassays to drug conjugates. However, it is becoming increasingly clear that in order to maximize an antibody's antigen binding ability and to produce homogeneous antibody-conjugates, the conjugated molecule should be attached onto IgG site-specifically. We previously developed a facile method for the site-specific modification of full length, native IgGs by engineering a recombinant Protein Z that forms a covalent link to the Fc domain of IgG upon exposure to long wavelength UV light. To further improve the efficiency of Protein Z production and IgG conjugation, we constructed a panel of 13 different Protein Z variants with the UV-active amino acid benzoylphenylalanine (BPA) in different locations. By using this panel of Protein Z to cross-link a range of IgGs from different hosts, including human, mouse, and rat, we discovered two previously unknown Protein Z variants, L17BPA and K35BPA, that are capable of cross-linking many commonly used IgG isotypes with efficiencies ranging from 60% to 95% after only 1 h of UV exposure. When compared to existing site-specific methods, which often require cloning or enzymatic reactions, the Protein Z-based method described here, utilizing the L17BPA, K35BPA, and the previously described Q32BPA variants, represents a vastly more accessible and efficient approach that is compatible with nearly all native IgGs, thus making site-specific conjugation more accessible to the general research community.

  5. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics.

    Science.gov (United States)

    Davis, Caitlin M; Reddish, Michael J; Dyer, R Brian

    2017-05-05

    Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Fast and easy protocol for the purification of recombinant S-layer protein for synthetic biology applications

    KAUST Repository

    Norville, Julie E.; Kelly, Deborah F.; Knight, Thomas F.; Belcher, Angela M.; Walz, Thomas

    2011-01-01

    A goal of synthetic biology is to make biological systems easier to engineer. One of the aims is to design, with nanometer-scale precision, biomaterials with well-defined properties. The surface-layer protein SbpA forms 2D arrays naturally

  7. Designing a fully automated multi-bioreactor plant for fast DoE optimization of pharmaceutical protein production.

    Science.gov (United States)

    Fricke, Jens; Pohlmann, Kristof; Jonescheit, Nils A; Ellert, Andree; Joksch, Burkhard; Luttmann, Reiner

    2013-06-01

    The identification of optimal expression conditions for state-of-the-art production of pharmaceutical proteins is a very time-consuming and expensive process. In this report a method for rapid and reproducible optimization of protein expression in an in-house designed small-scale BIOSTAT® multi-bioreactor plant is described. A newly developed BioPAT® MFCS/win Design of Experiments (DoE) module (Sartorius Stedim Systems, Germany) connects the process control system MFCS/win and the DoE software MODDE® (Umetrics AB, Sweden) and enables therefore the implementation of fully automated optimization procedures. As a proof of concept, a commercial Pichia pastoris strain KM71H has been transformed for the expression of potential malaria vaccines. This approach has allowed a doubling of intact protein secretion productivity due to the DoE optimization procedure compared to initial cultivation results. In a next step, robustness regarding the sensitivity to process parameter variability has been proven around the determined optimum. Thereby, a pharmaceutical production process that is significantly improved within seven 24-hour cultivation cycles was established. Specifically, regarding the regulatory demands pointed out in the process analytical technology (PAT) initiative of the United States Food and Drug Administration (FDA), the combination of a highly instrumented, fully automated multi-bioreactor platform with proper cultivation strategies and extended DoE software solutions opens up promising benefits and opportunities for pharmaceutical protein production. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

    Science.gov (United States)

    Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

    2017-05-01

    We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

  9. irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules--a GPU solver using the fast multipole method and statistical thermodynamics.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2015-04-05

    A cluster of strongly interacting ionization groups in protein molecules with irregular ionization behavior is suggestive for specific structure-function relationship. However, their computational treatment is unconventional (e.g., lack of convergence in naive self-consistent iterative algorithm). The stringent evaluation requires evaluation of Boltzmann averaged statistical mechanics sums and electrostatic energy estimation for each microstate. irGPU: Irregular strong interactions in proteins--a GPU solver is novel solution to a versatile problem in protein biophysics--atypical protonation behavior of coupled groups. The computational severity of the problem is alleviated by parallelization (via GPU kernels) which is applied for the electrostatic interaction evaluation (including explicit electrostatics via the fast multipole method) as well as statistical mechanics sums (partition function) estimation. Special attention is given to the ease of the service and encapsulation of theoretical details without sacrificing rigor of computational procedures. irGPU is not just a solution-in-principle but a promising practical application with potential to entice community into deeper understanding of principles governing biomolecule mechanisms. © 2015 Wiley Periodicals, Inc.

  10. relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins

    International Nuclear Information System (INIS)

    Bieri, Michael; D’Auvergne, Edward J.; Gooley, Paul R.

    2011-01-01

    Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

  11. relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

    Science.gov (United States)

    Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

    2011-06-01

    Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

  12. LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

    Science.gov (United States)

    Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

    2018-05-07

    Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

  13. Fast track, dynein-dependent nuclear targeting of human immunodeficiency virus Vpr protein; impaired trafficking in a clinical isolate

    Energy Technology Data Exchange (ETDEWEB)

    Caly, Leon [Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800 (Australia); Kassouf, Vicki T. [Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145 (Australia); Moseley, Gregory W. [Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800 (Australia); Diefenbach, Russell J.; Cunningham, Anthony L. [Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145 (Australia); Jans, David A., E-mail: david.jans@monash.edu [Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800 (Australia)

    2016-02-12

    Nuclear import of the accessory protein Vpr is central to infection by human immunodeficiency virus (HIV). We previously identified the Vpr F72L mutation in a HIV-infected, long-term non-progressor, showing that it resulted in reduced Vpr nuclear accumulation and altered cytoplasmic localisation. Here we demonstrate for the first time that the effects of nuclear accumulation of the F72L mutation are due to impairment of microtubule-dependent-enhancement of Vpr nuclear import. We use high resolution imaging approaches including fluorescence recovery after photobleaching and other approaches to document interaction between Vpr and the dynein light chain protein, DYNLT1, and impaired interaction of the F72L mutant with DYNLT1. The results implicate MTs/DYNLT1 as drivers of Vpr nuclear import and HIV infection, with important therapeutic implications. - Highlights: • HIV-1 Vpr utilizes the microtubule network to traffic towards the nucleus. • Mechanism relies on interaction between Vpr and dynein light chain protein DYNLT1. • Long-term non-progressor derived mutation (F72L) impairs this interaction. • Key residues in the vicinity of F72 contribute to interaction with DYNLT1.

  14. Fast and easy protocol for the purification of recombinant S-layer protein for synthetic biology applications

    KAUST Repository

    Norville, Julie E.

    2011-06-17

    A goal of synthetic biology is to make biological systems easier to engineer. One of the aims is to design, with nanometer-scale precision, biomaterials with well-defined properties. The surface-layer protein SbpA forms 2D arrays naturally on the cell surface of Lysinibacillus sphaericus, but also as the purified protein in solution upon the addition of divalent cations. The high propensity of SbpA to form crystalline arrays, which can be simply controlled by divalent cations, and the possibility to genetically alter the protein, make SbpA an attractive molecule for synthetic biology. To be a useful tool, however, it is important that a simple protocol can be used to produce recombinant wild-type and modified SbpA in large quantities and in a biologically active form. The present study addresses this requirement by introducing a mild and non-denaturing purification protocol to produce milligram quantities of recombinant, active SbpA.

  15. Essential corrections of interference reactions in the determination of protein contents of Nigeria foodstuffs using fast neutron activation analysis

    International Nuclear Information System (INIS)

    Adesanmi, C.A.; Essiett, A.A.; Balogun, F.A.

    2003-01-01

    Using the 14 N(n, zn) 13 N reaction, the protein contents of some Nigeria staple foods were estimated. The contribution of some elements in these foods such as Br, P, K and the recoil proton to the 511 KeV photopeak commonly used in this technique was investigated. While Br was found absent from the high carbohydrate foods such as the cassava tuber based 'gari', maize and rice, this element was shown to produce significant interference in broad beans and soya beans. The contribution of Br to the 511 Kev line in protein measurement in the latter set of food materials ranged between 12% and 62%. Proton recoil were found to be a significant source of interference in virtually all the food stuffs investigated. The result of protein contents using 14 MeV compared favourably, within experimental errors, with that of the wet kjeldahl method, except in the case of soya beans which indicates an underestimation of the contribution from the recoil proton

  16. Fast track, dynein-dependent nuclear targeting of human immunodeficiency virus Vpr protein; impaired trafficking in a clinical isolate

    International Nuclear Information System (INIS)

    Caly, Leon; Kassouf, Vicki T.; Moseley, Gregory W.; Diefenbach, Russell J.; Cunningham, Anthony L.; Jans, David A.

    2016-01-01

    Nuclear import of the accessory protein Vpr is central to infection by human immunodeficiency virus (HIV). We previously identified the Vpr F72L mutation in a HIV-infected, long-term non-progressor, showing that it resulted in reduced Vpr nuclear accumulation and altered cytoplasmic localisation. Here we demonstrate for the first time that the effects of nuclear accumulation of the F72L mutation are due to impairment of microtubule-dependent-enhancement of Vpr nuclear import. We use high resolution imaging approaches including fluorescence recovery after photobleaching and other approaches to document interaction between Vpr and the dynein light chain protein, DYNLT1, and impaired interaction of the F72L mutant with DYNLT1. The results implicate MTs/DYNLT1 as drivers of Vpr nuclear import and HIV infection, with important therapeutic implications. - Highlights: • HIV-1 Vpr utilizes the microtubule network to traffic towards the nucleus. • Mechanism relies on interaction between Vpr and dynein light chain protein DYNLT1. • Long-term non-progressor derived mutation (F72L) impairs this interaction. • Key residues in the vicinity of F72 contribute to interaction with DYNLT1.

  17. Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

    Science.gov (United States)

    The, Matthew; MacCoss, Michael J.; Noble, William S.; Käll, Lukas

    2016-11-01

    Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method—grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein—in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license.

  18. Effects of beta-hydroxy-beta-methylbutyrate (HMB) on the expression of ubiquitin ligases, protein synthesis pathways and contractile function in extensor digitorum longus (EDL) of fed and fasting rats.

    Science.gov (United States)

    Gerlinger-Romero, Frederico; Guimarães-Ferreira, Lucas; Yonamine, Caio Yogi; Salgueiro, Rafael Barrera; Nunes, Maria Tereza

    2018-03-01

    Beta-hydroxy-beta-methylbutyrate (HMB), a leucine metabolite, enhances the gain of skeletal muscle mass by increasing protein synthesis or attenuating protein degradation or both. The aims of this study were to investigate the effect of HMB on molecular factors controlling skeletal muscle protein synthesis and degradation, as well as muscle contractile function, in fed and fasted conditions. Wistar rats were supplied daily with HMB (320 mg/kg body weight diluted in NaCl-0.9%) or vehicle only (control) by gavage for 28 days. After this period, some of the animals were subjected to a 24-h fasting, while others remained in the fed condition. The EDL muscle was then removed, weighed and used to evaluate the genes and proteins involved in protein synthesis (AKT/4E-BP1/S6) and degradation (Fbxo32 and Trim63). A sub-set of rats were used to measure in vivo muscle contractile function. HMB supplementation increased AKT phosphorylation during fasting (three-fold). In the fed condition, no differences were detected in atrogenes expression between control and HMB supplemented group; however, HMB supplementation did attenuate the fasting-induced increase in their expression levels. Fasting animals receiving HMB showed improved sustained tetanic contraction times (one-fold) and an increased muscle to tibia length ratio (1.3-fold), without any cross-sectional area changes. These results suggest that HMB supplementation under fasting conditions increases AKT phosphorylation and attenuates the increased of atrogenes expression, followed by a functional improvement and gain of skeletal muscle weight, suggesting that HMB protects skeletal muscle against the deleterious effects of fasting.

  19. Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm.

    Science.gov (United States)

    Yanagisawa, Keisuke; Komine, Shunta; Kubota, Rikuto; Ohue, Masahito; Akiyama, Yutaka

    2018-03-16

    The need to accelerate large-scale protein-ligand docking in virtual screening against a huge compound database led researchers to propose a strategy that entails memorizing the evaluation result of the partial structure of a compound and reusing it to evaluate other compounds. However, the previous method required frequent disk accesses, resulting in insufficient acceleration. Thus, more efficient memory usage can be expected to lead to further acceleration, and optimal memory usage could be achieved by solving the minimum cost flow problem. In this research, we propose a fast algorithm for the minimum cost flow problem utilizing the characteristics of the graph generated for this problem as constraints. The proposed algorithm, which optimized memory usage, was approximately seven times faster compared to existing minimum cost flow algorithms. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

    Science.gov (United States)

    Shcherbakova, Inna; Mitra, Somdeb; Beer, Robert H.; Brenowitz, Michael

    2006-01-01

    ‘Footprinting’ describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (·OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved ·OH footprinting has been developed based on the Fenton reaction, Fe(II) + H2O2 → Fe(III) + ·OH + OH−. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function. PMID:16582097

  1. Myosin Binding Protein-C Slow Phosphorylation is Altered in Duchenne Dystrophy and Arthrogryposis Myopathy in Fast-Twitch Skeletal Muscles.

    Science.gov (United States)

    Ackermann, Maegen A; Ward, Christopher W; Gurnett, Christina; Kontrogianni-Konstantopoulos, Aikaterini

    2015-08-19

    Myosin Binding Protein-C slow (sMyBP-C), encoded by MYBPC1, comprises a family of regulatory proteins of skeletal muscles that are phosphorylated by PKA and PKC. MYBPC1 missense mutations are linked to the development of Distal Arthrogryposis-1 (DA-1). Although structure-function details for this myopathy are evolving, function is undoubtedly driven by sequence variations and post-translational modifications in sMyBP-C. Herein, we examined the phosphorylation profile of sMyBP-C in mouse and human fast-twitch skeletal muscles. We used Flexor Digitorum Brevis (FDB) isolated from young (~2-months old) and old (~14-months old) wild type and mdx mice, and human Abductor Hallucis (AH) and gastrocnemious muscles carrying the DA-1 mutations. Our results indicate both constitutive and differential phosphorylation of sMyBP-C in aged and diseased muscles. We report a 7-35% reduction in the phosphorylation levels of select sites in old wild type and young or old mdx FDB mouse muscles, compared to young wild type tissue. Similarly, we observe a 30-70% decrease in the phosphorylation levels of all PKA and PKC phospho-sites in the DA-1 AH, but not gastrocnemius, muscle. Overall, our studies show that the phosphorylation pattern of sMyBP-C is differentially regulated in response to age and disease, suggesting that phosphorylation plays important roles in these processes.

  2. qPMS7: a fast algorithm for finding (ℓ, d-motifs in DNA and protein sequences.

    Directory of Open Access Journals (Sweden)

    Hieu Dinh

    Full Text Available Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is useful in the detection of transcription factor binding sites and transcriptional regulatory elements that are very crucial in understanding gene function, human disease, drug design, etc. Many versions of the motif search problem have been proposed in the literature. One such is the (ℓ, d-motif search (or Planted Motif Search (PMS. A generalized version of the PMS problem, namely, Quorum Planted Motif Search (qPMS, is shown to accurately model motifs in real data. However, solving the qPMS problem is an extremely difficult task because a special case of it, the PMS Problem, is already NP-hard, which means that any algorithm solving it can be expected to take exponential time in the worse case scenario. In this paper, we propose a novel algorithm named qPMS7 that tackles the qPMS problem on real data as well as challenging instances. Experimental results show that our Algorithm qPMS7 is on an average 5 times faster than the state-of-art algorithm. The executable program of Algorithm qPMS7 is freely available on the web at http://pms.engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com.

  3. A Simple, Fast, Low Cost, HPLC/UV Validated Method for Determination of Flutamide: Application to Protein Binding Studies.

    Science.gov (United States)

    Esmaeilzadeh, Sara; Valizadeh, Hadi; Zakeri-Milani, Parvin

    2016-06-01

    The main goal of this study was development of a reverse phase high performance liquid chromatography (RP-HPLC) method for flutamide quantitation which is applicable to protein binding studies. Ultrafilteration method was used for protein binding study of flutamide. For sample analysis, flutamide was extracted by a simple and low cost extraction method using diethyl ether and then was determined by HPLC/UV. Acetanilide was used as an internal standard. The chromatographic system consisted of a reversed-phase C8 column with C8 pre-column, and the mobile phase of a mixture of 29% (v/v) methanol, 38% (v/v) acetonitrile and 33% (v/v) potassium dihydrogen phosphate buffer (50 mM) with pH adjusted to 3.2. Acetanilide and flutamide were eluted at 1.8 and 2.9 min, respectively. The linearity of method was confirmed in the range of 62.5-16000 ng/ml (r(2) > 0.99). The limit of quantification was shown to be 62.5 ng/ml. Precision and accuracy ranges found to be (0.2-1.4%, 90-105%) and (0.2-5.3 %, 86.7-98.5 %) respectively. Acetanilide and flutamide capacity factor values of 1.35 and 2.87, tailing factor values of 1.24 and 1.07 and resolution values of 1.8 and 3.22 were obtained in accordance with ICH guidelines. Based on the obtained results a rapid, precise, accurate, sensitive and cost-effective analysis procedure was proposed for quantitative determination of flutamide.

  4. Role of calpain in eccentric contraction-induced proteolysis of Ca2+-regulatory proteins and force depression in rat fast-twitch skeletal muscle.

    Science.gov (United States)

    Kanzaki, Keita; Watanabe, Daiki; Kuratani, Mai; Yamada, Takashi; Matsunaga, Satoshi; Wada, Masanobu

    2017-02-01

    The aim of this study was to examine the in vivo effects of eccentric contraction (ECC) on calpain-dependent proteolysis of Ca 2+ -regulatory proteins and force production in fast-twitch skeletal muscles. Rat extensor digitorum longus muscles were exposed to 200 repeated ECC in situ and excised immediately [recovery 0 (REC0)] or 3 days [recovery 3 (REC3)] after cessation of ECC. Calpain inhibitor (CI)-treated rats were intraperitoneally injected with MDL-28170 before ECC and during REC3. Tetanic force was markedly reduced at REC0 and remained reduced at REC3. CI treatment ameliorated the ECC-induced force decline but only at REC3. No evidence was found for proteolysis of dihydropyridine receptor (DHPR), junctophilin (JP)1, JP2, ryanodine receptor (RyR), sarcoplasmic reticulum Ca 2+ -ATPase (SERCA)1a, or junctional face protein-45 at REC0. At REC3, ECC resulted in decreases in DHPR, JP1, JP2, RyR, and SERCA1a. CI treatment prevented the decreases in DHPR, JP1, and JP2, whereas it had little effect on RyR and SERCA1a. These findings suggest that DHPR, JP1, and JP2, but not RyR and SERCA1a, undergo calpain-dependent proteolysis in in vivo muscles subjected to ECC and that impaired function of DHPR and/or JP might cause prolonged force deficits with ECC. NEW & NOTEWORTHY Calpain-dependent proteolysis is one of the contributing factors to muscle damage that occurs with eccentric contraction (ECC). It is unclear, however, whether calpains account for proteolysis of Ca 2+ -regulatory proteins in in vivo muscles subjected to ECC. Here, we provide evidence that dihydropyridine receptor and junctophilin, but not ryanodine receptor and sarcoplasmic reticulum Ca 2+ -ATPase, undergo calpain-dependent proteolysis. Copyright © 2017 the American Physiological Society.

  5. Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics

    Science.gov (United States)

    Han, Zhou; Jin, Lei; Platisa, Jelena; Cohen, Lawrence B.; Baker, Bradley J.; Pieribone, Vincent A.

    2013-01-01

    We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms) are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ) less than 6ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9%) is not as large as the Ciona-based ArcLight (~35%), they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals. PMID:24312287

  6. Fluorescent protein voltage probes derived from ArcLight that respond to membrane voltage changes with fast kinetics.

    Directory of Open Access Journals (Sweden)

    Zhou Han

    Full Text Available We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ less than 6 ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9% is not as large as the Ciona-based ArcLight (~35%, they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals.

  7. Association between fasting plasma glucose and high-sensitivity C-reactive protein: gender differences in a Japanese community-dwelling population

    Directory of Open Access Journals (Sweden)

    Takayama Shuzo

    2011-06-01

    Full Text Available Abstract Background High sensitivity C-reactive protein (hsCRP is an acute phase reactant and a sensitive marker of inflammation. Hyperglycemia can potentially promote the production of CRP. The aim of this study was to determine whether increased fasting plasma glucose (FPG levels are associated with elevated hsCRP concentrations by gender. Methods We recruited 822 men (mean age, 61 ± 14 years and 1,097 women (63 ± 12 years during their annual health examination from a single community. We cross-sectionally examined whether FPG levels are associated with hsCRP concentrations, and whether this association is independent of gender, body mass index (BMI and other components of the metabolic syndrome. Results In women only, hsCRP increased significantly and progressively with increasing FPG (r = 0.169, P 2 and higher FPG than in men. Conclusions These results suggested that hsCRP levels increase continuously across the FPG spectrum starting from the lowest FPG in both men and women. However, increase in hsCRP levels was greater in women than men.

  8. Piscine reovirus, but not Jaundice Syndrome, was transmissible to Chinook Salmon, Oncorhynchus tshawytscha (Walbaum), Sockeye Salmon, Oncorhynchus nerka (Walbaum), and Atlantic Salmon, Salmo salar L.

    Science.gov (United States)

    Garver, Kyle A.; Marty, Gary D.; Cockburn, Sarah N.; Richard, Jon; Hawley, Laura M.; Müller, Anita; Thompson, Rachel L.; Purcell, Maureen K.; Saksida, Sonja M.

    2015-01-01

    A Jaundice Syndrome occurs sporadically among sea-pen-farmed Chinook Salmon in British Columbia, the westernmost province of Canada. Affected salmon are easily identified by a distinctive yellow discolouration of the abdominal and periorbital regions. Through traditional diagnostics, no bacterial or viral agents were cultured from tissues of jaundiced Chinook Salmon; however, piscine reovirus (PRV) was identified via RT-rPCR in all 10 affected fish sampled. By histopathology, Jaundice Syndrome is an acute to peracute systemic disease, and the time from first clinical signs to death is likely jaundiced Chinook Salmon, developed no gross or microscopic evidence of jaundice despite persistence of PRV for the 5-month holding period. The results from this study demonstrate that the Jaundice Syndrome was not transmissible by injection of material from infected fish and that PRV was not the sole aetiological factor for the condition. Additionally, these findings showed the Pacific coast strain of PRV, while transmissible, was of low pathogenicity for Atlantic Salmon, Chinook Salmon and Sockeye Salmon.

  9. Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay (NASBA-ELISA).

    Science.gov (United States)

    Zeng, Weiwei; Yao, Wei; Wang, Yingying; Li, Yingying; Bermann, Sven M; Ren, Yan; Shi, Cunbin; Song, Xinjian; Huang, Qiwen; Zheng, Shuchen; Wang, Qing

    2017-05-01

    Grass carp reovirus (GCRV) is the causative agent of the grass carp hemorrhagic disease that has resulted in severe economic losses in the grass carp (Ctenopharyngodon idella) farming industry in China. Early diagnosis and vaccine administration are important priorities for GCRV control. In this study, a nucleic acid sequence-based amplification with enzyme-linked immunosorbent assay (NASBA-ELISA) was developed for to detect genotype II GCRV (GCRV- II). Primers specifically targeting viral RNA genome segment 6 were utilized for amplification in an isothermal digoxigenin-labeling NASBA process, resulting in DIG-labeled RNA amplicons. The amplicons were hybridized to specific biotinylated DNA probes and the products were detected colorimetrically using horseradish peroxidase and a microplate reader. The new method is able to detect GCRV at 14 copies/μL within 5h and had a diagnostic sensitivity and a specificity of 100% when GCRV-II and non-target virus were tested. This NASBA-ELISA was evaluated using a panel of clinical samples (n=103) to demonstrate that it is a rapid, effective and sensitive method for GCRV detection in grass carp aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Proportions of myosin heavy chain mRNAs, protein isoforms and fiber types in the slow and fast skeletal muscles are maintained after alterations of thyroid status in rats.

    Science.gov (United States)

    Soukup, T; Diallo, M

    2015-01-01

    Recently, we have established that slow soleus (SOL) and fast extensor digitorum longus (EDL) muscles of euthyroid (EU) Lewis rats posses the same proportions between their four myosin heavy chain (MyHC) mRNAs, protein isoforms and fiber types as determined by real time RT-PCR, SDS-PAGE and 2-D stereological fiber type analysis, respectively. In the present paper we investigated if these proportions are maintained in adult Lewis rats with hyperthyroid (HT) and hypothyroid (HY) status. Although HT and HY states change MyHC isoform expression, results from all three methods showed that proportion between MyHC mRNA-1, 2a, -2x/d, -2b, protein isoforms MyHC-1, -2a, -2x/d, -2b and to lesser extent also fiber types 1, 2A, 2X/D, 2B were preserved in both SOL and EDL muscles. Furthermore, in the SOL muscle mRNA expression of slow MyHC-1 remained up to three orders higher compared to fast MyHC transcripts, which explains the predominance of MyHC-1 isoform and fiber type 1 even in HT rats. Although HT status led in the SOL to increased expression of MyHC-2a mRNA, MyHC-2a isoform and 2A fibers, it preserved extremely low expression of MyHC-2x and -2b mRNA and protein isoforms, which explains the absence of pure 2X/D and 2B fibers. HY status, on the other hand, almost completely abolished expression of all three fast MyHC mRNAs, MyHC protein isoforms and fast fiber types in the SOL muscle. Our data present evidence that a correlation between mRNA, protein content and fiber type composition found in EU status is also preserved in HT and HY rats.

  11. Profiling hepatic microRNAs in zebrafish: fluoxetine exposure mimics a fasting response that targets AMP-activated protein kinase (AMPK.

    Directory of Open Access Journals (Sweden)

    Paul M Craig

    Full Text Available This study examined the similarities in microRNA profiles between fasted and fluoxetine (FLX exposed zebrafish and downstream target transcripts and biological pathways. Using a custom designed microarray targeting 270 zebrafish miRNAs, we identified 9 differentially expressed miRNAs targeting transcripts in biological pathways associated with anabolic metabolism, such as adipogenesis, cholesterol biosynthesis, triacylglycerol synthesis, and insulin signaling. Exposure of female zebrafish to 540 ng/L FLX, an environmentally relevant concentration and a known metabolic repressor, increased specific miRNAs indicating greater inhibition of these pathways in spite of continued feeding. Further examination revealed two specific miRNAs, dre-let-7d and dre-miR-140-5p, were predicted in silico to bind to a primary regulator of metabolism, adenosine monophosphate-activated protein kinase (AMPK, and more specifically the two isoforms of the catalytic subunit, AMPKα1 and α2, respectively. Real-time analysis of the relative transcript abundance of the α1 and α2 mRNAs indicated a significant inverse relationship between specific miRNA and target transcript. This suggests that AMPK-related pathways may be compromised during FLX exposure as a result of increased miRNA abundance. The mechanism by which FLX regulates miRNA abundance is unknown but may be direct at the liver. The serotonin transporter, slc6a4, is the target of FLX and other selective serotonin reuptake inhibitors (SSRI and it was found to be expressed in the liver, although treatment did not alter expression of this transporter. Exposure to FLX disrupts key hepatic metabolic pathways, which may be indicative of reduced overall fitness and these effects may be linked to specific miRNA abundance. This has important implications for the heath of fish because concentrations of SSRIs in aquatic ecosystems are continually increasing.

  12. A Newly Emergent Turkey Arthritis Reovirus Shows Dominant Enteric Tropism and Induces Significantly Elevated Innate Antiviral and T Helper-1 Cytokine Responses.

    Directory of Open Access Journals (Sweden)

    Tamer A Sharafeldin

    Full Text Available Newly emergent turkey arthritis reoviruses (TARV were isolated from tendons of lame 15-week-old tom turkeys that occasionally had ruptured leg tendons. Experimentally, these TARVs induced remarkable tenosynovitis in gastrocnemius tendons of turkey poults. The current study aimed to characterize the location and the extent of virus replication as well as the cytokine response induced by TARV during the first two weeks of infection. One-week-old male turkeys were inoculated orally with TARV (O'Neil strain. Copy numbers of viral genes were estimated in intestines, internal organs and tendons at ½, 1, 2, 3, 4, 7, 14 days Post inoculation (dpi. Cytokine profile was measured in intestines, spleen and leg tendons at 0, 4, 7 and 14 dpi. Viral copy number peaked in jejunum, cecum and bursa of Fabricius at 4 dpi. Copy numbers increased dramatically in leg tendons at 7 and 14 dpi while minimal copies were detected in internal organs and blood during the same period. Virus was detected in cloacal swabs at 1-2 dpi, and peaked at 14 dpi indicating enterotropism of the virus and its early shedding in feces. Elevation of IFN-α and IFN-β was observed in intestines at 7 dpi as well as a prominent T helper-1 response (IFN-γ at 7 and 14 dpi. IFN-γ and IL-6 were elevated in gastrocnemius tendons at 14 dpi. Elevation of antiviral cytokines in intestines occurred at 7dpi when a significant decline of viral replication in intestines was observed. T helper-1 response in intestines and leg tendons was the dominant T-helper response. These results suggest the possible correlation between viral replication and cytokine response in early infection of TARV in turkeys. Our findings provide novel insights which help elucidate viral pathogenesis in turkey tendons infected with TARV.

  13. Protein Supplementation Does Not Further Increase Latissimus Dorsi Muscle Fiber Hypertrophy after Eight Weeks of Resistance Training in Novice Subjects, but Partially Counteracts the Fast-to-Slow Muscle Fiber Transition

    Directory of Open Access Journals (Sweden)

    Antonio Paoli

    2016-06-01

    Full Text Available The response to resistance training and protein supplementation in the latissimus dorsi muscle (LDM has never been investigated. We investigated the effects of resistance training (RT and protein supplementation on muscle mass, strength, and fiber characteristics of the LDM. Eighteen healthy young subjects were randomly assigned to a progressive eight-week RT program with a normal protein diet (NP or high protein diet (HP (NP 0.85 vs. HP 1.8 g of protein·kg−1·day−1. One repetition maximum tests, magnetic resonance imaging for cross-sectional muscle area (CSA, body composition, and single muscle fibers mechanical and phenotype characteristics were measured. RT induced a significant gain in strength (+17%, p < 0.0001, whole muscle CSA (p = 0.024, and single muscle fibers CSA (p < 0.05 of LDM in all subjects. Fiber isometric force increased in proportion to CSA (+22%, p < 0.005 and thus no change in specific tension occurred. A significant transition from 2X to 2A myosin expression was induced by training. The protein supplementation showed no significant effects on all measured outcomes except for a smaller reduction of 2X myosin expression. Our results suggest that in LDM protein supplementation does not further enhance RT-induced muscle fiber hypertrophy nor influence mechanic muscle fiber characteristics but partially counteracts the fast-to-slow fiber shift.

  14. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin

    2015-04-09

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  15. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin; Parthasarathy, Sudhakar; Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

    2015-01-01

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  16. Functional feeds reduce heart inflammation and pathology in Atlantic Salmon (Salmo salar L. following experimental challenge with Atlantic salmon reovirus (ASRV.

    Directory of Open Access Journals (Sweden)

    Laura Martinez-Rubio

    Full Text Available Heart and Skeletal Muscle Inflammation (HSMI, recently associated with a novel Atlantic salmon reovirus (ASRV, is currently one of the most prevalent inflammatory diseases in commercial Atlantic salmon farms in Norway. Mortality varies from low to 20%, but morbidity can be very high, reducing growth performance and causing considerable financial impact. Clinical symptoms, including myocarditis, myocardial and red skeletal muscle necrosis, correlate with the intensity of the inflammatory response. In the present study, the effects of two functional feeds (FF1 and FF2 were compared to a standard commercial reference feed (ST in Atlantic salmon subjected to an ASRV challenge. The functional feeds had reduced levels of total lipid and digestible energy, and different levels and proportions of long-chain polyunsaturated fatty acids (LC-PUFA. The objective was to determine whether these feeds could provide effective protection by decreasing the inflammatory response associated with HSMI. Histopathology, viral load, fatty acid composition and gene expression of heart tissue were assessed over a period of 16 weeks post-infection with ASRV. The viral load and histopathology scores in heart tissue in response to ASRV infection were reduced in fish fed both functional feeds, with FF1 showing the greatest effect. Microarray hierarchical cluster analysis showed that the functional feeds greatly affected expression of inflammation/immune related genes over the course of the ASRV infection. Viral load correlated with up-regulation of pro-inflammatory genes at the early-mid stages of infection in fish fed the ST diet. Expression of inflammatory genes 16-weeks after ASRV challenge reflected the difference in efficacy between the functional feeds, with fish fed FF1 showing lower expression. Thus, severity of the lesions in heart tissue correlated with the intensity of the innate immune response and was associated with tissue fatty acid compositions. The present

  17. Fast reactors

    International Nuclear Information System (INIS)

    Vasile, A.

    2001-01-01

    Fast reactors have capacities to spare uranium natural resources by their breeding property and to propose solutions to the management of radioactive wastes by limiting the inventory of heavy nuclei. This article highlights the role that fast reactors could play for reducing the radiotoxicity of wastes. The conversion of 238 U into 239 Pu by neutron capture is more efficient in fast reactors than in light water reactors. In fast reactors multi-recycling of U + Pu leads to fissioning up to 95% of the initial fuel ( 238 U + 235 U). 2 strategies have been studied to burn actinides: - the multi-recycling of heavy nuclei is made inside the fuel element (homogeneous option); - the unique recycling is made in special irradiation targets placed inside the core or at its surroundings (heterogeneous option). Simulations have shown that, for the same amount of energy produced (400 TWhe), the mass of transuranium elements (Pu + Np + Am + Cm) sent to waste disposal is 60,9 Kg in the homogeneous option and 204.4 Kg in the heterogeneous option. Experimental programs are carried out in Phenix and BOR60 reactors in order to study the feasibility of such strategies. (A.C.)

  18. Fast ejendom

    DEFF Research Database (Denmark)

    Pagh, Peter

    Bogen omfatter en gennemgang af lovgivning, praksis og teori vedrørende køb af fast ejendom og offentligretlig og privatretlig regulering. Bogen belyser bl.a. de privatretlige emner: købers misligholdelsesbeføjelser, servitutter, naboret, hævd og erstatningsansvar for miljøskader samt den...

  19. Analysis of myofibrillar proteins and transcripts in adult skeletal muscles of the American lobster Homarus americanus: variable expression of myosins, actin and troponins in fast, slow-twitch and slow-tonic fibres.

    Science.gov (United States)

    Medler, Scott; Mykles, Donald L

    2003-10-01

    Skeletal muscles are diverse in their contractile properties, with many of these differences being directly related to the assemblages of myofibrillar isoforms characteristic of different fibers. Crustacean muscles are similar to other muscles in this respect, although the majority of information about differences in muscle organization comes from vertebrate species. In the present study, we examined the correlation between myofibrillar protein isoforms and the patterns of myofibrillar gene expression in fast, slow-phasic (S(1)) and slow-tonic (S(2)) fibers of the American lobster Homarus americanus. SDS-PAGE and western blotting were used to identify isoform assemblages of myosin heavy chain (MHC), P75, troponin T (TnT) and troponin I (TnI). RT-PCR was used to monitor expression of fast and slow (S(1)) MHC, P75 and actin in different fiber types, and the MHC and actin levels were quantified by real-time PCR. Fast and slow fibers from the claw closers predominantly expressed fast and S(1) MHC, respectively, but also lower levels of the alternate MHC. By contrast, fast fibers from the deep abdominal muscle expressed fast MHC exclusively. In addition, slow muscles expressed significantly higher levels of actin than fast fibers. A distal bundle of fibers in the cutter claw closer muscle was found to be composed of a mixture of S(1) and S(2) fibers, many of which possessed a mixture of S(1) and S(2) MHC isoforms. This pattern supports the idea that S(1) and S(2) fibers represent extremes in a continuum of slow muscle phenotype. Overall, these patterns demonstrate that crustacean skeletal muscles cannot be strictly categorized into discrete fiber types, but a muscle's properties probably represent a point on a continuum of fiber types. This trend may result from differences in innervation pattern, as each muscle is controlled by a unique combination of phasic, tonic or both phasic and tonic motor nerves. In this respect, future studies examining how muscle phenotype

  20. Flow cytometric immunobead assay for fast and easy detection of PML-RARA fusion proteins for the diagnosis of acute promyelocytic leukemia

    NARCIS (Netherlands)

    E.H.A. Dekking (E. H A); V.H.J. van der Velden (Vincent); A. Varro (Andras); H. Wai; S. Böttcher (Stephan); M. Kneba (Michael); E. Sonneveld (Edwin); A. Koning; N. Boeckx; N. Van Poecke; P. Lucio (Paulo); A. Mendonça; L. Sedek (Lukasz); T. Szczepanski (Tomasz); T. Kalina (Tomas); V. Kanderová (V.); P.G. Hoogeveen (Patricia); J. Flores-Montero (Juan); C. Chillón (Carmen); A. Orfao (Alberto); J.M.M. Almeida (Julia); P.A.S. Evans; C. Cullen; A.L. Noordijk; P.M. Vermeulen (P.); M.T. de Man (M.); E.P. Dixon (Eric); W.M. Comans-Bitter; J.J.M. van Dongen (Jacques)

    2012-01-01

    textabstractThe PML-RARA fusion protein is found in approximately 97% of patients with acute promyelocytic leukemia (APL). APL can be associated with life-threatening bleeding complications when undiagnosed and not treated expeditiously. The PML-RARA fusion protein arrests maturation of myeloid

  1. Homozygous missense mutation (G56R in glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPI-HBP1 in two siblings with fasting chylomicronemia (MIM 144650

    Directory of Open Access Journals (Sweden)

    Hegele Robert A

    2007-09-01

    Full Text Available Abstract Background Mice with a deleted Gpihbp1 gene encoding glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPI-HBP1 develop severe chylomicronemia. We screened the coding regions of the human homologue – GPIHBP1 – from the genomic DNA of 160 unrelated adults with fasting chylomicronemia and plasma triglycerides >10 mmol/L, each of whom had normal sequence of the LPL and APOC2 genes. Results One patient with severe type 5 hyperlipoproteinemia (MIM 144650, fasting chylomicronemia and relapsing pancreatitis resistant to standard therapy was found to be homozygous for a novel GPIHBP1 missense variant, namely G56R. This mutation was absent from the genomes of 600 control subjects and 610 patients with hyperlipidemia. The GPIHBP1 G56 residue has been conserved throughout evolution and the G56R mutation was predicted to have compromised function. Her homozygous brother also had refractory chylomicronemia and relapsing pancreatitis together with early coronary heart disease. G56R heterozygotes in the family had fasting mild hypertriglyceridemia. Conclusion Thus, a very rare GPIHBP1 missense mutation appears to be associated with severe hypertriglyceridemia and chylomicronemia.

  2. imFASP: An integrated approach combining in-situ filter-aided sample pretreatment with microwave-assisted protein digestion for fast and efficient proteome sample preparation.

    Science.gov (United States)

    Zhao, Qun; Fang, Fei; Wu, Ci; Wu, Qi; Liang, Yu; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

    2016-03-17

    An integrated sample preparation method, termed "imFASP", which combined in-situ filter-aided sample pretreatment and microwave-assisted trypsin digestion, was developed for preparation of microgram and even nanogram amounts of complex protein samples with high efficiency in 1 h. For imFASP method, proteins dissolved in 8 M urea were loaded onto a filter device with molecular weight cut off (MWCO) as 10 kDa, followed by in-situ protein preconcentration, denaturation, reduction, alkylation, and microwave-assisted tryptic digestion. Compared with traditional in-solution sample preparation method, imFASP method generated more protein and peptide identifications (IDs) from preparation of 45 μg Escherichia coli protein sample due to the higher efficiency, and the sample preparation throughput was significantly improved by 14 times (1 h vs. 15 h). More importantly, when the starting amounts of E. coli cell lysate decreased to nanogram level (50-500 ng), the protein and peptide identified by imFASP method were improved at least 30% and 44%, compared with traditional in-solution preparation method, suggesting dramatically higher peptide recovery of imFASP method for trace amounts of complex proteome samples. All these results demonstrate that the imFASP method developed here is of high potential for high efficient and high throughput preparation of trace amounts of complex proteome samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. A Gene Family Coding for Salivary Proteins (SHOT) of the Polyphagous Spider Mite Tetranychus urticae Exhibits Fast Host-Dependent Transcriptional Plasticity.

    Science.gov (United States)

    Jonckheere, Wim; Dermauw, Wannes; Khalighi, Mousaalreza; Pavlidi, Nena; Reubens, Wim; Baggerman, Geert; Tirry, Luc; Menschaert, Gerben; Kant, Merijn R; Vanholme, Bartel; Van Leeuwen, Thomas

    2018-01-01

    The salivary protein repertoire released by the herbivorous pest Tetranychus urticae is assumed to hold keys to its success on diverse crops. We report on a spider mite-specific protein family that is expanded in T. urticae. The encoding genes have an expression pattern restricted to the anterior podocephalic glands, while peptide fragments were found in the T. urticae secretome, supporting the salivary nature of these proteins. As peptide fragments were identified in a host-dependent manner, we designated this family as the SHOT (secreted host-responsive protein of Tetranychidae) family. The proteins were divided in three groups based on sequence similarity. Unlike TuSHOT3 genes, TuSHOT1 and TuSHOT2 genes were highly expressed when feeding on a subset of family Fabaceae, while expression was depleted on other hosts. TuSHOT1 and TuSHOT2 expression was induced within 24 h after certain host transfers, pointing toward transcriptional plasticity rather than selection as the cause. Transfer from an 'inducer' to a 'noninducer' plant was associated with slow yet strong downregulation of TuSHOT1 and TuSHOT2, occurring over generations rather than hours. This asymmetric on and off regulation points toward host-specific effects of SHOT proteins, which is further supported by the diversity of SHOT genes identified in Tetranychidae with a distinct host repertoire.

  4. Ion-Exchange Sample Displacement Chromatography as a Method for Fast and Simple Isolation of Low- and High-Abundance Proteins from Complex Biological Mixtures

    Directory of Open Access Journals (Sweden)

    Martina Srajer Gajdosik

    2014-01-01

    Full Text Available Sample displacement chromatography (SDC in reversed phase and ion-exchange modes was introduced at the end of 1980s. This chromatographic method was first used for preparative purification of synthetic peptides, and subsequently adapted for protein fractionation, mainly in anion-exchange mode. In the past few years, SDC has been successfully used for enrichment of low- and medium-abundance proteins from complex biological fluids on both monolithic and bulk chromatographic supports. If aqueous mobile phase is used with the application of mild chromatographic conditions, isolated proteins are not denatured and can also keep their biological activity. In this paper, the use of SDC in anion-exchange mode on a high-capacity chromatographic resin for separation of proteins from complex biological mixtures such as human plasma is demonstrated. By use of three and more columns coupled in series during sample application, and subsequent parallel elution of detached columns, additional separation of bound proteins was achieved. Highly enriched human serum albumin fraction and a number of physiologically active medium- and low-abundance proteins could be fractionated and detected by electrospray ionization tandem mass spectrometry (ESI-MS/MS and matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS. The use of the aforementioned columns that can be sanitized with 1 M sodium hydroxide for further application of SDC in biotechnology and food technology was discussed.

  5. Skeletal muscle protein synthesis and the abundance of the mRNA translation initiation repressor PDCD4 are inversely regulated by fasting and refeeding in rats.

    Science.gov (United States)

    Zargar, Sana; Moreira, Tracy S; Samimi-Seisan, Helena; Jeganathan, Senthure; Kakade, Dhanshri; Islam, Nushaba; Campbell, Jonathan; Adegoke, Olasunkanmi A J

    2011-06-01

    Optimal skeletal muscle mass is vital to human health, because defects in muscle protein metabolism underlie or exacerbate human diseases. The mammalian target of rapamycin complex 1 is critical in the regulation of mRNA translation and protein synthesis. These functions are mediated in part by the ribosomal protein S6 kinase 1 (S6K1) through mechanisms that are poorly understood. The tumor suppressor programmed cell death 4 (PDCD4) has been identified as a novel substrate of S6K1. Here, we examined 1) the expression of PDCD4 in skeletal muscle and 2) its regulation by feed deprivation (FD) and refeeding. Male rats (~100 g; n = 6) were subjected to FD for 48 h; some rats were refed for 2 h. FD suppressed muscle fractional rates of protein synthesis and Ser(67) phosphorylation of PDCD4 (-50%) but increased PDCD4 abundance (P muscle fractional rates of protein synthesis and reduced PDCD4 abundance relative to FD. Finally, when myoblasts were grown in amino acid- and serum-free medium, phenylalanine incorporation into proteins in cells depleted of PDCD4 more than doubled the values in cells with a normal level of PDCD4 (P skeletal muscle in parallel with the reduction of the abundance of this mRNA translation inhibitor.

  6. Fast tomosynthesis

    International Nuclear Information System (INIS)

    Klotz, E.; Linde, R.; Tiemens, U.; Weiss, H.

    1978-01-01

    A system has been constructed for fast tomosynthesis, whereby X-ray photographs are made of a single layer of an object. Twenty five X-ray tubes illuminate the object simultaneously at different angles. The resulting coded image is decoded by projecting it with a pattern of lenses that have the same form as the pattern of X-ray tubes. The coded image is optically correlated with the pattern of the sources. The scale of this can be adjusted so that the desired layer of the object is portrayed. Experimental results of its use in a hospital are presented. (C.F.)

  7. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. A high-protein diet increases postprandial but not fasting plasma total homocysteine concentrations: a dietary controlled, crossover trial in healthy volunteers

    NARCIS (Netherlands)

    Verhoef, P.; Vliet, van T.; Olthof, M.R.; Katan, M.B.

    2005-01-01

    Background: A high plasma concentration of total homocysteine (tHcy) is associated with increased risk of cardiovascular disease. A high protein intake and hence a high intake of methionine¿the sole dietary precursor of homocysteine¿may raise plasma tHcy concentrations. Objectives: We studied

  9. A high-protein diet increases postprandial but not fasting plasma total homocysteine concentrations: A dietary controlled, crossover trial in healthy volunteers

    NARCIS (Netherlands)

    Verhoef, P.; Vliet, T. van; Olthof, M.R.; Katan, M.B.

    2005-01-01

    Background: A high plasma concentration of total homocysteine (tHcy) is associated with increased risk of cardiovascular disease. A high protein intake and hence a high intake of methionine-the sole dietary precursor of homocysteine-may raise plasma tHcy concentrations. Objectives: We studied

  10. A high-protein diet increases postprandial but not fasting plasma total homocysteine concentrations : A dietary controlled, crossover trial in healthy volunteers

    NARCIS (Netherlands)

    Verhoef, Petra; Van Vliet, Trinette; Olthof, Margreet R.; Katan, Martijn B.

    2005-01-01

    Background: A high plasma concentration of total homocysteine (tHcy) is associated with increased risk of cardiovascular disease. A high protein intake and hence a high intake of methionine-the sole dietary precursor of homocysteine-may raise plasma tHcy concentrations. Objectives: We studied

  11. Genetic encoding of a bicyclo[6.1.0]nonyne-charged amino acid enables fast cellular protein imaging by metal-free ligation.

    Science.gov (United States)

    Borrmann, Annika; Milles, Sigrid; Plass, Tilman; Dommerholt, Jan; Verkade, Jorge M M; Wiessler, Manfred; Schultz, Carsten; van Hest, Jan C M; van Delft, Floris L; Lemke, Edward A

    2012-09-24

    Visualizing biomolecules by fluorescent tagging is a powerful method for studying their behaviour and function inside cells. We prepared and genetically encoded an unnatural amino acid (UAA) that features a bicyclononyne moiety. This UAA offered exceptional reactivity in strain-promoted azide-alkyne cycloadditions. Kinetic measurements revealed that the UAA reacted also remarkably fast in the inverse-electron-demand Diels-Alder cycloaddition with tetrazine-conjugated dyes. Genetic encoding of the new UAA inside mammalian cells and its subsequent selective labeling at low dye concentrations demonstrate the usefulness of the new amino acid for future imaging studies. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Enteric virus with segmented double-stranded RNA genome in broiler chicken: Rotavirus, Reovirus and Picobirnavirus / Virus entéricos RNA fita dupla, segmentado, em aves: Rotavírus, Reovírus e Picobirnavírus

    Directory of Open Access Journals (Sweden)

    Amauri Alcindo Alfieri

    2000-04-01

    Full Text Available Enteric infections account for considerable economic losses to the poultry industry through weight loss, low food conversion, direct and indirect expenses with treatments and increased death rates. Poultry intestinal pathologies, either with local or general manifestations, can be caused by bacteria, protozoa or virus, acting alone or in association. Regarding viral etiology, several genera have been isolated from poultry with enteric disease. However, two genera from the Reoviridae family, the rotavirus and the reovirus are found more frequently in broiler chicken and/or laying hen feces. These viruses have been associated with clinical signs of enteritis in most epidemiological research. This revision aims to present some topics on the etiological agents (rotavirus, reovirus and picobirnavirus, the clinical disease and the diagnostic and control methods and prophylaxis of the infection.As infecções entéricas são responsáveis por consideráveis prejuízos econômicos à indústria avícola representados por perda de peso, baixa conversão alimentar, custos diretos e indiretos com tratamentos e por aumento na taxa de mortalidade. As patologias intestinais em aves, tanto com manifestação local quanto geral, podem ser determinadas por bactérias, protozoários e vírus, atuando de forma isolada ou em associação. Com relação a etiologia virai, vários gêneros têm sido isolados a partir de aves com enteropatias. Porém, dois gêneros na família Reoviridae, o rotavírus e o reovírus são encontrados com maior freqüência em fezes de frangos de corte e/ou galinhas poedeiras. Na maioria dos inquéritos epidemiológicos esses vírus estão associados a sinais clínicos de enterite. Esta revisão tem por objetivo apresentar alguns tópicos relativos aos agentes etiológicos (Rotavírus, Reovírus e Picobirnavírus, à doença clínica e aos métodos de diagnóstico, controle e profilaxia da infecção.

  13. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  14. Fast Convolution Module (Fast Convolution Module)

    National Research Council Canada - National Science Library

    Bierens, L

    1997-01-01

    This report describes the design and realisation of a real-time range azimuth compression module, the so-called 'Fast Convolution Module', based on the fast convolution algorithm developed at TNO-FEL...

  15. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  16. Fasting and rheumatic diseases

    OpenAIRE

    Mohammad Hassan Jokar

    2015-01-01

    Fasting is one of the important religious practices of Muslims, in which the individuals abstain from eating and drinking from dawn to sunset. Fasting is not obligatory or even not allowed, in case it causes health problems to the fasting individual. Rheumatic diseases are a major group of chronic diseases which can bring about numerous problems while fasting. The aim of this article is to review the impact of Islamic fasting on rheumatic patients, based on the scientific evidences.

  17. A prospective audit of preprocedural fasting practices on a transplant ward: when fasting becomes starving.

    Science.gov (United States)

    Vidot, Helen; Teevan, Kate; Carey, Sharon; Strasser, Simone; Shackel, Nicholas

    2016-03-01

    To investigate the prevalence and duration of preprocedural medically ordered fasting during a period of hospitalisation in an Australian population of patients with hepatic cirrhosis or following liver transplantation and to identify potential solutions to reduce fasting times. Protein-energy malnutrition is a common finding in patients with hepatic cirrhosis and can impact significantly on survival and quality of life. Protein and energy requirements in patients with cirrhosis are higher than those of healthy individuals. A significant feature of cirrhosis is the induction of starvation metabolism following seven to eight hours of food deprivation. Many investigative and interventional procedures for patients with cirrhosis necessitate a period of fasting to comply with anaesthesia guidelines. An observational study of the fasting episodes for 34 hospitalised patients with hepatic cirrhosis or following liver transplantation. Nutritional status was estimated using subjective global assessment and handgrip strength. The prevalence and duration of fasting practices for diagnostic or investigational procedures were estimated using electronic records and patient notes. Thirty-three patients (97%) were malnourished. Twenty-two patients (65%) were fasted during the observation period. There were 43 occasions of fasting with a median fasting time of 13·5 hours. On 40 occasions fasting times exceeded the maximum six-hour guideline recommended prior to the administration of anaesthesia by the majority of Anaesthesiology Societies. The majority of procedures (77%) requiring fasting occurred after midday. Eating breakfast on the day of the procedure reduced fasting time by 45%. Medically ordered preprocedural fasting times almost always exceed existing guidelines in this nutritionally compromised group. Adherence to fasting guidelines and eating breakfast before the procedure can reduce fasting times significantly and avoid the potential induction of starvation metabolism

  18. HCUP Fast Stats

    Data.gov (United States)

    U.S. Department of Health & Human Services — HCUP Fast Stats provides easy access to the latest HCUP-based statistics for health information topics. HCUP Fast Stats uses visual statistical displays in...

  19. Fast food (image)

    Science.gov (United States)

    Fast foods are quick, reasonably priced, and readily available alternatives to home cooking. While convenient and economical for a busy lifestyle, fast foods are typically high in calories, fat, saturated fat, ...

  20. Fast food tips (image)

    Science.gov (United States)

    ... challenge to eat healthy when going to a fast food place. In general, avoiding items that are deep ... challenge to eat healthy when going to a fast food place. In general, avoiding items that are deep ...

  1. Physiology of Ramadan fasting

    OpenAIRE

    Shokoufeh Bonakdaran

    2016-01-01

    Considering the emphasis of Islam on the importance of fasting, Muslims attempt to fast from dawn until sunset during the holy month of Ramadan. Fasting is associated with several benefits for normal and healthy individuals. However, it could pose high risks to the health of diabetic patients due to certain physiological changes. This study aimed to compare the physiological changes associated with fasting in healthy individuals and diabetic patients during Ramadan. Furthermore, we reviewed t...

  2. The prototype fast reactor

    International Nuclear Information System (INIS)

    Broomfield, A.M.

    1985-01-01

    The paper concerns the Prototype Fast Reactor (PFR), which is a liquid metal cooled fast reactor power station, situated at Dounreay, Scotland. The principal design features of a Fast Reactor and the PFR are given, along with key points of operating history, and health and safety features. The role of the PFR in the development programme for commercial reactors is discussed. (U.K.)

  3. The fast reactor

    International Nuclear Information System (INIS)

    1980-02-01

    The subject is discussed as follows: brief description of fast reactors; advantage in conserving uranium resources; experience, in UK and elsewhere, in fast reactor design, construction and operation; safety; production of plutonium, security aspects; consideration of future UK fast reactor programme. (U.K.)

  4. Ramadan, fasting and pregnancy

    DEFF Research Database (Denmark)

    Ahmed, Urfan Zahoor; Lykke, Jacob Alexander

    2014-01-01

    In Islam, the month of Ramadan is a period of fasting lasting 29 or 30 days. Epidemiological studies among Muslims in Denmark have not been conducted, but studies show, that fasting among pregnant Muslim women is common. Fasting does not increase the risk of growth restriction or preterm delivery...

  5. Ramadan, fasting and pregnancy

    DEFF Research Database (Denmark)

    Ahmed, Urfan Zahoor; Lykke, Jacob Alexander

    2014-01-01

    In Islam, the month of Ramadan is a period of fasting lasting 29 or 30 days. Epidemiological studies among Muslims in Denmark have not been conducted, but studies show, that fasting among pregnant Muslim women is common. Fasting does not increase the risk of growth restriction or preterm delivery......, but there are reports of decreased foetal movements. Furthermore, the fasting may have long-term health consequences for the offspring, especially when they reach their middle age. According to Islam and the interpretation, pregnant and breast-feeding women are allowed to postpone the fasting of the month of Ramadan...

  6. Ramadan, faste og graviditet

    DEFF Research Database (Denmark)

    Ahmed, Urfan Zahoor; Lykke, Jacob Alexander

    2014-01-01

    In Islam, the month of Ramadan is a period of fasting lasting 29 or 30 days. Epidemiological studies among Muslims in Denmark have not been conducted, but studies show, that fasting among pregnant Muslim women is common. Fasting does not increase the risk of growth restriction or preterm delivery......, but there are reports of decreased foetal movements. Furthermore, the fasting may have long-term health consequences for the offspring, especially when they reach their middle age. According to Islam and the interpretation, pregnant and breast-feeding women are allowed to postpone the fasting of the month of Ramadan...

  7. Feasibility of protein-sparing modified fast by tube (ProMoFasT) in obesity treatment: a phase II pilot trial on clinical safety and efficacy (appetite control, body composition, muscular strength, metabolic pattern, pulmonary function test).

    Science.gov (United States)

    Sukkar, S G; Signori, A; Borrini, C; Barisione, G; Ivaldi, C; Romeo, C; Gradaschi, R; Machello, N; Nanetti, E; Vaccaro, A L

    2013-01-01

    Anecdotal data in the last few years suggest that protein-sparing modified diet (PSMF) delivered by naso-gastric tube enteral (with continuous feeding) could attain an significant weight loss and control of appetite oral feeding, but no phase II studies on safety and efficacy have been done up to now. To verify the safety and efficacy of a protein-sparing modified fast administered by naso-gastric tube (ProMoFasT) for 10 days followed by 20 days of a low-calorie diet, in patients with morbid obesity (appetite control, fat free mass maintenance, pulmonary function tests and metabolic pattern, side effects), 26 patients with a BMI ≥30 kg/m 2 have been selected. The patients had to follow a protein-sparing fast by enteral nutrition (ProMoFasT) for 24 h/day, for 10 days followed by 20 days of low-calorie diet (LCD). The endpoint was represented by body weight, BMI, abdominal circumference, Haber's appetite test, body composition by body impedance assessment (BIA), handgrip strength test, metabolic pattern, pulmonary function test. Safety was assessed by evaluation of complications and side effects of PSMF and/or enteral nutrition. In this report the results on safety and efficacy are described after 10 and 30 days of treatment. After the recruiting phase, a total of 22 patients out of 26 enrolled [14 (63.6 %) females] were evaluated in this study. Globally almost all clinical parameters changed significantly during first 10 days. Total body weight significantly decreased after 10 days (∆-6.1 ± 2; p  < 0.001) and this decrease is maintained in the following 20 days of LCD (∆ = -5.88 ± 1.79; p  < 0.001). Also the abdominal circumference significantly decreased after 10 days [median (range): -4.5 (-30 to 0); p  < 0.001] maintained then in the following 20 days of LCD [median (range) = -7 (-23.5 to -2); p  < 0.001]. All BIA parameters significantly changed after 10 and 30 days from baseline. All parameters except BF had a significant

  8. The fast breeder reactor

    International Nuclear Information System (INIS)

    Collier, J.

    1990-01-01

    The arguments for and against the fast breeder reactor are debated. The case for the fast reactor is that the world energy demand will increase due to increasing population over the next forty years and that the damage to the global environment from burning fossil fuels which contribute to the greenhouse effect. Nuclear fission is the only large scale energy source which can achieve a cut in the use of carbon based fuels although energy conservation and renewable sources will also be important. Fast reactors produce more energy from uranium than other types of (thermal) reactors such as AGRs and PWRs. Fast reactors would be important from about 2020 onwards especially as by then many thermal reactors will need to be replaced. Fast reactors are also safer than normal reactors. The arguments against fast reactors are largely economic. The cost, especially the capital cost is very high. The viability of the technology is also questioned. (UK)

  9. The fast breeder reactor

    International Nuclear Information System (INIS)

    Davis, D.A.; Baker, M.A.W.; Hall, R.S.

    1990-01-01

    Following submission of written evidence, the Energy Committee members asked questions of three witnesses from the Central Electricity Generating Board and Nuclear Electric (which will be the government owned company running nuclear power stations after privatisation). Both questions and answers are reported verbatim. The points raised include where the responsibility for the future fast reactor programme should lie, with government only or with private enterprise or both and the viability of fast breeder reactors in the future. The case for the fast reactor was stated as essentially strategic not economic. This raised the issue of nuclear cost which has both a construction and a decommissioning element. There was considerable discussion as to the cost of building a European Fast reactor and the cost of the electricity it would generate compared with PWR type reactors. The likely demand for fast reactors will not arrive for 20-30 years and the need to build a fast reactor now is questioned. (UK)

  10. Fast reactors worldwide

    International Nuclear Information System (INIS)

    Hall, R.S.; Vignon, D.

    1985-01-01

    The paper concerns the evolution of fast reactors over the past 30 years, and their present status. Fast reactor development in different countries is described, and the present position, with emphasis on cost reduction and collaboration, is examined. The French development of the fast breeder type reactor is reviewed, and includes: the acquisition of technical skills, the search for competitive costs and the spx2 project, and more advanced designs. Future prospects are also discussed. (U.K.)

  11. Fast breeder reactors

    International Nuclear Information System (INIS)

    Heinzel, V.

    1975-01-01

    The author gives a survey of 'fast breeder reactors'. In detail the process of breeding, the reasons for the development of fast breeders, the possible breeder reactors, the design criteria, fuels, cladding, coolant, and safety aspects are reported on. Design data of some experimental reactors already in operation are summarized in stabular form. 300 MWe Prototype-Reactors SNR-300 and PFR are explained in detail and data of KWU helium-cooled fast breeder reactors are given. (HR) [de

  12. Fast wave current drive

    International Nuclear Information System (INIS)

    Goree, J.; Ono, M.; Colestock, P.; Horton, R.; McNeill, D.; Park, H.

    1985-07-01

    Fast wave current drive is demonstrated in the Princeton ACT-I toroidal device. The fast Alfven wave, in the range of high ion-cyclotron harmonics, produced 40 A of current from 1 kW of rf power coupled into the plasma by fast wave loop antenna. This wave excites a steady current by damping on the energetic tail of the electron distribution function in the same way as lower-hybrid current drive, except that fast wave current drive is appropriate for higher plasma densities

  13. Fast multichannel analyser

    Energy Technology Data Exchange (ETDEWEB)

    Berry, A; Przybylski, M M; Sumner, I [Science Research Council, Daresbury (UK). Daresbury Lab.

    1982-10-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10/sup 7/ s/sup -1/ has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format.

  14. A fast multichannel analyser

    International Nuclear Information System (INIS)

    Berry, A.; Przybylski, M.M.; Sumner, I.

    1982-01-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10 7 s -1 has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format. (orig.)

  15. Islamic Fasting and Diabetes

    Directory of Open Access Journals (Sweden)

    Fereidoun Azizi

    2013-07-01

    Full Text Available The aim of this article is to review health-related aspects of Ramadan fasting in normal individuals and diabetics. During fasting days of Ramadan, glucose homeostasis is maintained by meal taken bepore dawn and by liver glycogen stores. Changes in serum lipids are variable and defend on the quality and quantity of food consumption and changes in weight. Compliant, well controlled type 2 diabetics may observe Ramadan fasting; but fasting is not recommended for type 1, non complaint, poorly controlled and pregnant diabetics. Although Ramadan fasting is safe for all healthy individuals and well controlled diabetics, those with uncontrolled diabetics and diabetics with complications should consult physicians and follow scientific recommendations.

  16. Fast Spectrum Reactors

    CERN Document Server

    Todd, Donald; Tsvetkov, Pavel

    2012-01-01

    Fast Spectrum Reactors presents a detailed overview of world-wide technology contributing to the development of fast spectrum reactors. With a unique focus on the capabilities of fast spectrum reactors to address nuclear waste transmutation issues, in addition to the well-known capabilities of breeding new fuel, this volume describes how fast spectrum reactors contribute to the wide application of nuclear power systems to serve the global nuclear renaissance while minimizing nuclear proliferation concerns. Readers will find an introduction to the sustainable development of nuclear energy and the role of fast reactors, in addition to an economic analysis of nuclear reactors. A section devoted to neutronics offers the current trends in nuclear design, such as performance parameters and the optimization of advanced power systems. The latest findings on fuel management, partitioning and transmutation include the physics, efficiency and strategies of transmutation, homogeneous and heterogeneous recycling, in addit...

  17. Fast ejendom III

    DEFF Research Database (Denmark)

    Munk-Hansen, Carsten

    Bogen er det tredje bind af tre planlagte bind om fast ejendom: I Overdragelsen, II Bolighandlen og III Ejerbeføjelsen. Fremstillingens giver et grundigt overblik over centrale områder af en omfattende regulering af fast ejendom, med angivelse af litteratur, hvor læseren kan søge yderligere...... oplysning. En ejer af fast ejendom er på særdeles mange områder begrænset i sin råden sammenlignet med ejeren af et formuegode i almindelighed. Fremstillingen tager udgangspunkt i ejerens perspektiv (fremfor samfundets eller myndighedernes). Både den privatretlige og offentligretlige regulering behandles......, eksempelvis ejendomsdannelsen, servitutter, naboretten, hævd, zoneinddelingen, den fysiske planlægning, beskyttelse af natur, beskyttelse af kultur, forurening fra fast ejendom, erstatning for forurening, jordforurening, ekspropriation, byggeri og adgang til fast ejendom....

  18. Fast fission phenomena

    International Nuclear Information System (INIS)

    Gregoire, Christian.

    1982-03-01

    Experimental studies of fast fission phenomena are presented. The paper is divided into three parts. In the first part, problems associated with fast fission processes are examined in terms of interaction potentials and a dynamic model is presented in which highly elastic collisions, the formation of compound nuclei and fast fission appear naturally. In the second part, a description is given of the experimental methods employed, the observations made and the preliminary interpretation of measurements suggesting the occurence of fast fission processes. In the third part, our dynamic model is incorporated in a general theory of the dissipative processes studied. This theory enables fluctuations associated with collective variables to be calculated. It is applied to highly inelastic collisions, to fast fission and to the fission dynamics of compound nuclei (for which a schematic representation is given). It is with these calculations that the main results of the second part can be interpreted [fr

  19. Fast and Accurate Identification of Cross-Linked Peptides for the Structural Analysis of Large Protein Complexes and Elucidation of Interaction Networks. / Tahir, Salman; Bukowski-Wills, Jimi-Carlo; Rasmussen, Morten; Rappsilber, Juri

    DEFF Research Database (Denmark)

    Rasmussen, Morten

    to investigate protein structure and protein-protein interactions. When applied to single proteins or small purified protein complexes, this methodology works well. However certain challenges arise when applied to more complex samples. One of the main problems is the combinatorial increase in the search space...... simplify a spectrum because we remove all peaks that are accounted for by the fragmentation of peptide one. This approach is highly sensitive and scales well as revealed by searching our data of synthetic cross-links against a large sequence database. Currently, against a protein database of >1300 proteins...... a spectrum is searched in 0.35 seconds - a vast improvement when compared to the exhaustive search method of combining every potential cross-link for each spectrum(60 hours). In fact the search time is comparable, if not better, than existing linear search engines. Furthermore, we auto-validate the results...

  20. The N-Terminal of Aquareovirus NS80 Is Required for Interacting with Viral Proteins and Viral Replication.

    Directory of Open Access Journals (Sweden)

    Jie Zhang

    Full Text Available Reovirus replication and assembly occurs within viral inclusion bodies that formed in specific intracellular compartments of cytoplasm in infected cells. Previous study indicated that aquareovirus NS80 is able to form inclusion bodies, and also can retain viral proteins within its inclusions. To better understand how NS80 performed in viral replication and assembly, the functional regions of NS80 associated with other viral proteins in aquareovirus replication were investigated in this study. Deletion mutational analysis and rotavirus NSP5-based protein association platform were used to detect association regions. Immunofluorescence images indicated that different N-terminal regions of NS80 could associate with viral proteins VP1, VP4, VP6 and NS38. Further co-immunoprecipitation analysis confirmed the interaction between VP1, VP4, VP6 or NS38 with different regions covering the N-terminal amino acid (aa, 1-471 of NS80, respectively. Moreover, removal of NS80 N-terminal sequences required for interaction with proteins VP1, VP4, VP6 or NS38 not only prevented the capacity of NS80 to support viral replication in NS80 shRNA-based replication complementation assays, but also inhibited the expression of aquareovirus proteins, suggesting that N-terminal regions of NS80 are necessary for viral replication. These results provided a foundational basis for further understanding the role of NS80 in viral replication and assembly during aquareovirus infection.

  1. Fast Breeder Reactor studies

    International Nuclear Information System (INIS)

    Till, C.E.; Chang, Y.I.; Kittel, J.H.; Fauske, H.K.; Lineberry, M.J.; Stevenson, M.G.; Amundson, P.I.; Dance, K.D.

    1980-07-01

    This report is a compilation of Fast Breeder Reactor (FBR) resource documents prepared to provide the technical basis for the US contribution to the International Nuclear Fuel Cycle Evaluation. The eight separate parts deal with the alternative fast breeder reactor fuel cycles in terms of energy demand, resource base, technical potential and current status, safety, proliferation resistance, deployment, and nuclear safeguards. An Annex compares the cost of decommissioning light-water and fast breeder reactors. Separate abstracts are included for each of the parts

  2. Fast track-hoftealloplastik

    DEFF Research Database (Denmark)

    Hansen, Torben Bæk; Gromov, Kirill; Kristensen, Billy B

    2017-01-01

    Fast-track surgery implies a coordinated perioperative approach aimed at reducing surgical stress and facilitating post-operative recovery. The fast-track programme has reduced post-operative length of stay and has led to shorter convalescence with more rapid functional recovery and decreased...... morbidity and mortality in total hip arthroplasty. It should now be a standard total hip arthroplasty patient pathway, but fine tuning of the multiple factors in the fast-track pathway is still needed in patients with special needs or high comorbidity burden....

  3. Fast Breeder Reactor studies

    Energy Technology Data Exchange (ETDEWEB)

    Till, C.E.; Chang, Y.I.; Kittel, J.H.; Fauske, H.K.; Lineberry, M.J.; Stevenson, M.G.; Amundson, P.I.; Dance, K.D.

    1980-07-01

    This report is a compilation of Fast Breeder Reactor (FBR) resource documents prepared to provide the technical basis for the US contribution to the International Nuclear Fuel Cycle Evaluation. The eight separate parts deal with the alternative fast breeder reactor fuel cycles in terms of energy demand, resource base, technical potential and current status, safety, proliferation resistance, deployment, and nuclear safeguards. An Annex compares the cost of decommissioning light-water and fast breeder reactors. Separate abstracts are included for each of the parts.

  4. Effect of fasting on renal physiology

    OpenAIRE

    Achraf Hendawy

    2014-01-01

    Total abstention from food and water from sunrise to sunset during the month of Ramadan, is practiced by hundreds of millions of Muslims throughout the world. This pattern of fasting during Ramadan is different from the usual fasting as people are allowed to eat and drink between sunset and dawn but not after dawn. The amount and type of food (rich in protein, fat and sugar) eaten during the night may also be significantly different to that usually consumed during the rest of the year, while ...

  5. FastStats: Measles

    Science.gov (United States)

    ... Women’s Health State and Territorial Data Reproductive Health Contraceptive Use Infertility Reproductive Health Notice Regarding FastStats Mobile ... measles, mumps, rubella: 91.9% (2015) Percent of adolescents aged 13-17 years vaccinated against measles, mumps, ...

  6. Fast neutrons dosimetry

    International Nuclear Information System (INIS)

    Rzyski, B.M.

    1977-01-01

    A proton recoil technique has been developed for inducing thermoluminescence with incident fast neutrons. CaF 2 was used as the TL phosphor, and cane sugar and polyethylene were used as proton radiators. The phosphor and the hydrogeneous material powders were well mixed, encapsulated in glass tubes and exposed to Am-Be sources, resulting in recoils from incident fast neutrons of energy between 0,25 and 11,25 MeV. The intrinsic response of pure CaF 2 to fast neutrons without a hydrogeneous radiator was checked by using LiF (TLD-700). Glow curves were recorded from room temperature up to 350 0 C after different doses of neutrons and gamma rays of 60 Co. First collision dose due to fast neutrons in tissue like materials such as cane sugar and polyethylene was also calculated [pt

  7. Dounreay fast reactor

    International Nuclear Information System (INIS)

    Maclennan, R.; Eggar, T.; Skeet, T.

    1992-01-01

    The short debate which followed a private notice question asking for a statement on Government policy on the future of the European fast breeder nuclear research programme is reported verbatim. In response to the question, the Minister for Energy said that the Government had decided in 1988 that the Dounreay prototype fast reactor would close in 1994. That decision had been confirmed. Funding of fast breeder research and development beyond 1993 is not a priority as commercialization is not expected until well into the next century. Dounreay will be supported financially until 1994 and then for its subsequent decommissioning and reprocessing of spent fuel. The debate raised issues such as Britain losing its lead in fast breeder research, loss of jobs and the Government's nuclear policy in general. However, the Government's position was that the research had reached a stage where it could be left and returned to in the future. (UK)

  8. CMS Fast Facts

    Data.gov (United States)

    U.S. Department of Health & Human Services — CMS has developed a new quick reference statistical summary on annual CMS program and financial data. CMS Fast Facts includes summary information on total program...

  9. Brug af faste vendinger

    DEFF Research Database (Denmark)

    Bergenholtz, Henning; Bjærge, Esben

    Ordbogen indelholder tekstproduktionsangivelser til ca. 17.000 idiomer, ordsprog, bevingede ord og andre faste vendinger. Det drejer sig bl.a. om angivelser til betydningen, grammatik, kollokationer, eksempler, synonymer og antonymer....

  10. Fasting and Urinary Stones

    Directory of Open Access Journals (Sweden)

    Ali Shamsa

    2013-11-01

    Full Text Available Introduction: Fasting is considered as one of the most important practices of Islam, and according to Prophet Mohammad, fasting is obligatory upon Muslims. The aim of this study is to evaluate the effects of fasting on urinary stones. Materials and Methods: Very few studies have been carried out on urinary stones and the effect of Ramadan fasting. The sources of the present study are Medline and articles presented by local and Muslim researchers. Meanwhile, since we are acquainted with three well-known researchers in the field of urology, we contacted them via email and asked for their professional opinions. Results: The results of studies about the relationship of urinary stones and their incidence in Ramadan are not alike, and are even sometimes contradictory. Some believe that increased incidence of urinary stones in Ramadan is related not to fasting, but to the rise of weather temperature in hot months, and an increase in humidity. Conclusion: Numerous biological and behavioral changes occur in people who fast in Ramadan and some researchers believe that urinary stone increases during this month.

  11. Fast form alpha-2-macroglobulin

    DEFF Research Database (Denmark)

    Biltoft, Daniel; Gram, Jørgen Brodersen; Larsen, Anette

    2017-01-01

    Objectives: Investigation of the blood compatibility requires a number of sensitive assays to quantify the activation of the blood protein cascades and cells induced by biomaterials. A global assay measuring the blood compatibility of biomaterials could be a valuable tool in such regard....... In this study, we investigated whether an enzyme-linked immunosorbent assay (ELISA), that specifically measures the electrophoretic "fast form" of α2-macroglobulin (F-α2M), could be a sensitive and global marker for activation of calcium dependent and in-dependent proteases in plasma exposed to biomaterials...... in vitro. Methods: A F-α2M specific monoclonal antibody was generated and applied in an ELISA setup. Using the F-α2M ELISA, we investigated activation of calcium dependent and in-dependent proteases by polyvinylchloride (n=10), polytetrafluoroethylene (n=10) and silicone (n=10) tubings as well as glass...

  12. Fast breeder reactors

    International Nuclear Information System (INIS)

    Waltar, A.E.; Reynolds, A.B.

    1981-01-01

    This book describes the major design features of fast breeder reactors and the methods used for their design and analysis. The foremost objective of this book is to fulfill the need for a textbook on Fast Breeder Reactor (FBR) technology at the graduate level or the advanced undergraduate level. It is assumed that the reader has an introductory understanding of reactor theory, heat transfer, and fluid mechanics. The book is expected to be used most widely for a one-semester general course on fast breeder reactors, with the extent of material covered to vary according to the interest of the instructor. The book could also be used effectively for a two-quarter or a two-semester course. In addition, the book could serve as a text for a course on fast reactor safety since many topics other than those appearing in the safety chapters relate to FBR safety. Methodology in fast reactor design and analysis, together with physical descriptions of systems, is emphasized in this text more than numerical results. Analytical and design results continue to change with the ongoing evolution of FBR design whereas many design methods have remained fundamentally unchanged for a considerable time

  13. Fast reactor programme

    International Nuclear Information System (INIS)

    Plakman, J.C.

    1982-01-01

    This progress report summarizes the fast reactor research carried out by ECN during the period covering the year 1980. This research is mainly concerned with the cores of sodium-cooled breeders, in particular the SNR-300, and its related safety aspects. It comprises six items: A programme to determine relevant nuclear data of fission- and corrosion-products; A fuel performance programme comprising in-pile cladding failure experiments and a study of the consequences of loss-of-cooling and overpower; Basic research on fuel; Investigation of the changes in the mechanical properties of austenitic stainless steel DIN 1.4948 due to fast neutron doses, this material has been used in the manufacture of the reactor vessel and its internal components; Study of aerosols which could be formed at the time of a fast reactor accident and their progressive behaviour on leaking through cracks in the concrete containment; Studies on heat transfer in a sodium-cooled fast reactor core. As fast breeders operate at high power densities, an accurate knowledge of the heat transfer phenomena under single-phase and two-phase conditions is sought. (Auth.)

  14. The fast breeder reactor

    International Nuclear Information System (INIS)

    Patterson, W.

    1990-01-01

    The author criticises the United Kingdom Atomic Energy Authority's fast breeder reactor programme in his evidence to the House of Commons Select Committee on Energy in January 1990. He argues for power generation by renewable means and greater efficiency in the use rather than in the generation of electricity. He refutes the arguments for nuclear power on the basis of reduced global warming as he claims support technology produces significant amounts of carbon dioxide in any case. Serious doubts are raised about the costs of a fast breeder reactor programme compared to, say, generation by pressurised water reactors. The idea of a uranium scarcity in several decades is also refuted. The reliability of fast breeder reactor technology is called into question. He argues against reprocessing plutonium for economic, health and safety reasons. (UK)

  15. The fast code

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, L.N.; Wilson, R.E. [Oregon State Univ., Dept. of Mechanical Engineering, Corvallis, OR (United States)

    1996-09-01

    The FAST Code which is capable of determining structural loads on a flexible, teetering, horizontal axis wind turbine is described and comparisons of calculated loads with test data are given at two wind speeds for the ESI-80. The FAST Code models a two-bladed HAWT with degrees of freedom for blade bending, teeter, drive train flexibility, yaw, and windwise and crosswind tower motion. The code allows blade dimensions, stiffnesses, and weights to differ and models tower shadow, wind shear, and turbulence. Additionally, dynamic stall is included as are delta-3 and an underslung rotor. Load comparisons are made with ESI-80 test data in the form of power spectral density, rainflow counting, occurrence histograms, and azimuth averaged bin plots. It is concluded that agreement between the FAST Code and test results is good. (au)

  16. Fast harmonic field mapper

    International Nuclear Information System (INIS)

    Au, R.; Fowler, M.; Hanawa, H.; Riedel, J.; Qua, Z.G.

    1984-01-01

    In early 1983 it was decided to mount coils on arms separated by 120 degrees and buck them out so that the third harmonic dphi/dt component would be cancelled and thus the first and second field harmonics could be very accurately measured. The original intention was to do as others had done, namely, use fast ADC's to read the voltages, and computer process the result to get the Fourier components. However, because of the 100 to 1 dynamic range of the fast ADC's and the likelihood that noise would be a problem, the authors decided to do things differently. Using a fast Fourier transform analyzer was considered, but this instrument is very expensive, so they decided to use a completely electronic analog approach: The authors decided to use active bandpass filters to render the harmonic components

  17. Fast beam radiofrequency spectroscopy

    International Nuclear Information System (INIS)

    Pipkin, F.M.

    1983-01-01

    The combination of a fast atom or ion beam derived from a small accelerator with radiofrequency spectroscopy methods provides a powerful method for measuring the fine structure of atomic and molecular systems. The fast beam makes possible measurements in which two separated oscillatory fields are used to obtain resonance lines whose widths are less than the natural line width due to the lifetimes of the states. The separated oscillatory field lines have, in addition, a number of features which make possible measurements with greater precision and less sensitivity to systematic errors. The fast beam also makes accessible multiple photon radiofrequency transitions whose line width is intrinsically narrower than that of the single photon transitions and which offer great potential for high precision measurements. This report focuses on the techniques and their promise. Recent measurements of the fine structure of H and He + are used as illustrations

  18. The fast breeder reactor

    International Nuclear Information System (INIS)

    Keck, O.

    1984-01-01

    Nowadays the fast-breeder reactor is a negative symbol of advanced technology which is getting out of control and, due to its complexity, is incomprehensible for politicians and therefore by-passes the established order. The author lists the most important decisions over state aid to the fast-breeder-reactors up until the mid-seventies and uses documents from the appropriate advisory bodies as reference. He was also aided by interviews with those directly involved with the project. The empirical facts forces us to discard our traditional view of the relationship between state and industry with regard to advanced technology. The author explains that it is impossible to find any economic value in the fast-breeder reactor. The insight gained through this project allows him to draw conclusions which apply to all aspects of state aid to advanced technology. (orig.) [de

  19. Adopting preoperative fasting guidelines.

    Science.gov (United States)

    Anderson, Megan; Comrie, Rhonda

    2009-07-01

    In 1999, the American Society of Anesthesiologists adopted preoperative fasting guidelines to enhance the quality and efficiency of patient care. Guidelines suggest that healthy, non-pregnant patients should fast six hours from solids and two hours from liquids. Although these guidelines are in place, studies suggest that providers are still using the blanket statement "NPO after midnight" without regard to patient characteristics, the procedure, or the time of the procedure. Using theory to help change provider's beliefs may help make change more successful. Rogers' Theory of Diffusion of Innovations can assist in changing long-time practice by laying the groundwork for an analysis of the benefits and disadvantages of proposed changes, such as changes to fasting orders, while helping initiate local protocols instead of additional national guidelines.

  20. Proton Fast Ignition

    International Nuclear Information System (INIS)

    Key, M H; Freeman, R R; Hatchett, S P; MacKinnon, A J; Patel, P K; Snavely, R A; Stephens, R B

    2006-04-01

    Fast ignition (FI) by a laser generated ballistically focused proton beam is a more recently proposed alternative to the original concept of FI by a laser generated beam of relativistic electrons. It has potential advantages in less complex energy transport into dense plasma. Recent successful target heating experiments motivate further investigation of the feasibility of proton fast ignition. The concept, the physics and characteristics of the proton beams, the recent experimental work on focusing of the beams and heating of solid targets and the overall prospects for proton FI are discussed

  1. Fast breeder project (PSB)

    International Nuclear Information System (INIS)

    1976-07-01

    Activities performed during the 1st quarter of 1976 at or on behalf of the Gesellschaft fuer Kernforschung mbH, Karlsruhe, within the framework of the Fast Breeder Project are given a survey. The following project subdivisions are dealt with: Fuel rod development; materials testing and developments; corrosion studies and coolant analyses; physical experiments; reactor theory; safety of fast breeders; instrumentation and signal processing for core monitoring; effects on the environment; sodium technology tests; thermodynamic and fluid flow tests in gas. (HR) [de

  2. Magnetically Assisted Fast Ignition

    OpenAIRE

    Wang, W.-M.; Gibbon, P.; Sheng, Z.-M.; Li, Y.-T.

    2015-01-01

    Fast ignition (FI) is investigated via integrated particle-in-cell simulation including both generation andtransport of fast electrons, where petawatt ignition lasers of 2 ps and compressed targets of a peak density of300 g cm−3 and areal density of 0.49 g cm−2 at the core are taken. When a 20 MG static magnetic field isimposed across a conventional cone-free target, the energy coupling from the laser to the core is enhancedby sevenfold and reaches 14%. This value even exceeds that obtained u...

  3. Fast neutron dosimetry

    International Nuclear Information System (INIS)

    DeLuca, P.M. Jr.; Pearson, D.W.

    1993-01-01

    Research concentrated on three major areas during the last twelve months: (1) investigations of energy fluence and absorbed dose measurements using crystalline and hot pressed TLD materials exposes to ultrasoft beams of photons, (2) fast neutron kerma factor measurements for several important elements as well as NE-213 scintillation material response function determinations at the intense ''white'' source available at the WNR facility at LAMPF, and (3) kerma factor ratio determinations for carbon and oxygen to A-150 tissue equivalent plastic at the clinical fast neutron radiation facility at Harper Hospital, Detroit, MI. Progress summary reports of these efforts are given in this report

  4. Moms og fast ejendom

    DEFF Research Database (Denmark)

    Edlund, Hans Henrik

    1999-01-01

    I artiklen gives et overblik over, hvorledes fast ejendom behandles momsmæssigt. Derfor findes en kort skitsering af reglerne for moms på byggearbejder, afgrænsningen mellem momspligtig og momsfri udlejning, muligheden for frivillig registrering af udlejning samt opgørelse af reguleringsforpligte......I artiklen gives et overblik over, hvorledes fast ejendom behandles momsmæssigt. Derfor findes en kort skitsering af reglerne for moms på byggearbejder, afgrænsningen mellem momspligtig og momsfri udlejning, muligheden for frivillig registrering af udlejning samt opgørelse af...

  5. Fast ejendom II

    DEFF Research Database (Denmark)

    Munk-Hansen, Carsten

    Fremstillingen påviser, at lov om forbrugerbeskyttelse ved erhvervelse af fast ejendom mv. lider af en række svagheder og at ankenævnspraksis bevæger sig væk fra retspraksis på en række områder.......Fremstillingen påviser, at lov om forbrugerbeskyttelse ved erhvervelse af fast ejendom mv. lider af en række svagheder og at ankenævnspraksis bevæger sig væk fra retspraksis på en række områder....

  6. [Preoperative fasting. An update].

    Science.gov (United States)

    Spies, C D; Breuer, J P; Gust, R; Wichmann, M; Adolph, M; Senkal, M; Kampa, U; Weissauer, W; Schleppers, A; Soreide, E; Martin, E; Kaisers, U; Falke, K J; Haas, N; Kox, W J

    2003-11-01

    In Germany the predominant standard of preoperative care for elective surgery is fasting after midnight, with the aim of reducing the risk of pulmonary aspiration. However, for the past several years the scientific evidence supporting such a practice has been challenged. Experimental and clinical studies prove a reliable gastric emptying within 2 h suggesting that, particularly for limited intake of clear fluids up to 2 h preoperatively, there would be no increased risk for the patient. In addition, the general incidence of pulmonary aspiration during general anaesthesia (before induction, during surgery and during recovery) is extremely low, has a good prognosis and is more a consequence of insufficient airway protection and/or inadequate anaesthetic depth rather than due to the patient's fasting state. Therefore, primarily to decrease perioperative discomfort for patients, several national anaesthesia societies have changed their guidelines for preoperative fasting. They recommend a more liberal policy regarding per os intake of both liquid and solid food, with consideration of certain conditions and contraindications. The following article reviews the literature and gives an overview of the scientific background on which the national guidelines are based. The intention of this review is to propose recommendations for preoperative fasting regarding clear fluids for Germany as well.

  7. Integral Fast Reactor concept

    International Nuclear Information System (INIS)

    Till, C.E.; Chang, Y.I.

    1986-01-01

    The Integral Fast Reactor (IFR) is an innovative LMR concept, being developed at Argonne National Laboratory, that fully exploits the inherent properties of liquid metal cooling and metallic fuel to achieve breakthroughs in economics and inherent safety. This paper describes key features and potential advantages of the IFR concept, technology development status, fuel cycle economics potential, and future development path

  8. FastStats: Immunization

    Science.gov (United States)

    ... Women’s Health State and Territorial Data Reproductive Health Contraceptive Use Infertility Reproductive Health Notice Regarding FastStats Mobile ... 69 [PDF – 9.8 MB] Vaccination coverage among adolescents 13-17 years of age Health, United States, ...

  9. Integral Fast Reactor concept

    Energy Technology Data Exchange (ETDEWEB)

    Till, C.E.; Chang, Y.I.

    1986-01-01

    The Integral Fast Reactor (IFR) is an innovative LMR concept, being developed at Argonne National Laboratory, that fully exploits the inherent properties of liquid metal cooling and metallic fuel to achieve breakthroughs in economics and inherent safety. This paper describes key features and potential advantages of the IFR concept, technology development status, fuel cycle economics potential, and future development path.

  10. Parallel Fast Legendre Transform

    NARCIS (Netherlands)

    Alves de Inda, M.; Bisseling, R.H.; Maslen, D.K.

    1998-01-01

    We discuss a parallel implementation of a fast algorithm for the discrete polynomial Legendre transform We give an introduction to the DriscollHealy algorithm using polynomial arithmetic and present experimental results on the eciency and accuracy of our implementation The algorithms were

  11. The Integral Fast Reactor

    International Nuclear Information System (INIS)

    Till, C.E.; Chang, Y.I.; Lineberry, M.J.

    1990-01-01

    Argonne National Laboratory, since 1984, has been developing the Integral Fast Reactor (IFR). This paper will describe the way in which this new reactor concept came about; the technical, public acceptance, and environmental issues that are addressed by the IFR; the technical progress that has been made; and our expectations for this program in the near term. 5 refs., 3 figs

  12. Viden om faste vendinger

    DEFF Research Database (Denmark)

    Bergenholtz, Henning; Bjærge, Esben

    2012-01-01

    Ordbogen indeholder ca. 17.000 idiomer, ordsprog, bevingede ord og andre faste vendinger, som der oplyses mest muligt om. Hertil hører oplysninger om betydningen, grammatik, kollokationer, synonymer, stil, ordforbindelsestype, etymologiske angivelser og andre baggrundsoplysninger, links til...

  13. Integral Fast Reactor Program

    International Nuclear Information System (INIS)

    Chang, Y.I.; Walters, L.C.; Laidler, J.J.; Pedersen, D.R.; Wade, D.C.; Lineberry, M.J.

    1993-06-01

    This report summarizes highlights of the technical progress made in the Integral Fast Reactor (IFR) Program in FY 1992. Technical accomplishments are presented in the following areas of the IFR technology development activities: (1) metal fuel performance, (2) pyroprocess development, (3) safety experiments and analyses, (4) core design development, (5) fuel cycle demonstration, and (6) LMR technology R ampersand D

  14. FAST goes underground

    International Nuclear Information System (INIS)

    Fridlund, P.S.

    1985-01-01

    The FAST-M Cost Estimating Model is a parametric model designed to determine the costs associated with mining and subterranean operations. It is part of the FAST (Freiman Analysis of Systems Techniques) series of parametric models developed by Freiman Parametric Systems, Inc. The rising cost of fossil fuels has created a need for a method which could be used to determine and control costs in mining and subterranean operations. FAST-M fills this need and also provides scheduling information. The model works equally well for a variety of situations including underground vaults for hazardous waste storage, highway tunnels, and mass transit tunnels. In addition, costs for above ground structures and equipment can be calculated. The input for the model may be on a macro or a micro level. This allows the model to be used at various stages in a project. On the macro level, only general conditions and specifications need to be known. On the micro level, the smallest details may be included. As with other FAST models, reference cases are used to more accurately predict costs and scheduling. This paper will address how the model can be used for a variety of subterranean purposes

  15. Fast Air Temperature Sensors

    DEFF Research Database (Denmark)

    Hendricks, Elbert

    1998-01-01

    The note documents briefly work done on a newly developed sensor for making fast temperature measurements on the air flow in the intake ports of an SI engine and in the EGR input line. The work reviewed has been carried out in close cooperation with Civ. Ing. Michael Føns, the author (IAU...

  16. Project fast breeder (PSB)

    International Nuclear Information System (INIS)

    1978-01-01

    The annual report of the fast breeder project (PSB) contains contributions of the participating institutes on the four subjects: 1) Development of oxidic fuel rods and materials for the SNR line, 2) Physics and safety investigations for the SNR line, 3) Carbidic fuel elements, and 4) Back-up solution with gaseous coolant. (HK) [de

  17. Fast ejendom, I

    DEFF Research Database (Denmark)

    Munk-Hansen, Carsten

    , værdiforringende forhold, der ligger uden for ejendommen og andre særlige tilfælde. Bogen uddyber andre emner omtalt i 1. udgave, eksempelvis erhvervelsesbetingelser, købsoptioner, ansvarsfraskrivelse, licitationssalg mv. Bogen er det første af tre planlagte bind om fast ejendom: I Overdragelsen, II Bolighandlen...

  18. Handel med fast ejendom

    DEFF Research Database (Denmark)

    Edlund, Hans Henrik

    Bogen tilstræber at give et overblik over nogle af de vigtigste generelle problemområder på markedet for ejendomshandel, der jo bliver mere og mere kompliceret. Værket er opdelt i følgende hovedafsnit: Ejendomsbegrebet. Indgåelse af aftale om salg af fast ejendom. Begrænsninger i adgangen til...

  19. Fast Harmonic Chirp Summation

    DEFF Research Database (Denmark)

    Nielsen, Jesper Kjær; Jensen, Tobias Lindstrøm; Jensen, Jesper Rindom

    2017-01-01

    -robust to noise, or very computationally inten- sive. In this paper, we propose a fast algorithm for the harmonic chirp summation method which has been demonstrated in the liter- ature to be accurate and robust to noise. The proposed algorithm is orders of magnitudes faster than previous algorithms which is also...

  20. Nanolensed Fast Radio Bursts

    Science.gov (United States)

    Eichler, David

    2017-12-01

    It is suggested that fast radio bursts can probe gravitational lensing by clumpy dark matter objects that range in mass from 10-3 M ⊙-102 M ⊙. They may provide a more sensitive probe than observations of lensings of objects in the Magellanic Clouds, and could find or rule out clumpy dark matter with an extended mass spectrum.

  1. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    The ATLAS Collaboration has set up a framework to automatically process the rapidly growing dataset and produce performance and physics plots for the most interesting analyses. The system is designed to give fast feedback. The histograms are produced within hours of data reconstruction (2–3 days after data taking).

  2. Calorie count - fast food

    Science.gov (United States)

    ... GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Calorie count - fast food URL of this page: //medlineplus.gov/ency/patientinstructions/ ...

  3. Fast breeder reactor research

    International Nuclear Information System (INIS)

    1975-01-01

    Full text: The meeting was attended by 15 participants from seven countries and two international organizations. The Eighth Annual Meeting of the International Working Group on Fast Reactors (IWGFR) was attended by representatives from France, Fed. Rep. Germany, Italy, Japan, United Kingdom, Union of Soviet Socialist Republics and the United States of America - countries that have made significant progress in developing the technology and physics of sodium cooled fast reactors and have extensive national programmes in this field - as well as by representatives of the Commission of the European Communities and the IAEA. The design of fast-reactor power plants is a more difficult task than developing facilities with thermal reactors. Different reactor kinetics and dynamics, a hard neutron spectrum, larger integral doses of fuel and structural material irradiation, higher core temperatures, the use of an essentially novel coolant, and, as a result of all these factors, the additional reliability and safety requirements that are imposed on the planning and operation of sodium cooled fast reactors - all these factors pose problems that can be solved comprehensively only by countries with a high level of scientific and technical development. The exchange of experience between these countries and their combined efforts in solving the fundamental problems that arise in planning, constructing and operating fast reactors are promoting technical progress and reducing the relative expenditure required for various studies on developing and introducing commercial fast reactors. For this reason, the meeting concentrated on reviewing and discussing national fast reactor programmes. The situation with regard to planning, constructing and operating fast experimental and demonstration reactors in the countries concerned, the experience accumulated in operating them, the difficulties arising during operation and ways of over-coming them, the search for optimal designs for the power

  4. Out-and-back {sup 13}C-{sup 13}C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS

    Energy Technology Data Exchange (ETDEWEB)

    Barbet-Massin, Emeline; Pell, Andrew J. [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Franks, W. Trent; Retel, Joren S. [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars [Biomedical Research and Study Center (Latvia); Emsley, Lyndon [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Oschkinat, Hartmut [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Lesage, Anne; Pintacuda, Guido, E-mail: guido.pintacuda@ens-lyon.fr [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France)

    2013-08-15

    We present here {sup 1}H-detected triple-resonance H/N/C experiments that incorporate CO-CA and CA-CB out-and-back scalar-transfer blocks optimized for robust resonance assignment in biosolids under ultra-fast magic-angle spinning (MAS). The first experiment, (H)(CO)CA(CO)NH, yields {sup 1}H-detected inter-residue correlations, in which we record the chemical shifts of the CA spins in the first indirect dimension while during the scalar-transfer delays the coherences are present only on the longer-lived CO spins. The second experiment, (H)(CA)CB(CA)NH, correlates the side-chain CB chemical shifts with the NH of the same residue. These high sensitivity experiments are demonstrated on both fully-protonated and 100 %-H{sup N} back-protonated perdeuterated microcrystalline samples of Acinetobacter phage 205 (AP205) capsids at 60 kHz MAS.

  5. Preoperative fasting times: Prescribed and actual fasting times at ...

    African Journals Online (AJOL)

    The current international guidelines for preoperative fasting for elective surgery are 6 ... to determine whether this policy was being followed and patients were being starved ..... recommended fasting time, so that autonomous patients take care.

  6. Damages to gladiolu corm caused by fast neutron irradiation

    International Nuclear Information System (INIS)

    Zhang Zhiwei; Wang Dan; Zhang Dongxue; Zheng Chun

    2007-01-01

    Gladiolus corms were irradiated to 100-500kGy by fast neutrons in the CFBR-II pulsed reactor, Scanning electron microscope images of the irradiated samples revealed significant radiation damages to the gladiolus corms, and the mutagenic effects were studied by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Within the dose range, radiation damage to the corm increased with the dose, with corm epidermis of the samples irradiated in vertical incidence being more serious than those irradiated in side-incidence to the same dose. Biological characters were investigated via field experiments, and the bands of protein subunit were analyzed by SDS-PAGE. The results showed that the fast neutrons irradiation inhibited growth of M1 generation seedling significantly. Protein expression was obviously inhibited by the irradiation. The study indicates that fast neutron induction is an effective way for gladiolus breeding. And the results may lay a foundation for studies on fast neutron mutation breeding. (authors)

  7. Inorganic component of saliva during fasting and after fast break

    OpenAIRE

    Samad, Rasmidar

    2016-01-01

    Oral health is closely related to salivary components. Saliva consists of water, inorganic and organic materials. Fasting changes one???s meal and drinking time that in turn can affect the environment in oral cavity, including inorganic componenet of saliva. The purpose of this study is to determine the inorganic component of saliva during fasting and after fast break.

  8. Fast Flux Test Facility

    International Nuclear Information System (INIS)

    Munn, W.I.

    1981-01-01

    The Fast Flux Test Facility (FFTF), located on the Hanford site a few miles north of Richland, Washington, is a major link in the chain of development required to sustain and advance Liquid Metal Fast Breeder Reactor (LMFBR) technology in the United States. This 400 MWt sodium cooled reactor is a three loop design, is operated by Westinghouse Hanford Company for the US Department of Energy, and is the largest research reactor of its kind in the world. The purpose of the facility is three-fold: (1) to provide a test bed for components, materials, and breeder reactor fuels which can significantly extend resource reserves; (2) to produce a complete body of base data for the use of liquid sodium in heat transfer systens; and (3) to demonstrate inherent safety characteristics of LMFBR designs

  9. Fast radiographic systems

    International Nuclear Information System (INIS)

    Domanus, J.C.

    1984-08-01

    Industrial radiography can be performed with shorter exposure times, when instead of X-ray film with lead intensifying screens the radiographic paper with fluorescent screen is used. With paper radiography one can obtain lower material, equipment, and labor costs, shorter exposure and processing times, and easier radiation protection. The speed of the radiographic inspection can also be increased by the use of fluorometallic intensifying screens together with a special brand of X-ray film. Before accepting either of the two fast radiographic systems one must be sure that they can produce radiographs of adequate image quality. Therefore an investigation was performed on that subject using ISO wire IQI's and ASTM penetrameters. The radiographic image quality was tested for aluminium and steel up to 30 mm thick using various brands of radiographic paper and X-ray film with fluorometallic screens and comparing them with fast X-ray films with lead screens. Both systems give satisfactory results. (author)

  10. Fast geometric algorithms

    International Nuclear Information System (INIS)

    Noga, M.T.

    1984-01-01

    This thesis addresses a number of important problems that fall within the framework of the new discipline of Computational Geometry. The list of topics covered includes sorting and selection, convex hull algorithms, the L 1 hull, determination of the minimum encasing rectangle of a set of points, the Euclidean and L 1 diameter of a set of points, the metric traveling salesman problem, and finding the superrange of star-shaped and monotype polygons. The main theme of all the work was to develop a set of very fast state-of-the-art algorithms that supersede any rivals in terms of speed and ease of implementation. In some cases existing algorithms were refined; for others new techniques were developed that add to the present database of fast adaptive geometric algorithms. What emerges is a collection of techniques that is successful at merging modern tools developed in analysis of algorithms with those of classical geometry

  11. The ELETTRA fast magnets

    International Nuclear Information System (INIS)

    Tommasini, D.

    1992-01-01

    The design of the fast magnets to be used to inject the electron beam into the 2 GeV storage ring Elettra is presented and discussed. Injection makes use of two types of fast magnets: the septa and the kickers. There are two identical septa magnets of the so called 'eddy current' type, which will be housed in a vacuum tank. The orbit bump is generated by four identical kicker magnets symmetrically placed around the mid-point of a single straight section: they will be in air with an internal vacuum chamber. Extensive electric and magnetic tests have been performed on prototypes, and the relevant results are presented and discussed. (author) 6 refs.; 6 figs.; 2 tabs

  12. Fast timing discriminator

    International Nuclear Information System (INIS)

    Lo, C.C.

    1977-01-01

    The processing of pulses with very fast risetimes for timing purposes involves many problems because of the large equivalent bandwidths involved. For pulses with risetimes in the 150 ps range (and full widths at half maximum (FWHM) of 400 ps) bandwidths in excess of 1GHz are required. Furthermore, these very narrow pulses with current amplitudes as small as 1 mA carry very small charges ( -12 coulomb), therefore, requiring very sensitive trigger circuits. The difficulty increases when timing characteristics in the picosecond range are sought especially when a wide input signal amplitude range causes a time-walk problem. The fast timing discriminator described has a time-walk of approximately +-75 ps over the input signal range from 80 mV to 3V. A schematic of the discriminator is included, and operation and performance are discussed

  13. Fast reactor database

    International Nuclear Information System (INIS)

    1996-02-01

    This publication contains detailed data on liquid metal cooled fast reactors (LMFRs), specifically plant parameters and design details. Each LMFR power plant is characterized by about 400 parameters, by design data and by relevant materials. The report provides general and detailed design characteristics including structural materials, data on experimental, demonstration, prototype and commercial size LMFRs. The focus is on practical issues that are useful to engineers, scientists, managers and university students and professors. The report includes updated information contained in IAEA previous publications on LMFR plant parameters: IWGRF/51 (1985) and IWGFR/80 (1991) and reflects experience gained from two consultants meetings held in Vienna (1993,1994). This compilation of data was produced by members of the IAEA International Working Group on Fast Reactors (IWGFR)

  14. Fast electrochemical actuator

    International Nuclear Information System (INIS)

    Uvarov, I V; Postnikov, A V; Svetovoy, V B

    2016-01-01

    Lack of fast and strong microactuators is a well-recognized problem in MEMS community. Electrochemical actuators can develop high pressure but they are notoriously slow. Water electrolysis produced by short voltage pulses of alternating polarity can overcome the problem of slow gas termination. Here we demonstrate an actuation regime, for which the gas pressure is relaxed just for 10 μs or so. The actuator consists of a microchamber filled with the electrolyte and covered with a flexible membrane. The membrane bends outward when the pressure in the chamber increases. Fast termination of gas and high pressure developed in the chamber are related to a high density of nanobubbles in the chamber. The physical processes happening in the chamber are discussed so as problems that have to be resolved for practical applications of this actuation regime. The actuator can be used as a driving engine for microfluidics. (paper)

  15. PHENIX Fast TOF

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Chiu, Mickey [Brookhaven National Lab. (BNL), Upton, NY (United States); Mannel, Eric [Brookhaven National Lab. (BNL), Upton, NY (United States); Stoll, Sean [Brookhaven National Lab. (BNL), Upton, NY (United States); Lynch, Don [Brookhaven National Lab. (BNL), Upton, NY (United States); Boose, Steve [Brookhaven National Lab. (BNL), Upton, NY (United States); Northacker, Dave [Brookhaven National Lab. (BNL), Upton, NY (United States); Alfred, Marcus [Howard Univ., Washington, DC (United States); Lindesay, James [Howard Univ., Washington, DC (United States); Chujo, Tatsuya [Univ. of Tsukuba (Japan); Inaba, Motoi [Univ. of Tsukuba (Japan); Nonaka, Toshihiro [Univ. of Tsukuba (Japan); Sato, Wataru [Univ. of Tsukuba (Japan); Sakatani, Ikumi [Univ. of Tsukuba (Japan); Hirano, Masahiro [Univ. of Tsukuba (Japan); Choi, Ihnjea [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2014-01-15

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of PHENIX Fast TOF group who have committed to participate in beam tests to be carried out during the FY2014 Fermilab Test Beam Facility program. The goals for this test beam experiment are to verify the timing performance of the two types of time-of-flight detector prototypes.

  16. Fast diamond photoconductors

    International Nuclear Information System (INIS)

    Pochet, T.

    1993-01-01

    Preliminary results on the response of type Ib and IIa diamond photodetectors to fast laser pulse exposures at 265 and 530 nm are presented. The influence of the applied bias, the laser wavelengths and the light intensity on the detector sensitivity is studied. Also, recent measurements with 1.25 MeV gamma ray pulses are reported. (authors). 13 refs., 7 figs., 1 tab

  17. Integral fast reactor

    International Nuclear Information System (INIS)

    Chang, Y.I.

    1989-01-01

    The Integral Fast Reactor (IFR) is an innovative liquid metal reactor concept being developed at Argonne National Laboratory. It seeks to specifically exploit the inherent properties of liquid metal cooling and metallic fuel in a way that leads to substantial improvements in the characteristics of the complete reactor system. This paper describes the key features and potential advantages of the IFR concept, with emphasis on its safety characteristics

  18. Fast antihydrogen beam spectroscopy

    International Nuclear Information System (INIS)

    Neumann, R.

    1989-01-01

    The motivation for production and precision spectroscopy of antihydrogen atoms is outlined. An experimental configuration is considered, concerning laser-microwave spectroscopy of a fast hydrogen beam with characteristics similar to those of an antihydrogen beam emanating from an antiproton-positron overlap region in an antiproton storage ring. In particular, a possible experiment for the measurement of the ground state hyperfine structure splitting is described. (orig.)

  19. The Integral Fast Reactor

    International Nuclear Information System (INIS)

    Chang, Y.I.

    1988-01-01

    The Integral Fast Reactor (IFR) is an innovative liquid metal reactor concept being developed at Argonne National Laboratory. It seeks to specifically exploit the inherent properties of liquid metal cooling and metallic fuel in a way that leads to substantial improvements in the characteristics of the complete reactor system. This paper describes the key features and potential advantages of the IFR concept, with emphasis on its safety characteristics. 3 refs., 4 figs., 1 tab

  20. Fasting - the ultimate diet?

    Science.gov (United States)

    Johnstone, A M

    2007-05-01

    Adult humans often undertake acute fasts for cosmetic, religious or medical reasons. For example, an estimated 14% of US adults have reported using fasting as a means to control body weight and this approach has long been advocated as an intermittent treatment for gross refractory obesity. There are unique historical data sets on extreme forms of food restriction that give insight into the consequences of starvation or semi-starvation in previously healthy, but usually non-obese subjects. These include documented medical reports on victims of hunger strike, famine and prisoners of war. Such data provide a detailed account on how the body adapts to prolonged starvation. It has previously been shown that fasting for the biblical period of 40 days and 40 nights is well within the overall physiological capabilities of a healthy adult. However, the specific effects on the human body and mind are less clearly documented, either in the short term (hours) or in the longer term (days). This review asks the following three questions, pertinent to any weight-loss therapy, (i) how effective is the regime in achieving weight loss, (ii) what impact does it have on psychology? and finally, (iii) does it work long-term?

  1. ADT fast losses MD

    CERN Document Server

    Priebe, A; Dehning, B; Redaelli, S; Salvachua Ferrando, BM; Sapinski, M; Solfaroli Camillocci, M; Valuch, D

    2013-01-01

    The fast beam losses in the order of 1 ms are expected to be a potential major luminosity limitation for higher beam energies after the LHC long shutdown (LS1). Therefore a Quench Test is planned in the winter 2013 to estimate the quench limit in this timescale and revise the current models. This experiment was devoted to determination the LHC Transverse Damper (ADT) as a system for fast losses induction. A non-standard operation of the ADT was used to develop the beam oscillation instead of suppressing them. The sign flip method had allowed us to create the fast losses within several LHC turns at 450 GeV during the previous test (26th March 2012). Thus, the ADT could be potentially used for the studies of the UFO ("Unidentied Falling Object") impact on the cold magnets. Verification of the system capability and investigations of the disturbed beam properties were the main objectives of this MD. During the experiment, the pilot bunches of proton beam were excited independently in the horizontal and vertical ...

  2. Fast Light Optical Gyroscopes

    Science.gov (United States)

    Smith, David D.

    2015-01-01

    Next-generation space missions are currently constrained by existing spacecraft navigation systems which are not fully autonomous. These systems suffer from accumulated dead-reckoning errors and must therefore rely on periodic corrections provided by supplementary technologies that depend on line-of-sight signals from Earth, satellites, or other celestial bodies for absolute attitude and position determination, which can be spoofed, incorrectly identified, occluded, obscured, attenuated, or insufficiently available. These dead-reckoning errors originate in the ring laser gyros themselves, which constitute inertial measurement units. Increasing the time for standalone spacecraft navigation therefore requires fundamental improvements in gyroscope technologies. One promising solution to enhance gyro sensitivity is to place an anomalous dispersion or fast light material inside the gyro cavity. The fast light essentially provides a positive feedback to the gyro response, resulting in a larger measured beat frequency for a given rotation rate as shown in figure 1. Game Changing Development has been investing in this idea through the Fast Light Optical Gyros (FLOG) project, a collaborative effort which began in FY 2013 between NASA Marshall Space Flight Center (MSFC), the U.S. Army Aviation and Missile Research, Development, and Engineering Center (AMRDEC), and Northwestern University. MSFC and AMRDEC are working on the development of a passive FLOG (PFLOG), while Northwestern is developing an active FLOG (AFLOG). The project has demonstrated new benchmarks in the state of the art for scale factor sensitivity enhancement. Recent results show cavity scale factor enhancements of approx.100 for passive cavities.

  3. Metabolic Effects of Intermittent Fasting.

    Science.gov (United States)

    Patterson, Ruth E; Sears, Dorothy D

    2017-08-21

    The objective of this review is to provide an overview of intermittent fasting regimens, summarize the evidence on the health benefits of intermittent fasting, and discuss physiological mechanisms by which intermittent fasting might lead to improved health outcomes. A MEDLINE search was performed using PubMed and the terms "intermittent fasting," "fasting," "time-restricted feeding," and "food timing." Modified fasting regimens appear to promote weight loss and may improve metabolic health. Several lines of evidence also support the hypothesis that eating patterns that reduce or eliminate nighttime eating and prolong nightly fasting intervals may result in sustained improvements in human health. Intermittent fasting regimens are hypothesized to influence metabolic regulation via effects on (a) circadian biology, (b) the gut microbiome, and (c) modifiable lifestyle behaviors, such as sleep. If proven to be efficacious, these eating regimens offer promising nonpharmacological approaches to improving health at the population level, with multiple public health benefits.

  4. Neighborhood fast food availability and fast food consumption.

    Science.gov (United States)

    Oexle, Nathalie; Barnes, Timothy L; Blake, Christine E; Bell, Bethany A; Liese, Angela D

    2015-09-01

    Recent nutritional and public health research has focused on how the availability of various types of food in a person's immediate area or neighborhood influences his or her food choices and eating habits. It has been theorized that people living in areas with a wealth of unhealthy fast-food options may show higher levels of fast-food consumption, a factor that often coincides with being overweight or obese. However, measuring food availability in a particular area is difficult to achieve consistently: there may be differences in the strict physical locations of food options as compared to how individuals perceive their personal food availability, and various studies may use either one or both of these measures. The aim of this study was to evaluate the association between weekly fast-food consumption and both a person's perceived availability of fast-food and an objective measure of fast-food presence - Geographic Information Systems (GIS) - within that person's neighborhood. A randomly selected population-based sample of eight counties in South Carolina was used to conduct a cross-sectional telephone survey assessing self-report fast-food consumption and perceived availability of fast food. GIS was used to determine the actual number of fast-food outlets within each participant's neighborhood. Using multinomial logistic regression analyses, we found that neither perceived availability nor GIS-based presence of fast-food was significantly associated with weekly fast-food consumption. Our findings indicate that availability might not be the dominant factor influencing fast-food consumption. We recommend using subjective availability measures and considering individual characteristics that could influence both perceived availability of fast food and its impact on fast-food consumption. If replicated, our findings suggest that interventions aimed at reducing fast-food consumption by limiting neighborhood fast-food availability might not be completely effective

  5. Serum Lipid Profile: Fasting or Non-fasting?

    OpenAIRE

    Nigam, P. K.

    2010-01-01

    Serum lipid profile has now become almost a routine test. It is usually done in fasting state due to certain limitations in non-fasting serum sample. In the recent past efforts have been made to simplify blood sampling by replacing fasting lipid profile with non-fasting lipid profile. However, fasting specimen is preferred if cardiovascular risk assessment is based on total cholesterol, LDL cholesterol or non-HDL cholesterol. A lot has yet to be done in this area. Till then we have to believe...

  6. Hispanics in Fast Food Jobs.

    Science.gov (United States)

    Charner, Ivan; Fraser, Bryna Shore

    A study examined the employment of Hispanics in the fast-food industry. Data were obtained from a national survey of employees at 279 fast-food restaurants from seven companies in which 194 (4.2 percent) of the 4,660 respondents reported being Hispanic. Compared with the total sample, Hispanic fast-food employees were slightly less likely to be…

  7. Fast reactors: potential for power

    International Nuclear Information System (INIS)

    1983-02-01

    The subject is discussed as follows: basic facts about conventional and fast reactors; uranium economy; plutonium and fast reactors; cooling systems; sodium coolant; safety engineering; handling and recycling plutonium; safeguards; development of fast reactors in Britain and abroad; future progress. (U.K.)

  8. Serum corticosteroid binding globulin expression is modulated by fasting in polar bears (Ursus maritimus).

    Science.gov (United States)

    Chow, Brian A; Hamilton, Jason; Cattet, Marc R L; Stenhouse, Gordon; Obbard, Martyn E; Vijayan, Mathilakath M

    2011-01-01

    Polar bears (Ursus maritimus) from several subpopulations undergo extended fasting during the ice-free season. However, the animals appear to conserve protein despite the prolonged fasting, though the mechanisms involved are poorly understood. We hypothesized that elevated concentrations of corticosteroid binding globulin (CBG), the primary cortisol binding protein in circulation, lead to cortisol resistance and provide a mechanism for protein conservation during extended fasting. The metabolic state (feeding vs. fasting) of 16 field sampled male polar bears was determined based on their serum urea to creatinine ratio (>25 for feeding vs. polar bears sampled. Serum CBG expression was greater in lactating females relative to non-lactating females and males. CBG expression was significantly higher in fasting males when compared to non-fasting males. This leads us to suggest that CBG expression may serve as a mechanism to conserve protein during extended fasting in polar bears by reducing systemic free cortisol concentrations. This was further supported by a lower serum glucose concentration in the fasting bears. As well, a lack of an enhanced adrenocortical response to acute capture stress supports our hypothesis that chronic hunger is not a stressor in this species. Overall, our results suggest that elevated serum CBG expression may be an important adaptation to spare proteins by limiting cortisol bioavailability during extended fasting in polar bears. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. Fast reactors in nuclear power

    Energy Technology Data Exchange (ETDEWEB)

    Kazachkovskii, O

    1981-02-01

    The possible applications are discussed of fast reactor nuclear power plants. Basic differences are explained in fast and thermal reactors, mainly with a view to nuclear fuel utilization. Discussed in more detail are the problems of nuclear fuel reproduction and the nost important technical problems of fast reactors. Flow charts are shown of heat transfer for fast reactors BN-350 (loop design) and BN-600 (integral coolant circuit design). Main specifications are given for demonstration and power fast reactors in operation, under construction and in project-stage.

  10. Knowledge management in fast reactors

    International Nuclear Information System (INIS)

    Kuriakose, K.K.; Satya Murty, S.A.V.; Swaminathan, P.; Raj, Baldev

    2010-01-01

    This paper highlights the work that is being carried out in Knowledge Management of Fast Reactors at Indira Gandhi Centre for Atomic Research (IGCAR) including a few examples of how the knowledge acquired because of various incidents in the initial years has been utilized for the successful operation of Fast Breeder Test Reactor. It also briefly refers to the features of the IAEA initiative on the preservation of Knowledge in the area of Fast Reactors in the form of 'Fast Reactor Knowledge Organization System' (FR-KOS), which is based on a taxonomy for storage and mining of Fast Reactor Knowledge. (author)

  11. Fast photomultiplier ELUP 151

    International Nuclear Information System (INIS)

    Andreeva, L.I.; Belokon', V.A.; Krasin, E.V.

    1992-01-01

    High-velocity photomultiplier is described. The latter is recommended to be used in nuclear physics, plasma physics, nuclear medical diagnostics and at measurement of fast-occurring process parameters. Main specifications are as follows: range of spectral sensitivity - 0.2-0.7 μm; limit of dinamic characteristic linearity - up to 5A; dark current at +20 deg C ambient temperature - maximum 10-8A, time of anode pulse growth - maximum 8 ns; photocathode quantum yield in the maximum of spectral characteristic (λ max =380-420 nm) - 24-26%; supply voltage - 4-5 kV

  12. Fast neutron dosimetry

    International Nuclear Information System (INIS)

    DeLuca, P.M. Jr.; Pearson, D.W.

    1992-01-01

    This progress report concentrates on two major areas of dosimetry research: measurement of fast neutron kerma factors for several elements for monochromatic and white spectrum neutron fields and determination of the response of thermoluminescent phosphors to various ultra-soft X-ray energies and beta-rays. Dr. Zhixin Zhou from the Shanghai Institute of Radiation Medicine, People's Republic of China brought with him special expertise in the fabrication and use of ultra-thin TLD materials. Such materials are not available in the USA. The rather unique properties of these materials were investigated during this grant period

  13. The fast encryption package

    Science.gov (United States)

    Bishop, Matt

    1988-01-01

    The organization of some tools to help improve passwork security at a UNIX-based site is described along with how to install and use them. These tools and their associated library enable a site to force users to pick reasonably safe passwords (safe being site configurable) and to enable site management to try to crack existing passworks. The library contains various versions of a very fast implementation of the Data Encryption Standard and of the one-way encryption functions used to encryp the password.

  14. Fast breeder reactors

    International Nuclear Information System (INIS)

    Ollier, J.L.

    1987-01-01

    The first industrial-scale fast breeder reactor (FBR) is the Superphenix I at Crays-Melville. It was designed and built by Novatome, a French company, and Ansaldo, an Italian company. The advantages of FBRs are summarized. The status of Superphenix and the testing schedule is given. The stages in its power escalation in 1986 are given. The article is optimistic about the future for FBRs and expects FBRs to take over from PWRs at the beginning of the 21st Century. To achieve economic viability, European financial cooperation for the research and development programme is advocated. (UK)

  15. Sodium cooled fast reactor

    Energy Technology Data Exchange (ETDEWEB)

    Hokkyo, N; Inoue, K; Maeda, H

    1968-11-21

    In a sodium cooled fast neutron reactor, an ultrasonic generator is installed at a fuel assembly hold-down mechanism positioned above a blanket or fission gas reservoir located above the core. During operation of the reactor an ultrsonic wave of frequency 10/sup 3/ - 10/sup 4/ Hz is constantly transmitted to the core to resonantly inject the primary bubble with ultrasonic energy to thereby facilitate its growth. Hence, small bubbles grow gradually to prevent the sudden boiling of sodium if an accident occurs in the cooling system during operation of the reactor.

  16. Fast multichannel scaler

    International Nuclear Information System (INIS)

    Okayasu, T.; Takeuchi, S.; Nagai, S.

    1987-01-01

    A fast multichannel scaler achieving the minimum dwell time of 50 ns is described. The dead time due to memory cycle is eliminated by 4-phase operation of parallel-4 groups of counter RAMs. The MCS has 4 k channels in total. Differential nonlinearity is less than 0.4%. If an input pulse arrives near the channel boundary, it is caught temporarily for both channels and then sorted to go into a proper channel. Thus, the dead time near the channel boundary is also eliminated

  17. Fast delta Hadamard transform

    International Nuclear Information System (INIS)

    Fenimore, E.E.; Weston, G.S.

    1981-01-01

    In many fields (e.g., spectroscopy, imaging spectroscopy, photoacoustic imaging, coded aperture imaging) binary bit patterns known as m sequences are used to encode (by multiplexing) a series of measurements in order to obtain a larger throughput. The observed measurements must be decoded to obtain the desired spectrum (or image in the case of coded aperture imaging). Decoding in the past has used a technique called the fast Hadamard transform (FHT) whose chief advantage is that it can reduce the computational effort from N 2 multiplies of N log 2 N additions or subtractions. However, the FHT has the disadvantage that it does not readily allow one to sample more finely than the number of bits used in the m sequence. This can limit the obtainable resolution and cause confusion near the sample boundaries (phasing errors). Both 1-D and 2-D methods (called fast delta Hadamard transforms, FDHT) have been developed which overcome both of the above limitations. Applications of the FDHT are discussed in the context of Hadamard spectroscopy and coded aperture imaging with uniformly redundant arrays. Special emphasis has been placed on how the FDHT can unite techniques used by both of these fields into the same mathematical basis

  18. Fast Fourier transform telescope

    International Nuclear Information System (INIS)

    Tegmark, Max; Zaldarriaga, Matias

    2009-01-01

    We propose an all-digital telescope for 21 cm tomography, which combines key advantages of both single dishes and interferometers. The electric field is digitized by antennas on a rectangular grid, after which a series of fast Fourier transforms recovers simultaneous multifrequency images of up to half the sky. Thanks to Moore's law, the bandwidth up to which this is feasible has now reached about 1 GHz, and will likely continue doubling every couple of years. The main advantages over a single dish telescope are cost and orders of magnitude larger field-of-view, translating into dramatically better sensitivity for large-area surveys. The key advantages over traditional interferometers are cost (the correlator computational cost for an N-element array scales as Nlog 2 N rather than N 2 ) and a compact synthesized beam. We argue that 21 cm tomography could be an ideal first application of a very large fast Fourier transform telescope, which would provide both massive sensitivity improvements per dollar and mitigate the off-beam point source foreground problem with its clean beam. Another potentially interesting application is cosmic microwave background polarization.

  19. The integral fast reactor

    International Nuclear Information System (INIS)

    Till, C.E.

    1987-01-01

    On April 3rd, 1986, two dramatic demonstrations of the inherent capability of sodium-cooled fast reactors to survive unprotected loss of cooling accidents were carried out on the experimental sodium-cooled power reactor, EBR-II, on the Idaho site of Argonne National Laboratory. Transients potentially of the most serious kind, one an unprotected loss of flow, the other an unprotected loss of heat sink, both initiated from full power. In both cases the reactor quietly shut itself down, without damage of any kind. These tests were a part of the on-going development program at Argonne to develop an advanced reactor with significant new inherent safety characteristics. Called the Integral Fast Reactor, or IFR, the basic thrust is to develop everything that is needed for a complete nuclear power system - reactor, closed fuel cycle, and waste processing - as a single optimized entity, and, for simplicity in concept, as an integral part of a single plant. The particular selection of reactor materials emphasizes inherent safety characteristics and also makes possible a simplified closed fuel cycle and waste process improvements

  20. The integral fast reactor

    International Nuclear Information System (INIS)

    Till, C.E.

    1987-01-01

    On April 3rd, 1986, two demonstrations of the inherent capability of sodium-cooled fast reactors to survive unprotected loss of cooling accidents were carried out on the experimental sodium-cooled power reactor, EBR-II, on the Idaho site of Argonne National Laboratory. Transients potentially of the most serious kind, one an unprotected loss of flow, the other an unprotected loss of heat sink, both initiated from full power. In both cases the reactor quietly shut itself down, without damage of any kind. These tests were a part of the on-going development program at Argonne to develop an advanced reactor with significant new inherent safety characteristics. Called the integral fast reactor, or IFR, the basic thrust is to develop everything that is needed for a complete nuclear power system - reactor, closed fuel cycle, and waste processing - as a single optimized entity, and, for simplicity in concept, as an integral part of a single plant. The particular selection of reactor materials emphasizes inherent safety characteristics also makes possible a simplified close fuel cycle and waste process improvements. The paper describes the IFR concept, the inherent safety, tests, and status of IFR development today

  1. Manufacturing process used to produce long-acting recombinant factor VIII Fc fusion protein.

    Science.gov (United States)

    McCue, Justin; Kshirsagar, Rashmi; Selvitelli, Keith; Lu, Qi; Zhang, Mingxuan; Mei, Baisong; Peters, Robert; Pierce, Glenn F; Dumont, Jennifer; Raso, Stephen; Reichert, Heidi

    2015-07-01

    Recombinant factor VIII Fc fusion protein (rFVIIIFc) is a long-acting coagulation factor approved for the treatment of hemophilia A. Here, the rFVIIIFc manufacturing process and results of studies evaluating product quality and the capacity of the process to remove potential impurities and viruses are described. This manufacturing process utilized readily transferable and scalable unit operations and employed multi-step purification and viral clearance processing, including a novel affinity chromatography adsorbent and a 15 nm pore size virus removal nanofilter. A cell line derived from human embryonic kidney (HEK) 293H cells was used to produce rFVIIIFc. Validation studies evaluated identity, purity, activity, and safety. Process-related impurity clearance and viral clearance spiking studies demonstrate robust and reproducible removal of impurities and viruses, with total viral clearance >8-15 log10 for four model viruses (xenotropic murine leukemia virus, mice minute virus, reovirus type 3, and suid herpes virus 1). Terminal galactose-α-1,3-galactose and N-glycolylneuraminic acid, two non-human glycans, were undetectable in rFVIIIFc. Biochemical and in vitro biological analyses confirmed the purity, activity, and consistency of rFVIIIFc. In conclusion, this manufacturing process produces a highly pure product free of viruses, impurities, and non-human glycan structures, with scale capabilities to ensure a consistent and adequate supply of rFVIIIFc. Copyright © 2015 Biogen. Published by Elsevier Ltd.. All rights reserved.

  2. Quantitation of mRNAs for α1-acid glycoprotein and for serum albumin in livers of normal, stressed, fasted, and refed rats. [125I or 131I radioimmunoassay for protein products of specific mRNA activity

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Linda Jean [Univ. of Rochester, NY (United States)

    1978-01-01

    A new procedure for determining the relative levels of a specific mRNA species was developed and applied to mRNA for rat serum albumin (RSA) and α1-AGP) in rat liver. The method is a radioimmunoassay (125In or 131I) for the completed protein, but which also detects antigenic determinants in nascent polypeptide chains on plysomes synthesizing the specific protein. Results show that 24 hs after stressing the rat by turpentine injection the total number of polysomes per mg DNA has increased by 20 to 25%; however, the number of RSA synthesizing polysomes per mg DNA has decreased slightly. In rats fasted for 6 days, the number of RSA synthesizing polysomes per mg polysomal RNA is only slightly below normal, but the total number of RSA synthesizing polysomes per mg DNA has decreased by 40%. Again, it is seen that RSA mRNA levels do not decrease as sharply as the rate of RSA synthesis. Twelve hours after refeeding the rats, the number of RSA synthesizing polysomes begins to increase, reaching a peak two to three times normal levels 24 to 48 hours after commencement of refeeding. During the first 24 hs after turpentine injection, there is a linear increase in the number of α1-AGP synthesizing polysomes. The increase is smaller during the next 24 hs and there is a small decrease between 48 and 72 hs. The serum concentrations of α1-AGP following turpentine treatment reflect these changes in polysome levels. It was not possible to compare the number of α1-AGP synthesizing polysomes in livers of normal, fasted, and refed rats because the levels detected were only slightly higher than those seen in rat and rat kidney polysome controls. This background activity must be eliminated before the technique can be applied to quantitating mRNA for proteins synthesized in very small quantities. This technique offers several advantages over other procedures commonly used to quantitate mRNA. (ERB)

  3. Islamic fasting and multiple sclerosis

    Science.gov (United States)

    2014-01-01

    Background Month-long daytime Ramadan fasting pose s major challenges to multiple sclerosis (MS) patients in Muslim countries. Physicians should have practical knowledge on the implications of fasting on MS. We present a summary of database searches (Cochrane Database of Systematic Reviews, PubMed) and a mini-symposium on Ramadan fasting and MS. In this symposium, we aimed to review the effect of fasting on MS and suggest practical guidelines on management. Discussion In general, fasting is possible for most stable patients. Appropriate amendment of drug regimens, careful monitoring of symptoms, as well as providing patients with available evidence on fasting and MS are important parts of management. Evidence from experimental studies suggests that calorie restriction before disease induction reduces inflammation and subsequent demyelination and attenuates disease severity. Fasting does not appear to have unfavorable effects on disease course in patients with mild disability (Expanded Disability Status Scale (EDSS) score ≤3). Most experts believed that during fasting (especially in summer), some MS symptoms (fatigue, fatigue perception, dizziness, spasticity, cognitive problems, weakness, vision, balance, gait) might worsen but return to normal levels during feasting. There was a general consensus that fasting is not safe for patients: on high doses of anti-convulsants, anti-spastics, and corticosteroids; with coagulopathy or active disease; during attacks; with EDSS score ≥7. Summary These data suggest that MS patients should have tailored care. Fasting in MS patients is a challenge that is directly associated with the spiritual belief of the patient. PMID:24655543

  4. Fast Food Jobs. National Study of Fast Food Employment.

    Science.gov (United States)

    Charner, Ivan; Fraser, Bryna Shore

    A study examined employment in the fast-food industry. The national survey collected data from employees at 279 fast-food restaurants from seven companies. Female employees outnumbered males by two to one. The ages of those fast-food employees in the survey sample ranged from 14 to 71, with fully 70 percent being in the 16- to 20-year-old age…

  5. Fasting in king penguin. II. Hormonal and metabolic changes during molt.

    Science.gov (United States)

    Cherel, Y; Leloup, J; Le Maho, Y

    1988-02-01

    The coincidence of fast and molt in penguins is an interesting condition for investigating the factors controlling protein metabolism; avian molt involves the utilization of amino acids for synthesis of new feathers, whereas a major factor for adaptation to fasting in birds, as for mammals, is reduction in net protein breakdown. Hormonal and biochemical changes were studied in seven molting king penguins. Their initial body mass was 18 kg. It decreased by 58% over 41 days of fasting. Feather synthesis lasted for the first 3 wk of the fast. It was marked by plasma concentrations of alanine and uric acid 1.5 to 2 times those for nonmolting fast, and plasma thyroxine was increased five times. At the completion of molt all these values returned to levels comparable to those in nonmolting fast. As indicated by high plasma levels of beta-hydroxybutyrate, lipid stores were mobilized readily during molting. The fast ended by a phase of enhancement in protein utilization that was characterized by a fivefold increase in uricacidemia and coincided with an 80% drop in plasma beta-hydroxybutyrate and a fourfold increase in plasma corticosterone. These data suggest that two different hormones control the two successive periods marked by an increased protein mobilization during the molting fast, i.e., thyroxine during feather growth and corticosterone toward the end of the fast, when the molt is completed.

  6. Materials analysis fast ions

    CERN Document Server

    Denker, A; Rauschenberg, J; Röhrich, J; Strub, E

    2006-01-01

    Materials analysis with ion beams exploits the interaction of ions with the electrons and nuclei in the sample. Among the vast variety of possible analytical techniques available with ion beams we will restrain to ion beam analysis with ion beams in the energy range from one to several MeV per mass unit. It is possible to use either the back-scattered projectiles (RBS – Rutherford Back Scattering) or the recoiled atoms itself (ERDA – Elastic Recoil Detection Analysis) from the elastic scattering processes. These techniques allow the simultaneous and absolute determination of stoichiometry and depth profiles of the detected elements. The interaction of the ions with the electrons in the sample produces holes in the inner electronic shells of the sample atoms, which recombine and emit X-rays characteristic for the element in question. Particle Induced X-ray Emission (PIXE) has shown to be a fast technique for the analysis of elements with an atomic number above 11.

  7. Fast multilevel radiative transfer

    International Nuclear Information System (INIS)

    Paletou, Frederic; Leger, Ludovick

    2007-01-01

    The vast majority of recent advances in the field of numerical radiative transfer relies on approximate operator methods better known in astrophysics as Accelerated Lambda-Iteration (ALI). A superior class of iterative schemes, in term of rates of convergence, such as Gauss-Seidel and successive overrelaxation methods were therefore quite naturally introduced in the field of radiative transfer by Trujillo Bueno and Fabiani Bendicho [A novel iterative scheme for the very fast and accurate solution of non-LTE radiative transfer problems. Astrophys J 1995;455:646]; it was thoroughly described for the non-LTE two-level atom case. We describe hereafter in details how such methods can be generalized when dealing with non-LTE unpolarised radiation transfer with multilevel atomic models, in monodimensional geometry

  8. Fast reactor programme

    International Nuclear Information System (INIS)

    Hoekstra, E.K.

    1976-11-01

    Estimated reactivity effects of fission products in the SNR-300 fast breeder are given. Neutron cross sections of 127 I and 129 I are also given. Results of the in-pile canning failure experiments on fuel pins R54-F35 and F39 are discussed. Sinter experiments using mixed UC-UN powders are reported. Results of tensile tests on high-dose and low-dose irradiated specimens of 18Cr1 1Ni stainless steel (DIN 1.4948) used in the SNR-300 reactor vessel are given. It is shown that the aerosol behaviour in condensing sodium vapour can be described by the same MADCA model developed for the decay of aerosols in condensing water vapour. Results of heat transfer measurements in the electrically heated 28-rod bundle under liquid-phase and subsequently under two-phase conditions are commented on

  9. The Integral Fast Reactor

    International Nuclear Information System (INIS)

    Till, C.E.

    1985-01-01

    During the past two years, scientists from Argonne have developed an advanced breeder reactor with a closed self contained fuel cycle. The Integral Fast Reactor (IFR) is a new reactor concept, adaptable to a variety of designs, that is based on a fuel cycle radically different from the CRBR line of breeder development. The essential features of the IFR are metal fuel, pool layout, and pyro- and electro-reprocessing in a facility integral with the reactor plant. The IFR shows promise to provide an inexhaustible, safe, economic, environmentally acceptable, and diversion resistant source of nuclear power. It shows potential for major improvement in all of the areas that have led to concern about nuclear power

  10. Fast reactors and nonproliferation

    International Nuclear Information System (INIS)

    Orlov, V.V.

    1997-01-01

    1.Three aspects of nonproliferation relevant to nuclear power are: Pu buildup in NPP spent fuel cooling ponds (∼ 104 t in case of consumption of ∼ 107 t cheap uranium). Danger of illegal radiochemical extraction of Pu for weapons production; Pu extraction from NPP fuel at the plants available in nuclear countries, its burning along with weapon-grade Pu in NPP reactors or in special-purpose burners; increased hazard of nuclear weapons sprawl with breeders and closed fuel cycle technology spreading all over the world. 2.The latter is one of major obstacles to creation of large-scale nuclear power. 3.Nuclear power of the first stage using 235 U will be able to meet the demands of certain fuel-deficient countries and regions, replacing ∼ 5-10% of conventional fuels in the global consumption for a number of decades. 4.Fast reactors of the first generation and the currently employed fuel technology are far from exhausting their potential for solving economic problems and meeting the challenges of safety, radioactive waste and nonproliferation. Development of large-scale nuclear power will become an option accepted by society for solving energy problems in the following century, provided a breeder technology is elaborated and demonstrated in the next 15-20 years, which would comply with the totality of the following requirement: full internal Pu breeding deterministic elimination of severe accidents involving fuel damage and high radioactivity releases: fast runaway, loss of coolant, fires, steam and hydrogen explosions, etc.; reaching a balance between radioactive wastes disposed of and uranium mined in terms of radiation hazard; technology of closed fuel cycle preventing its use for Pu extraction and permitting physical protection from fuel thefts;economic competitiveness of nuclear power for most of countries and regions, i.e. primarily the cost of NPPs with fat reactors is to be below the cost of modern LWR plants, etc

  11. Promotion and Fast Food Demand

    OpenAIRE

    Timothy J. Richards; Luis Padilla

    2009-01-01

    Many believe that fast food promotion is a significant cause of the obesity epidemic in North America. Industry members argue that promotion only reallocates brand shares and does not increase overall demand. We study the effect of fast food promotion on market share and total demand by estimating a discrete / continuous model of fast food restaurant choice and food expenditure that explicitly accounts for both spatial and temporal determinants of demand. Estimates are obtained using a unique...

  12. New fast reactor installation concept

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    The large size and complexity of fast reactor installations are emphasised and these difficulties will be increased with the advent of fast reactors of higher power. In this connection a new concept of fast reactor installation is described with a view to reducing the size of the installation and enabling most components, including even the primary vessel, to be constructed within the confines of a workshop. Full constructional details are given. (U.K.)

  13. Fast mixed spectrum reactor concept

    International Nuclear Information System (INIS)

    Kouts, H.J.C.; Fischer, G.J.; Cerbone, R.J.

    1979-04-01

    The Fast Mixed Spectrum Reactor is a highly promising concept for a fast reactor with improved features of proliferation resistance, and excellent utilization of uranium resources. In technology, it can be considered to be a branch of fast breeder development, though its operation and implications are different from those of FBR'S in important respects. Successful development programs are required in several areas to bring FMSR to reality, but the payoff from a successful program can be high

  14. FastChem: An ultra-fast equilibrium chemistry

    Science.gov (United States)

    Kitzmann, Daniel; Stock, Joachim

    2018-04-01

    FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.

  15. Prolonged fasting increases glutathione biosynthesis in postweaned northern elephant seals

    Science.gov (United States)

    Vázquez-Medina, José Pablo; Zenteno-Savín, Tania; Forman, Henry Jay; Crocker, Daniel E.; Ortiz, Rudy M.

    2011-01-01

    SUMMARY Northern elephant seals experience prolonged periods of absolute food and water deprivation (fasting) while breeding, molting or weaning. The postweaning fast in elephant seals is characterized by increases in the renin–angiotensin system, expression of the oxidant-producing protein Nox4, and NADPH oxidase activity; however, these increases are not correlated with increased oxidative damage or inflammation. Glutathione (GSH) is a potent reductant and a cofactor for glutathione peroxidases (GPx), glutathione-S transferases (GST) and 1-cys peroxiredoxin (PrxVI) and thus contributes to the removal of hydroperoxides, preventing oxidative damage. The effects of prolonged food deprivation on the GSH system are not well described in mammals. To test our hypothesis that GSH biosynthesis increases with fasting in postweaned elephant seals, we measured circulating and muscle GSH content at the early and late phases of the postweaning fast in elephant seals along with the activity/protein content of glutamate-cysteine ligase [GCL; catalytic (GCLc) and modulatory (GCLm) subunits], γ-glutamyl transpeptidase (GGT), glutathione disulphide reductase (GR), glucose-6-phosphate dehydrogenase (G6PDH), GST and PrxVI, as well as plasma changes in γ-glutamyl amino acids, glutamate and glutamine. GSH increased two- to four-fold with fasting along with a 40–50% increase in the content of GCLm and GCLc, a 75% increase in GGT activity, a two- to 2.5-fold increase in GR, G6PDH and GST activities and a 30% increase in PrxVI content. Plasma γ-glutamyl glutamine, γ-glutamyl isoleucine and γ-glutamyl methionine also increased with fasting whereas glutamate and glutamine decreased. Results indicate that GSH biosynthesis increases with fasting and that GSH contributes to counteracting hydroperoxide production, preventing oxidative damage in fasting seals. PMID:21430206

  16. Fast pitch softball injuries.

    Science.gov (United States)

    Meyers, M C; Brown, B R; Bloom, J A

    2001-01-01

    The popularity of fast pitch softball in the US and throughout the world is well documented. Along with this popularity, there has been a concomitant increase in the number of injuries. Nearly 52% of cases qualify as major disabling injuries requiring 3 weeks or more of treatment and 2% require surgery. Interestingly, 75% of injuries occur during away games and approximately 31% of traumas occur during nonpositional and conditioning drills. Injuries range from contusions and tendinitis to ligamentous disorders and fractures. Although head and neck traumas account for 4 to 12% of cases, upper extremity traumas account for 23 to 47% of all injuries and up to 19% of cases involve the knee. Approximately 34 to 42% of injuries occur when the athlete collides with another individual or object. Other factors involved include the quality of playing surface, athlete's age and experience level, and the excessive physical demands associated with the sport. Nearly 24% of injuries involve base running and are due to poor judgement, sliding technique, current stationary base design, unorthodox joint and extremity position during ground impact and catching of cleats. The increasing prevalence of overtraining syndrome among athletes has been attributed to an unclear definition of an optimal training zone, poor communication between player and coach, and the limited ability of bone and connective tissue to quickly respond to match the demands of the sport. This has led routinely to arm, shoulder and lumbar instability, chronic nonsteroidal anti-inflammatory drug (NSAID) use and time loss injuries in 45% of pitching staff during a single season. Specific attention to a safer playing environment, coaching and player education, and sport-specific training and conditioning would reduce the risk, rate and severity of fast pitch traumas. Padding of walls, backstops, rails and dugout areas, as well as minimising use of indoor facilities, is suggested to decrease the number of collision

  17. PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

    KAUST Repository

    Li, Chuanxi; Chen, Peng; Wang, Rujing; Wang, Xiujie; Su, Yaru; Li, Jinyan

    2014-01-01

    Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea

  18. The polarization of fast neutrons

    International Nuclear Information System (INIS)

    Talov, V.V.

    2000-01-01

    The present work is the review of polarization of fast neutrons and methods of polarization analysis. This also includes information about polarization of fast neutrons from first papers, which described polarization in the D(d,n) 3 He, 7 Li(p,n) 7 Be, and T(p,n) 3 He reactions. (authors)

  19. FastStats: Child Health

    Science.gov (United States)

    ... Women’s Health State and Territorial Data Reproductive Health Contraceptive Use Infertility Reproductive Health Notice Regarding FastStats Mobile ... table 6 [PDF – 2.7 MB] Related FastStats Adolescent Health ADHD Asthma Infant Health More data: reports ...

  20. Fast feedback in classroom practice

    NARCIS (Netherlands)

    Emmett, K.M.; Klaassen, K.; Eijkelhof, H.

    2009-01-01

    In this article we describe one application of the fast feedback method (see Berg 2003 Aust. Sci. Teach. J. 28–34) in secondary mechanics education. Two teachers tried out a particular sequence twice, in consecutive years, once with and once without the use of fast feedback. We found the method to

  1. Uranium and the fast reactor

    International Nuclear Information System (INIS)

    Price, T.

    1982-01-01

    The influence of uranium availability upon the future of the fast reactor is reviewed. The important issues considered are uranium reserves and resources, uranium market prices, fast reactor economics and the political availability of uranium to customers in other countries. (U.K.)

  2. Fasting and nonfasting lipid levels

    DEFF Research Database (Denmark)

    Langsted, Anne; Freiberg, Jacob J; Nordestgaard, Børge G

    2008-01-01

    Lipid profiles are usually measured after fasting. We tested the hypotheses that these levels change only minimally in response to normal food intake and that nonfasting levels predict cardiovascular events.......Lipid profiles are usually measured after fasting. We tested the hypotheses that these levels change only minimally in response to normal food intake and that nonfasting levels predict cardiovascular events....

  3. Oil Analysis by Fast DSC

    NARCIS (Netherlands)

    Wetten, I.A.; Herwaarden, A.W.; Splinter, R.; Ruth, van S.M.

    2014-01-01

    Thermal analysis of Olive and Sunflower Oil is done by Fast DSC to evaluate its potential to replace DSC for adulteration detection. DSC measurements take hours, Fast DSC minutes. Peak temperatures of the crystallisation peak in cooling for different Olive and Sunflower Oils are both comparable to

  4. The safety of fast reactors

    International Nuclear Information System (INIS)

    Justin, F.

    1976-01-01

    A response is made to the main questions that a man in the street may arise concerning fast breeder reactors, in particular: the advantages of this line, dangerous materials contained in fast breeder reactors, containment shells protecting the environment from radiations, main studies now in progress [fr

  5. Fast reactor programme

    International Nuclear Information System (INIS)

    Plakman, J.C.

    1981-06-01

    The accuracy requirements and the status of the evaluated fission-product cross sections for fast reactors are reviewed; the work on calculating the sensitivity of the sodium void effect to fission-product cross sections is described; some results of the intercomparison of adjusted data sets for capture cross sections of fission-products (RCN-2A and CARNAVAL-IV) are discussed; the applicability of the maximum-likelihood method for the analysis of resolved resonance parameters for a large class of fission-product nuclides is demonstrated; the neutron cross sections for corrosion product 64 Ni are evaluated. Some results of post-irradiation examination of a loss-of-cooling experiment are given; the progress in testing the equipment and instrumentation for transient-overpower experiments is reported. The proceedings in the thermochemical investigations on uranium compounds with some fission-products are described. The creep behaviour of a heat of DIN 1.4948 parent metal is investigated with respect to the changes in strain with different test temperatures. Sodium smoke aerosols have been produced and analysed with respect to their aerodynamic behaviour and morphology. The two-phase local boiling experiments have been analysed to find criteria for the occurrence of different boiling regimes with the objection to deduce general dryout correlations

  6. Fast ignition breakeven scaling

    International Nuclear Information System (INIS)

    Slutz, Stephen A.; Vesey, Roger Alan

    2005-01-01

    A series of numerical simulations have been performed to determine scaling laws for fast ignition break even of a hot spot formed by energetic particles created by a short pulse laser. Hot spot break even is defined to be when the fusion yield is equal to the total energy deposited in the hot spot through both the initial compression and the subsequent heating. In these simulations, only a small portion of a previously compressed mass of deuterium-tritium fuel is heated on a short time scale, i.e., the hot spot is tamped by the cold dense fuel which surrounds it. The hot spot tamping reduces the minimum energy required to obtain break even as compared to the situation where the entire fuel mass is heated, as was assumed in a previous study [S. A. Slutz, R. A. Vesey, I. Shoemaker, T. A. Mehlhorn, and K. Cochrane, Phys. Plasmas 7, 3483 (2004)]. The minimum energy required to obtain hot spot break even is given approximately by the scaling law E T = 7.5(ρ/100) -1.87 kJ for tamped hot spots, as compared to the previously reported scaling of E UT = 15.3(ρ/100) -1.5 kJ for untamped hotspots. The size of the compressed fuel mass and the focusability of the particles generated by the short pulse laser determines which scaling law to use for an experiment designed to achieve hot spot break even

  7. Fast liner proposal

    International Nuclear Information System (INIS)

    Sherwood, A.R.; Freeman, B.L.; Gerwin, R.A.; Jarboe, T.R.; Krakowski, R.A.; Malone, R.C.; Marshall, J.; Miller, R.L.; Suydam, B.

    1977-08-01

    This is a proposal to study, both theoretically and experimentally, the possibility of making a fusion reactor by magnetically imploding a cylindrical metallic shell on a prepared plasma. The approach is characterized by the following features: (1) the nonrotating liner would be driven by an axial current, (2) the plasma would also carry an axial current that provides an azimuthal magnetic field for thermal insulation in both the radial and longitudinal directions, (3) solid end plugs would be utilized to prevent axial loss of particles, and (4) liner speeds would be in the 10 6 cm/s range. The preliminary calculations indicate (1) that the energetics are favorable (energy inputs of about 10 MJ might produce a machine in the break-even regime), (2) that radiation and heat losses could be made tolerable, (3) that alpha-particle heating could be made very effective, and (4) that Taylor instabilities in a fast liner might be harmless because of the large viscosities at high pressures. A preliminary conceptual design of the sort of fusion reactor that might result from such an approach is discussed, as are some of the relevant reactor scaling arguments

  8. Fast reactor recharging device

    International Nuclear Information System (INIS)

    Artemiev, L.N.; Kurilkin, V.V.

    1979-01-01

    Disclosure is made of a device for recharging a fast-neutron reactor, intended for the transfer of fuel assemblies and rods of the control and safety system, having profiled heads to be gripped on the outside. The device comprises storage drums whose compartments for rods of the control and safety system are identical to compartments for fuel assemblies. In order to store and transport rods of the control and safety system from the storage drums to the recharging mechanism provision is made for sleeve-type holders. When placed in such a holder, the dimensions of a rod of the control and safety system are equal to those of a fuel assembly. To join a holder to a rod of the control and safety system, on the open end of each holder there is mounted a collet, whereas on the surface of each rod of the control and safety system, close to its head, there is provided an encircling groove to interact with the collet. The grip of the recharging mechanism is provided with a stop interacting with the collet in order to open the latter and withdraw the safety and control system rod from its holder

  9. The ATLAS Fast Tracker

    CERN Document Server

    Volpi, Guido; The ATLAS collaboration

    2015-01-01

    The use of tracking information at the trigger level in the LHC Run II period is crucial for the trigger an data acquisition (TDAQ) system. The tracking precision is in fact important to identify specific decay products of the Higgs boson or new phenomena, a well as to distinguish the contributions coming from many contemporary collisions that occur at every bunch crossing. However, the track reconstruction is among the most demanding tasks performed by the TDAQ computing farm; in fact, full reconstruction at full Level-1 trigger accept rate (100 KHz) is not possible. In order to overcome this limitation, the ATLAS experiment is planning the installation of a specific processor: the Fast Tracker (FTK), which is aimed at achieving this goal. The FTK is a pipeline of high performance electronic, based on custom and commercial devices, which is expected to reconstruct, with high resolution, the trajectories of charged tracks with a transverse momentum above 1 GeV, using the ATLAS inner tracker information. Patte...

  10. Fast breeder fuel cycle

    International Nuclear Information System (INIS)

    1978-07-01

    This contribution is prepared for the answer to the questionnaire of working group 5, subgroup B. B.1. is the short review of the fast breeder fuel cycles based on the reference large commercial Japanese LMFBR. The LMFBRs are devided into two types. FBR-A is the reactor to be used before 2000, and its burnup and breeding ratio are relatively low. The reference fuel cycle requirement is calculated based on the FBR-A. FBR-B is the one to be used after 2000, and its burnup and breeding ratio are relatively high. B.2. is basic FBR fuel reprocessing scheme emphasizing the differences with LWR reprocessing. This scheme is based on the conceptual design and research and development work on the small scale LMFBR reprocessing facility of Japan. The facility adopts a conventional PUREX process except head end portions. The report also describes the effects of technical modifications of conventional reprocessing flow sheets, and the problems to be solved before the adoption of these alternatives

  11. Fast Aerial Video Stitching

    Directory of Open Access Journals (Sweden)

    Jing Li

    2014-10-01

    Full Text Available The highly efficient and robust stitching of aerial video captured by unmanned aerial vehicles (UAVs is a challenging problem in the field of robot vision. Existing commercial image stitching systems have seen success with offline stitching tasks, but they cannot guarantee high-speed performance when dealing with online aerial video sequences. In this paper, we present a novel system which has an unique ability to stitch high-frame rate aerial video at a speed of 150 frames per second (FPS. In addition, rather than using a high-speed vision platform such as FPGA or CUDA, our system is running on a normal personal computer. To achieve this, after the careful comparison of the existing invariant features, we choose the FAST corner and binary descriptor for efficient feature extraction and representation, and present a spatial and temporal coherent filter to fuse the UAV motion information into the feature matching. The proposed filter can remove the majority of feature correspondence outliers and significantly increase the speed of robust feature matching by up to 20 times. To achieve a balance between robustness and efficiency, a dynamic key frame-based stitching framework is used to reduce the accumulation errors. Extensive experiments on challenging UAV datasets demonstrate that our approach can break through the speed limitation and generate an accurate stitching image for aerial video stitching tasks.

  12. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  13. Comparison of three methods for determination of protein ...

    African Journals Online (AJOL)

    However, a six fold greater amount of protein was obtained when FastPrep was applied to lyse LAB cells. Our results also indicate that, this fast and easy extraction method allows more spot-abundant polyacrylamide gels. More clear and consistent strips were detected by SDS-PAGE when proteins were extracted by ...

  14. Fast-prototyping of VLSI

    International Nuclear Information System (INIS)

    Saucier, G.; Read, E.

    1987-01-01

    Fast-prototyping will be a reality in the very near future if both straightforward design methods and fast manufacturing facilities are available. This book focuses, first, on the motivation for fast-prototyping. Economic aspects and market considerations are analysed by European and Japanese companies. In the second chapter, new design methods are identified, mainly for full custom circuits. Of course, silicon compilers play a key role and the introduction of artificial intelligence techniques sheds a new light on the subject. At present, fast-prototyping on gate arrays or on standard cells is the most conventional technique and the third chapter updates the state-of-the art in this area. The fourth chapter concentrates specifically on the e-beam direct-writing for submicron IC technologies. In the fifth chapter, a strategic point in fast-prototyping, namely the test problem is addressed. The design for testability and the interface to the test equipment are mandatory to fulfill the test requirement for fast-prototyping. Finally, the last chapter deals with the subject of education when many people complain about the lack of use of fast-prototyping in higher education for VLSI

  15. FAST MRI breast screening revisited

    International Nuclear Information System (INIS)

    Jain, Manish; Jain, Arushi; Hyzy, Marek D.; Werth, Graziella

    2017-01-01

    Screening for breast cancer in high-risk women takes about 40 minutes to acquire an MRI scan and is time-intensive to report. There is recent interest in the performance of an abbreviated MRI protocol (FAST) in the screening setting. FAST scans have a reported negative predictive value of 99.8%. This study evaluates the false positive rates (FPR) and recall rates for FAST scans as compared to full diagnostic studies (FD). A database of all screening breast MRI scans performed at our institution between 30 June 2013 and 1 July 2014 (n = 591) was created by one of the researchers, who did not subsequently analyse the MRI scans. The T1W and first post-contrast and subtracted images from each of these scans (FAST protocol) were assessed by experienced breast MRI radiologists, blinded to the final diagnosis. The findings were then compared with the FD result. The recall rates were 6.6% for FAST scans and 5.8% for FD scans. FPR rates were 4.7% and 3.9% respectively. There is no statistically significant difference in the recall rates or FPR of FAST scans in comparison with full diagnostic studies. Given the absence of statistically significant difference in the FPR and recall rates in comparison with FD, FAST scans can replace FD for screening of breast cancer.

  16. Fast food: unfriendly and unhealthy.

    Science.gov (United States)

    Stender, S; Dyerberg, J; Astrup, A

    2007-06-01

    Although nutrition experts might be able to navigate the menus of fast-food restaurant chains, and based on the nutritional information, compose apparently 'healthy' meals, there are still many reasons why frequent fast-food consumption at most chains is unhealthy and contributes to weight gain, obesity, type 2 diabetes and coronary artery disease. Fast food generally has a high-energy density, which, together with large portion sizes, induces over consumption of calories. In addition, we have found it to be a myth that the typical fast-food meal is the same worldwide. Chemical analyses of 74 samples of fast-food menus consisting of French fries and fried chicken (nuggets/hot wings) bought in McDonalds and KFC outlets in 35 countries in 2005-2006 showed that the total fat content of the same menu varies from 41 to 65 g at McDonalds and from 42 to 74 g at KFC. In addition, fast food from major chains in most countries still contains unacceptably high levels of industrially produced trans-fatty acids (IP-TFA). IP-TFA have powerful biological effects and may contribute to increased weight gain, abdominal obesity, type 2 diabetes and coronary artery disease. The food quality and portion size need to be improved before it is safe to eat frequently at most fast-food chains.

  17. Fast reactor physics - an overview

    International Nuclear Information System (INIS)

    Lee, S.M.

    2004-01-01

    An introduction to the basic features of fast neutron reactors is made, highlighting the differences from the more conventional thermal neutron reactors. A discussion of important feedback reactivity mechanisms is given. Then an overview is presented of the methods of fast reactor physics, which play an important role in the successful design and operation of fast reactors. The methods are based on three main elements, namely (i) nuclear data bases, (ii) numerical methods and computer codes, and (iii) critical experiments. These elements are reviewed and the present status and future trends are summarized. (author)

  18. [Fast food promotes weight gain].

    Science.gov (United States)

    Stender, Steen; Dyerberg, Jørn; Astrup, Arne V

    2007-05-07

    The total amounts of fat in a fast food menu consisting of French fries and fried Chicken Nuggets from McDonald's and KFC, respectively, bought in 35 different countries vary from 41 to 71 gram. In most countries the menu contained unacceptably high amounts of industrially-produced trans fat which contributes to an increased risk of ischaemic heart disease, weight gain, abdominal fat accumulation and type 2 diabetes. The quality of the ingredients in fast food ought to be better and the size of the portions smaller and less energy-dense so that frequent fast food meals do not increase the risk of obesity and diseases among customers.

  19. Molecular packing, hydrogen bonding, and fast dynamics in lysozyme/trehalose/glycerol and trehalose/glycerol glasses at low hydration

    OpenAIRE

    Lerbret, Adrien; Affouard, Frédéric

    2017-01-01

    Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\\sim$ \\AA ) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme...

  20. FastStats: Contraceptive Use

    Science.gov (United States)

    ... Growth (data are for 2011-2015) Related FastStats Infertility Reproductive Health More data Condom Use During Sexual Intercourse Among Females and Males 15-44 in the United States [PDF – 430 ...

  1. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  2. Allegheny County Fast Food Establishments

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Allegheny County Health Department has generated this list of fast food restaurants by exporting all chain restaurants without an alcohol permit from the...

  3. FastStats: Mental Health

    Science.gov (United States)

    ... Women’s Health State and Territorial Data Reproductive Health Contraceptive Use Infertility Reproductive Health Notice Regarding FastStats Mobile ... Use of Selected Nonmedication Mental Health Services by Adolescent Boys and Girls With Serious Emotional or Behavioral ...

  4. Fast neutron spectrometry and dosimetry

    International Nuclear Information System (INIS)

    Blaize, S.; Ailloud, J.; Mariani, J.; Millot, J.P.

    1958-01-01

    We have studied fast neutron spectrometry and dosimetry through the recoil protons they produce in hydrogenated samples. In spectrometric, we used nuclear emulsions, in dosimetric, we used polyethylene coated with zinc sulphide and placed before a photomultiplier. (author) [fr

  5. The Fast Theater Model (FATHM)

    National Research Council Canada - National Science Library

    Brown, Gerald G; Washburn, Alan R

    2002-01-01

    The Fast Theater Model (FATHM) is an aggregated joint theater combat model that fuses Air Force Air-to-Ground attack sortie optimization with Ground-to-Ground deterministic Lanchester fire-exchange battles using attrition rates...

  6. The price of fast fashion

    Science.gov (United States)

    2018-01-01

    The fashion industry has changed rapidly in recent years with the increased prevalence of fast fashion, impacting the environment. Efforts to green this polluting industry require action from businesses and consumers.

  7. FastStats: Body Measurements

    Science.gov (United States)

    ... this? Submit What's this? Submit Button NCHS Home Body Measurements Recommend on Facebook Tweet Share Compartir Data ... 7 MB] Related FastStats Obesity/Overweight Related Links Body Mass Index table CDC Growth Charts National Health ...

  8. Fast generation of dendritic cells

    DEFF Research Database (Denmark)

    Kvistborg, P; Bøgh, Marie; Pedersen, A W

    2009-01-01

    we have developed fast DC protocol by comparing two different fast DC protocols with SDDC. DC were evaluated by FACS analysis, and the optimal profile was considered: CD14(low), CD80(high), CD83(high), CD86(high), CCR7(high), HLA class I and II(high). FACS profiles were used as the selection criteria...... together with yield and morphology. Two fast DC protocols fulfilled these criteria and were selected for functional analysis. Our results demonstrate that DC generated within 5days or 48h are comparable with SDDC both phenotypically and functionally. However, we found that 48h DC were more susceptible than...... SDDC to the IL-10 inducing stimulus of TLR ligands (R848 and LPS). Thus to determine the clinical relevance of fast DC protocols in cancer settings, small phase I trials should be conducted monitoring regulatory T cells carefully....

  9. Contraband detection with fast neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Buffler, Andy E-mail: abuffler@science.uct.ac.za

    2004-11-01

    Recent terror events and the increase in the trade of illicit drugs have fuelled the exploration of the use of fast neutrons as probes for the detection of hidden contraband, especially explosives, in packages ranging in size from small mail items to cargo containers. The various approaches using fast neutrons for contraband detection, presently under development, are reviewed. The role that a neutron system might play in the non-intrusive interrogation of airline luggage is discussed.

  10. Review of fast reactor activities

    International Nuclear Information System (INIS)

    1982-01-01

    A description of some highlights of the activities performed by the Commission of the European Communities in the field of fast reactors is given. They fall into two categories: coordinating and harmonizing activities and research activities. The former are essentially performed in the frame of the Fast Reactor Coordinating Committee (FRCC), the latter in the Commission's Joint Research Center and to some extent under contract in research centers of the Member States

  11. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

  12. Physiological responses to food deprivation in the house sparrow, a species not adapted to prolonged fasting.

    Science.gov (United States)

    Khalilieh, Anton; McCue, Marshall D; Pinshow, Berry

    2012-09-01

    Many wild birds fast during reproduction, molting, migration, or because of limited food availability. Species that are adapted to fasting sequentially oxidize endogenous fuels in three discrete phases. We hypothesized that species not adapted to long fasts have truncated, but otherwise similar, phases of fasting, sequential changes in fuel oxidization, and similar changes in blood metabolites to fasting-adapted species. We tested salient predictions in house sparrows (Passer domesticus biblicus), a subspecies that is unable to tolerate more than ~32 h of fasting. Our main hypothesis was that fasting sparrows sequentially oxidize substrates in the order carbohydrates, lipids, and protein. We dosed 24 house sparrows with [(13)C]glucose, palmitic acid, or glycine and measured (13)CO(2) in their breath while they fasted for 24 h. To ascertain whether blood metabolite levels reflect fasting-induced changes in metabolic fuels, we also measured glucose, triacylglycerides, and β-hydroxybutyrate in the birds' blood. The results of both breath (13)CO(2) and plasma metabolite analyses did not support our hypothesis; i.e., that sparrows have the same metabolic responses characteristic of fasting-adapted species, but on a shorter time scale. Contrary to our main prediction, we found that recently assimilated (13)C-tracers were oxidized continuously in different patterns with no definite peaks corresponding to the three phases of fasting and also that changes in plasma metabolite levels accurately tracked the changes found by breath analysis. Notably, the rate of recently assimilated [(13)C]glycine oxidization was significantly higher (P fast for longer than 32 h is likely related to their inability to accrue large lipid stores, separately oxidize different fuels, and/or spare protein during fasting.

  13. Upgrading ATLAS Fast Calorimeter Simulation

    CERN Document Server

    Heath, Matthew Peter; The ATLAS collaboration

    2017-01-01

    Producing the very large samples of simulated events required by many physics and performance studies with the ATLAS detector using the full GEANT4 detector simulation is highly CPU intensive. Fast simulation tools are a useful way of reducing CPU requirements when detailed detector simulations are not needed. During the LHC Run-1, a fast calorimeter simulation (FastCaloSim) was successfully used in ATLAS. FastCaloSim provides a simulation of the particle energy response at the calorimeter read-out cell level, taking into account the detailed particle shower shapes and the correlations between the energy depositions in the various calorimeter layers. It is interfaced to the standard ATLAS digitization and reconstruction software, and it can be tuned to data more easily than Geant4. Now an improved version of FastCaloSim is in development, incorporating the experience with the version used during Run-1. The new FastCaloSim aims to overcome some limitations of the first version by improving the description of s...

  14. Direct Fast-Neutron Detection

    International Nuclear Information System (INIS)

    DC Stromswold; AJ Peurrung; RR Hansen; PL Reeder

    2000-01-01

    Direct fast-neutron detection is the detection of fast neutrons before they are moderated to thermal energy. We have investigated two approaches for using proton-recoil in plastic scintillators to detect fast neutrons and distinguish them from gamma-ray interactions. Both approaches use the difference in travel speed between neutrons and gamma rays as the basis for separating the types of events. In the first method, we examined the pulses generated during scattering in a plastic scintillator to see if they provide a means for distinguishing fast-neutron events from gamma-ray events. The slower speed of neutrons compared to gamma rays results in the production of broader pulses when neutrons scatter several times within a plastic scintillator. In contrast, gamma-ray interactions should produce narrow pulses, even if multiple scattering takes place, because the time between successive scattering is small. Experiments using a fast scintillator confirmed the presence of broader pulses from neutrons than from gamma rays. However, the difference in pulse widths between neutrons and gamma rays using the best commercially available scintillators was not sufficiently large to provide a practical means for distinguishing fast neutrons and gamma rays on a pulse-by-pulse basis. A faster scintillator is needed, and that scintillator might become available in the literature. Results of the pulse-width studies were presented in a previous report (peurrung et al. 1998), and they are only summarized here

  15. Fast Calorimeter Simulation in ATLAS

    CERN Document Server

    Schaarschmidt, Jana; The ATLAS collaboration

    2017-01-01

    Producing the very large samples of simulated events required by many physics and performance studies with the ATLAS detector using the full GEANT4 detector simulation is highly CPU intensive. Fast simulation tools are a useful way of reducing CPU requirements when detailed detector simulations are not needed. During the LHC Run-1, a fast calorimeter simulation (FastCaloSim) was successfully used in ATLAS. FastCaloSim provides a simulation of the particle energy response at the calorimeter read-out cell level, taking into account the detailed particle shower shapes and the correlations between the energy depositions in the various calorimeter layers. It is interfaced to the standard ATLAS digitization and reconstruction software, and it can be tuned to data more easily than GEANT4. It is 500 times faster than full simulation in the calorimeter system. Now an improved version of FastCaloSim is in development, incorporating the experience with the version used during Run-1. The new FastCaloSim makes use of mach...

  16. Role of plasma adiponectin /C-reactive protein ratio in obesity and ...

    African Journals Online (AJOL)

    African Health Sciences ... Objective(s): We examined relations between fasting plasma adiponectin (ADIP), C-reactive protein (CRP) ... Methods: Fasting plasma ADIP, CRP, Insulin (IN), HOMA-IR, lipid profiles, body fat percent (%BF), waist ...

  17. Protein Detection with Aptamer Biosensors

    Directory of Open Access Journals (Sweden)

    Regina Stoltenburg

    2008-07-01

    Full Text Available Aptamers have been developed for different applications. Their use as new biological recognition elements in biosensors promises progress for fast and easy detection of proteins. This new generation of biosensor (aptasensors will be more stable and well adapted to the conditions of real samples because of the specific properties of aptamers.

  18. Fast reactor database. 2006 update

    International Nuclear Information System (INIS)

    2006-12-01

    Liquid metal cooled fast reactors (LMFRs) have been under development for about 50 years. Ten experimental fast reactors and six prototype and commercial size fast reactor plants have been constructed and operated. In many cases, the overall experience with LMFRs has been rather good, with the reactors themselves and also the various components showing remarkable performances, well in accordance with the design expectations. The fast reactor system has also been shown to have very attractive safety characteristics, resulting to a large extent from the fact that the fast reactor is a low pressure system with large thermal inertia and negative power and temperature coefficients. In addition to the LMFRs that have been constructed and operated, more than ten advanced LMFR projects have been developed, and the latest designs are now close to achieving economic competitivity with other reactor types. In the current world economic climate, the introduction of a new nuclear energy system based on the LMFR may not be considered by utilities as a near future option when compared to other potential power plants. However, there is a strong agreement between experts in the nuclear energy field that, for sustainability reasons, long term development of nuclear power as a part of the world's future energy mix will require the fast reactor technology, and that, given the decline in fast reactor development projects, data retrieval and knowledge preservation efforts in this area are of particular importance. This publication contains detailed design data and main operational data on experimental, prototype, demonstration, and commercial size LMFRs. Each LMFR plant is characterized by about 500 parameters: physics, thermohydraulics, thermomechanics, by design and technical data, and by relevant sketches. The focus is on practical issues that are useful to engineers, scientists, managers, university students and professors with complete technical information of a total of 37 LMFR

  19. Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2008-05-01

    Full Text Available Abstract Members of the genus Cypovirus (family Reoviridae are common pathogens of insects. These viruses have linear dsRNA genomes divided into 10–11 segments, which have generally been assumed to be monocistronic. Here, bioinformatic evidence is presented for a short overlapping coding sequence (CDS in the cypovirus genome segment encoding the major core capsid protein VP1, overlapping the 5'-terminal region of the VP1 ORF in the +1 reading frame. In Cypovirus type 1 (CPV-1, a 62-codon AUG-initiated open reading frame (hereafter ORFX is present in all four available segment 1 sequences. The pattern of base variations across the sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP1 reading frame are taken into account; MLOGD software. In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP1. The genomic location of ORFX is consistent with translation via leaky scanning. A 62–64 codon AUG-initiated ORF is present in a corresponding location and reading frame in other available cypovirus sequences (2 CPV-14, 1 CPV-15 and an 87-codon ORFX homologue may also be present in Aedes pseudoscutellaris reovirus. The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5–10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels.

  20. FAST: An advanced code system for fast reactor transient analysis

    International Nuclear Information System (INIS)

    Mikityuk, Konstantin; Pelloni, Sandro; Coddington, Paul; Bubelis, Evaldas; Chawla, Rakesh

    2005-01-01

    One of the main goals of the FAST project at PSI is to establish a unique analytical code capability for the core and safety analysis of advanced critical (and sub-critical) fast-spectrum systems for a wide range of different coolants. Both static and transient core physics, as well as the behaviour and safety of the power plant as a whole, are studied. The paper discusses the structure of the code system, including the organisation of the interfaces and data exchange. Examples of validation and application of the individual programs, as well as of the complete code system, are provided using studies carried out within the context of designs for experimental accelerator-driven, fast-spectrum systems

  1. Protein synthesis and degradation during starvation-induced cardiac atrophy in rabbits

    International Nuclear Information System (INIS)

    Samarel, A.M.; Parmacek, M.S.; Magid, N.M.; Decker, R.S.; Lesch, M.

    1987-01-01

    To determine the relative importance of protein degradation in the development of starvation-induced cardiac atrophy, in vivo fractional synthetic rates of total cardiac protein, myosin heavy chain, actin, light chain 1, and light chain 2 were measured in fed and fasted rabbits by continuous infusion of [ 3 H] leucine. In addition, the rate of left ventricular protein accumulation and loss were assessed in weight-matched control and fasted rabbits. Rates of total cardiac protein degradation were then estimated as the difference between rates of synthesis and growth. Fasting produced left ventricular atrophy by decreasing the rate of left ventricular protein synthesis (34.8 +/- 1.4, 27.3 +/- 3.0, and 19.3 +/- 1.2 mg/day of left ventricular protein synthesized for 0-, 3-, and 7-day fasted rabbits, respectively). Inhibition of contractile protein synthesis was evident by significant reductions in the fractional synthetic rates of all myofibrillar protein subunits. Although fractional rates of protein degradation increased significantly within 7 days of fasting, actual amounts of left ventricular protein degraded per day were unaffected. Thus, prolonged fasting profoundly inhibits the synthesis of new cardiac protein, including the major protein constituents of the myofibril. Both this inhibition in new protein synthesis as well as a smaller but significant reduction in the average half-lives of cardiac proteins are responsible for atrophy of the heart in response to fasting

  2. Preoperative fasting time in children.

    LENUS (Irish Health Repository)

    Adeel, S

    2012-02-01

    The aim of preoperative fasting is to prevent regurgitation and pulmonary aspiration while limiting potential problems of thirst, dehydration and hypoglycaemia. The American Society of Anaesthesiologists (ASA) has suggested guidelines for preoperative fasting for children undergoing elective surgery. We did a postal survey to determine the current practice regarding these guidelines amongst all specialist registrars in anaesthesia in Ireland. A questionnaire was sent to all specialist registrars in anaesthesia (90 in total), 60 (67%) were returned and analysed. The question asked was how long children should be kept fasting before elective surgery. The results of our survey suggest that most of the respondents are following the ASA guidelines for clear fluids and solids however there were differing opinion regarding the duration of fasting for formula milk and breast milk. In conclusion, we would recommend greater awareness and collaboration between anaesthetists, nurses and surgeons to ensure that fasting instructions are consistent with the ASA guidelines and that patient and their parents understand these directives as well.

  3. δ15N value does not reflect fasting in mysticetes.

    Science.gov (United States)

    Aguilar, Alex; Giménez, Joan; Gómez-Campos, Encarna; Cardona, Luís; Borrell, Asunción

    2014-01-01

    The finding that tissue δ(15)N values increase with protein catabolism has led researchers to apply this value to gauge nutritive condition in vertebrates. However, its application to marine mammals has in most occasions failed. We investigated the relationship between δ(15)N values and the fattening/fasting cycle in a model species, the fin whale, a migratory capital breeder that experiences severe seasonal variation in body condition. We analyzed two tissues providing complementary insights: one with isotopic turnover (muscle) and one that keeps a permanent record of variations in isotopic values (baleen plates). In both tissues δ(15)N values increased with intensive feeding but decreased with fasting, thus contradicting the pattern previously anticipated. The apparent inconsistency during fasting is explained by the fact that a) individuals migrate between different isotopic isoscapes, b) starvation may not trigger significant negative nitrogen balance, and c) excretion drops and elimination of 15N-depleted urine is minimized. Conversely, when intensive feeding is resumed in the northern grounds, protein anabolism and excretion start again, triggering 15N enrichment. It can be concluded that in whales and other mammals that accrue massive depots of lipids as energetic reserves and which have limited access to drinking water, the δ15N value is not affected by fasting and therefore cannot be used as an indication of nutritive condition.

  4. Chromatin damage induced by fast neutrons or UV laser radiation

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I

    2002-07-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m{sup -2}. The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  5. Chromatin damage induced by fast neutrons or UV laser radiation

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I.

    2002-01-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m -2 . The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  6. Review of fast reactor activities in India

    International Nuclear Information System (INIS)

    Paranjpe, S.R.

    1982-01-01

    A review of fast reactor activities in India is introduced. One stage of construction of the Fast Breeder Test Reactor (FBTR) and design studies for 500MWe Prototype Fast Breeder Reactor (PFBR) are briefly summarized. The emphasis is on fast reactor physics, materials studies, radiochemistry, and the safety and fuel reprocessing programme

  7. Observations of fast variable objects

    International Nuclear Information System (INIS)

    Alekseev, G.N.

    1978-01-01

    A problem on studying fast variable astronomic objects is considered. The basis of the method used in the experiment is a detailed photoelectric study of a fast variableness along with spectroscopy of a high time resolution. Power spectrum of the SS Cyg brightness oscillations and autocorrelation function of the AX Mon brightness are analyzed as an example. To provide a reliable identification of parameters of star active regions responsible for the fast variableness, an experiment is proposed, the ''synchronous spectroscopy'' method being used. The method is based on the supposition about temporary stationarity of occasional processes within the limits of the time scale of several hours. The block diagram of the experiment is described

  8. Review of fast reactor activities

    Energy Technology Data Exchange (ETDEWEB)

    Balz, W [Commission of the European Communities, Brussels (Belgium)

    1978-07-01

    The Commission of the European Communities continued its activities on the following lines: activities aimed at preparing for commercialization of fast breeder reactors which are essentially performed in the frame of Fast Reactor Coordinating Committee (FRCC); the execution of its own research program in the Joint Research Center. The report covers activities of the FRCC, of the Safety Working Group (SWG), the Whole Core Accident Code (WAC) subgroup, Containment (CONT) subgroup, Codes and Standards Working Group (CSWG). Research and development activities are concerned with LMFBR safety, subassembly thermal hydraulics, fuel-coolant interactions, post-accident heat removal, dynamic load response, safety related material properties, utilization limits of fast breeder fuels, plutonium and actinide aspects of nuclear fuel cycle.

  9. Fast reactor collaboration in Europe

    International Nuclear Information System (INIS)

    Smith, G.E.I.

    1987-01-01

    Fast reactors have been developed in several European countries, the United Kingdom, France, Germany and Italy. A suggestion to collaborate on fast reactor research and development resulted in an Intergovernmental Memorandum of Understanding signed in 1984 by the UK, France, Germany, Italy and Belgium. Holland was expected to join later. This provided for co-operation between electric utilities, reactor design, research and development companies and fuel cycle companies. Three steering committees have so far been set up, the European fast reactor utilities Group, the European research and development and the European fuel cycle steering committees. Progress on these is detailed. The main areas of technology exchange are listed in the Appendix. The possibility exists for a series of three large demonstration plants to be built in Europe and a fuel reprocessing plant to confirm the reactor system. (U.K.)

  10. Future Assets, Student Talent (FAST)

    Science.gov (United States)

    1992-01-01

    Future Assets, Student Talent (FAST) motivates and prepares talented students with disabilities to further their education and achieve High Tech and professional employment. The FAST program is managed by local professionals, business, and industry leaders; it is modeled after High School High Tech project TAKE CHARGE started in Los Angeles in 1983. Through cooperative efforts of Alabama Department of Education, Vocational Rehabilitation, Adult and Children Services, and the President's Committee on Employment of People with Disabilities, north central Alabama was chosen as the second site for a High School High Tech project. In 1986 local business, industry, education, government agencies, and rehabilitation representatives started FAST. The program objectives and goals, results and accomplishments, and survey results are included.

  11. Review of fast reactor activities

    International Nuclear Information System (INIS)

    Balz, W.

    1978-01-01

    The Commission of the European Communities continued its activities on the following lines: activities aimed at preparing for commercialization of fast breeder reactors which are essentially performed in the frame of Fast Reactor Coordinating Committee (FRCC); the execution of its own research program in the Joint Research Center. The report covers activities of the FRCC, of the Safety Working Group (SWG), the Whole Core Accident Code (WAC) subgroup, Containment (CONT) subgroup, Codes and Standards Working Group (CSWG). Research and development activities are concerned with LMFBR safety, subassembly thermal hydraulics, fuel-coolant interactions, post-accident heat removal, dynamic load response, safety related material properties, utilization limits of fast breeder fuels, plutonium and actinide aspects of nuclear fuel cycle

  12. The polarization of fast neutrons

    International Nuclear Information System (INIS)

    Talov, V.V.

    2001-01-01

    It is insufficient to know coordinates and momentum to describe a state of a neutron. It is necessary to define a spin orientation. As far as it is known from quantum mechanics, a half spin has a projection in the positive direction or in the negative direction. The probability of both projections in an unpolarized beam is equal. If a direction exists, in which the projection is more probably then beam is called polarized in this direction. It is essential to know polarization of neutrons for characteristics of a neutron source, which is emitting it. The question of polarization of fast neutrons came up in 50's. The present work is the review of polarization of fast neutrons and methods of polarization analysis. This also includes information about polarization of fast neutrons from first papers, which described polarization in the D(d,n) 3 He, 7 Li (p,n) 7 Be, T(p,n) 3 He reactions. (authors)

  13. The Proteins API: accessing key integrated protein and genome information.

    Science.gov (United States)

    Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

    2017-07-03

    The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

    Science.gov (United States)

    Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomáš; Stamatakis, Alexandros; von Haeseler, Arndt; Minh, Bui Quang

    2018-02-02

    The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony. To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3-63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased. MPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot .

  15. [Preoperative fasting period of fluids in bariatric surgery].

    Science.gov (United States)

    Simon, P; Pietsch, U-C; Oesemann, R; Dietrich, A; Wrigge, H

    2017-07-01

    Aspiration of stomach content is a severe complication during general anaesthesia. The DGAI (German Society for Anesthesiology and Intensive Care Medicine) guidelines recommend a fasting period for liquids of 2 h, with a maximum of 400 ml. Preoperative fasting can affect the patients' recovery after surgery due to insulin resistance and higher protein catabolism as a response to surgical stress. The aim of the study was to compare a liberal fasting regimen consisting of up to 1000 ml of liquids until 2 h before surgery with the DGAI recommendation. The prospective observational clinical study was approved by the ethics committee of the University of Leipzig. In the liberal fasting group (G lib ) patients undergoing bariatric surgery were asked to drink 1000 ml of tea up to 2 h before surgery. Patients assigned to the restrictive fasting group (G res ) who were undergoing nonbariatric abdominal surgery were asked to drink no more than 400 ml of water up to 2 h preoperatively. Right after anaesthesia induction and intubation a gastric tube was placed, gastric residual volume was measured and the pH level of gastric fluid was determined. Moreover, the occurrence of aspiration was monitored. In all, 98 patients with a body mass index (BMI) of G lib 51.1 kg/m 2 and G res 26.5 kg/m 2 were identified. The preoperative fasting period of liquids was significantly different (G lib 170 min vs. G res 700 min, p fasting regimen (1000 ml of fluid) in the preoperative period is safe in patients undergoing bariatric surgery.

  16. Resolving Fast, Confined Diffusion in Bacteria with Image Correlation Spectroscopy.

    Science.gov (United States)

    Rowland, David J; Tuson, Hannah H; Biteen, Julie S

    2016-05-24

    By following single fluorescent molecules in a microscope, single-particle tracking (SPT) can measure diffusion and binding on the nanometer and millisecond scales. Still, although SPT can at its limits characterize the fastest biomolecules as they interact with subcellular environments, this measurement may require advanced illumination techniques such as stroboscopic illumination. Here, we address the challenge of measuring fast subcellular motion by instead analyzing single-molecule data with spatiotemporal image correlation spectroscopy (STICS) with a focus on measurements of confined motion. Our SPT and STICS analysis of simulations of the fast diffusion of confined molecules shows that image blur affects both STICS and SPT, and we find biased diffusion rate measurements for STICS analysis in the limits of fast diffusion and tight confinement due to fitting STICS correlation functions to a Gaussian approximation. However, we determine that with STICS, it is possible to correctly interpret the motion that blurs single-molecule images without advanced illumination techniques or fast cameras. In particular, we present a method to overcome the bias due to image blur by properly estimating the width of the correlation function by directly calculating the correlation function variance instead of using the typical Gaussian fitting procedure. Our simulation results are validated by applying the STICS method to experimental measurements of fast, confined motion: we measure the diffusion of cytosolic mMaple3 in living Escherichia coli cells at 25 frames/s under continuous illumination to illustrate the utility of STICS in an experimental parameter regime for which in-frame motion prevents SPT and tight confinement of fast diffusion precludes stroboscopic illumination. Overall, our application of STICS to freely diffusing cytosolic protein in small cells extends the utility of single-molecule experiments to the regime of fast confined diffusion without requiring advanced

  17. Review of fast reactor activities

    International Nuclear Information System (INIS)

    Haeussermann, W.; Royen, J.

    1978-01-01

    Since 1971, when the Co-ordinating Group on Gas-Cooled Fast reactors Development was set up, the participating countries have maintained an interest in keeping this option as a back-up solution to the sodium cooled fast reactors. Two different concepts were investigated, one based on coated particle type fuel elements and the other on pin type fuel elements. The coated particles studies have been brought to an end, and resources were concentrated on the further development of the pin type concept. The work done in previous years covered design and safety investigations, heat transfer studies and irradiation experiments in thermal reactors

  18. Overview of tritium fast-fission yields

    International Nuclear Information System (INIS)

    Tanner, J.E.

    1981-03-01

    Tritium production rates are very important to the development of fast reactors because tritium may be produced at a greater rate in fast reactors than in light water reactors. This report focuses on tritium production and does not evaluate the transport and eventual release of the tritium in a fast reactor system. However, if an order-of-magnitude increase in fast fission yields for tritium is confirmed, fission will become the dominant production source of tritium in fast reactors

  19. Causes And Effects Of Fast Food

    Directory of Open Access Journals (Sweden)

    Eman Al-Saad

    2015-08-01

    Full Text Available Fast food affects our life in many aspects. In fact There are many reasons that have been shown why people continuing eating fast food while they knew about its negative effects on their health and family because of eating fast food. The commercial advertisements play a major role in consuming fast food. In this research I will focus on causes and effects of eating fast food.

  20. Causes And Effects Of Fast Food

    OpenAIRE

    Eman Al-Saad

    2015-01-01

    Fast food affects our life in many aspects. In fact There are many reasons that have been shown why people continuing eating fast food while they knew about its negative effects on their health and family because of eating fast food. The commercial advertisements play a major role in consuming fast food. In this research I will focus on causes and effects of eating fast food.

  1. Temporal partitioning of adaptive responses of the murine heart to fasting.

    Science.gov (United States)

    Brewer, Rachel A; Collins, Helen E; Berry, Ryan D; Brahma, Manoja K; Tirado, Brian A; Peliciari-Garcia, Rodrigo A; Stanley, Haley L; Wende, Adam R; Taegtmeyer, Heinrich; Rajasekaran, Namakkal Soorappan; Darley-Usmar, Victor; Zhang, Jianhua; Frank, Stuart J; Chatham, John C; Young, Martin E

    2018-03-15

    Recent studies suggest that the time of day at which food is consumed dramatically influences clinically-relevant cardiometabolic parameters (e.g., adiposity, insulin sensitivity, and cardiac function). Meal feeding benefits may be the result of daily periods of feeding and/or fasting, highlighting the need for improved understanding of the temporal adaptation of cardiometabolic tissues (e.g., heart) to fasting. Such studies may provide mechanistic insight regarding how time-of-day-dependent feeding/fasting cycles influence cardiac function. We hypothesized that fasting during the sleep period elicits beneficial adaptation of the heart at transcriptional, translational, and metabolic levels. To test this hypothesis, temporal adaptation was investigated in wild-type mice fasted for 24-h, or for either the 12-h light/sleep phase or the 12-h dark/awake phase. Fasting maximally induced fatty acid responsive genes (e.g., Pdk4) during the dark/active phase; transcriptional changes were mirrored at translational (e.g., PDK4) and metabolic flux (e.g., glucose/oleate oxidation) levels. Similarly, maximal repression of myocardial p-mTOR and protein synthesis rates occurred during the dark phase; both parameters remained elevated in the heart of fasted mice during the light phase. In contrast, markers of autophagy (e.g., LC3II) exhibited peak responses to fasting during the light phase. Collectively, these data show that responsiveness of the heart to fasting is temporally partitioned. Autophagy peaks during the light/sleep phase, while repression of glucose utilization and protein synthesis is maximized during the dark/active phase. We speculate that sleep phase fasting may benefit cardiac function through augmentation of protein/cellular constituent turnover. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Energy metabolism and fasting in male and female insectivorous bats Molossus molossus (Chiroptera: Molossidae

    Directory of Open Access Journals (Sweden)

    MB. Freitas

    Full Text Available Metabolic adaptations induced by 24 and 48 hours of fasting were investigated in male and female insectivorous bats (Molossus molossus Pallas, 1766. For this purpose, plasma glucose, non esterified fatty acids (NEFA, glycogen, protein and lipids concentrations in liver and muscles were obtained. Data presented here demonstrate that fed bats showed plasma glucose levels similar to those reported for other mammal species. In response to fasting, glycemia was decreased only in 48 hours fasted females. Plasma NEFA levels were similar in both sexes, and did not exhibit any changes during fasting. Considering the data from energy reserve variations, fed females presented an increased content of liver glycogen as well as higher breast muscle protein and limbs lipids concentrations, compared to fed males. In response to fasting, liver and muscle glycogen levels remained unchanged. Considering protein and lipid reserves, only females showed decreased values following fasting, as seen in breast, limbs and carcass lipids and breast muscle protein reserves, but still fail to keep glucose homeostasis after 48 hours without food. Taken together, our data suggest that the energy metabolism of insectivorous bats may vary according to sexual differences, a pattern that might be associated to different reproduction investments and costs between genders.

  3. Glucocorticoids activate the ATP-ubiquitin-dependent proteolytic system in skeletal muscle during fasting

    Science.gov (United States)

    Wing, S. S.; Goldberg, A. L.; Goldberger, A. L. (Principal Investigator)

    1993-01-01

    Glucocorticoids are essential for the increase in protein breakdown in skeletal muscle normally seen during fasting. To determine which proteolytic pathway(s) are activated upon fasting, leg muscles from fed and fasted normal rats were incubated under conditions that block or activate different proteolytic systems. After food deprivation (1 day), the nonlysosomal ATP-dependent process increased by 250%, as shown in experiments involving depletion of muscle ATP. Also, the maximal capacity of the lysosomal process increased 60-100%, but no changes occurred in the Ca(2+)-dependent or the residual energy-independent proteolytic processes. In muscles from fasted normal and adrenalectomized (ADX) rats, the protein breakdown sensitive to inhibitors of the lysosomal or Ca(2+)-dependent pathways did not differ. However, the ATP-dependent process was 30% slower in muscles from fasted ADX rats. Administering dexamethasone to these animals or incubating their muscles with dexamethasone reversed this defect. During fasting, when the ATP-dependent process rises, muscles show a two- to threefold increase in levels of ubiquitin (Ub) mRNA. However, muscles of ADX animals failed to show this response. Injecting dexamethasone into the fasted ADX animals increased muscle Ub mRNA within 6 h. Thus glucocorticoids activate the ATP-Ub-dependent proteolytic pathway in fasting apparently by enhancing the expression of components of this system such as Ub.

  4. Physiological adaptations to fasting in an actively wintering canid, the Arctic blue fox (Alopex lagopus).

    Science.gov (United States)

    Mustonen, Anne-Mari; Pyykönen, Teija; Puukka, Matti; Asikainen, Juha; Hänninen, Sari; Mononen, Jaakko; Nieminen, Petteri

    2006-01-01

    This study investigated the physiological adaptations to fasting using the farmed blue fox (Alopex lagopus) as a model for the endangered wild arctic fox. Sixteen blue foxes were fed throughout the winter and 32 blue foxes were fasted for 22 d in Nov-Dec 2002. Half of the fasted blue foxes were food-deprived again for 22 d in Jan-Feb 2003. The farmed blue fox lost weight at a slower rate (0.97-1.02% body mass d(-1)) than observed previously in the arctic fox, possibly due to its higher initial body fat content. The animals experienced occasional fasting-induced hypoglycaemia, but their locomotor activity was not affected. The plasma triacylglycerol and glycerol concentrations were elevated during phase II of fasting indicating stimulated lipolysis, probably induced by the high growth hormone concentrations. The total cholesterol, HDL- and LDL-cholesterol, urea, uric acid and total protein levels and the urea:creatinine ratio decreased during fasting. Although the plasma levels of some essential amino acids increased, the blue foxes did not enter phase III of starvation characterized by stimulated proteolysis during either of the 22-d fasting procedures. Instead of excessive protein catabolism, it is liver dysfunction, indicated by the increased plasma bilirubin levels and alkaline phosphatase, alanine aminotransferase and aspartate aminotransferase activities, that may limit the duration of fasting in the species.

  5. A Fasting-Responsive Signaling Pathway that Extends Life Span in C. elegans

    Directory of Open Access Journals (Sweden)

    Masaharu Uno

    2013-01-01

    Full Text Available Intermittent fasting is one of the most effective dietary restriction regimens that extend life span in C. elegans and mammals. Fasting-stimulus responses are key to the longevity response; however, the mechanisms that sense and transduce the fasting stimulus remain largely unknown. Through a comprehensive transcriptome analysis in C. elegans, we find that along with the FOXO transcription factor DAF-16, AP-1 (JUN-1/FOS-1 plays a central role in fasting-induced transcriptional changes. KGB-1, one of the C. elegans JNKs, acts as an activator of AP-1 and is activated in response to fasting. KGB-1 and AP-1 are involved in intermittent fasting-induced longevity. Fasting-induced upregulation of the components of the SCF E3 ubiquitin ligase complex via AP-1 and DAF-16 enhances protein ubiquitination and reduces protein carbonylation. Our results thus identify a fasting-responsive KGB-1/AP-1 signaling pathway, which, together with DAF-16, causes transcriptional changes that mediate longevity, partly through regulating proteostasis.

  6. Fast data processing with Spark

    CERN Document Server

    Sankar, Krishna

    2015-01-01

    Fast Data Processing with Spark - Second Edition is for software developers who want to learn how to write distributed programs with Spark. It will help developers who have had problems that were too big to be dealt with on a single computer. No previous experience with distributed programming is necessary. This book assumes knowledge of either Java, Scala, or Python.

  7. A fast fractional difference algorithm

    DEFF Research Database (Denmark)

    Jensen, Andreas Noack; Nielsen, Morten Ørregaard

    2014-01-01

    We provide a fast algorithm for calculating the fractional difference of a time series. In standard implementations, the calculation speed (number of arithmetic operations) is of order T 2, where T is the length of the time series. Our algorithm allows calculation speed of order T log...

  8. A Fast Fractional Difference Algorithm

    DEFF Research Database (Denmark)

    Jensen, Andreas Noack; Nielsen, Morten Ørregaard

    We provide a fast algorithm for calculating the fractional difference of a time series. In standard implementations, the calculation speed (number of arithmetic operations) is of order T 2, where T is the length of the time series. Our algorithm allows calculation speed of order T log...

  9. Fast Timing for Collider Detectors

    CERN Multimedia

    CERN. Geneva

    2017-01-01

    Advancements in fast timing particle detectors have opened up new possibilities to design collider detectors that fully reconstruct and separate event vertices and individual particles in the time domain. The applications of these techniques are considered for the physics at HL-LHC.

  10. Fast and Objective MRTD measurement

    NARCIS (Netherlands)

    Jong, A.N. de; Bakker, S.J.M.

    1988-01-01

    Manufacturers and Users of the Thermal Imagers have spent very much time upon the definition and measurement of the generally accepted performance curve: MRTD (Minimum Resolvable Temperature Difference). The need for a cheap and fast, objective measurement method has considerably increased since the

  11. Fast algorithm of track detection

    International Nuclear Information System (INIS)

    Nehrguj, B.

    1980-01-01

    A fast algorithm of variable-slope histograms is proposed, which allows a considerable reduction of computer memory size and is quite simple to carry out. Corresponding FORTRAN subprograms given a triple speed gain have been included in spiral reader data handling software

  12. Enhanced Model for Fast Ignition

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Rodney J. [Research Applications Corporation, Los Alamos, NM (United States)

    2010-10-12

    Laser Fusion is a prime candidate for alternate energy production, capable of serving a major portion of the nation's energy needs, once fusion fuel can be readily ignited. Fast Ignition may well speed achievement of this goal, by reducing net demands on laser pulse energy and timing precision. However, Fast Ignition has presented a major challenge to modeling. This project has enhanced the computer code ePLAS for the simulation of the many specialized phenomena, which arise with Fast Ignition. The improved code has helped researchers to understand better the consequences of laser absorption, energy transport, and laser target hydrodynamics. ePLAS uses efficient implicit methods to acquire solutions for the electromagnetic fields that govern the accelerations of electrons and ions in targets. In many cases, the code implements fluid modeling for these components. These combined features, "implicitness and fluid modeling," can greatly facilitate calculations, permitting the rapid scoping and evaluation of experiments. ePLAS can be used on PCs, Macs and Linux machines, providing researchers and students with rapid results. This project has improved the treatment of electromagnetics, hydrodynamics, and atomic physics in the code. It has simplified output graphics, and provided new input that avoids the need for source code access by users. The improved code can now aid university, business and national laboratory users in pursuit of an early path to success with Fast Ignition.

  13. Fast simulation of ultrasound images

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Nikolov, Svetoslav

    2000-01-01

    , and a whole image can take a full day. Simulating 3D images and 3D flow takes even more time. A 3D image of 64 by 64 lines can take 21 days, which is not practical for iterative work. This paper presents a new fast simulation method based on the Field II program. In imaging the same spatial impulse response...

  14. The Integral Fast Reactor concept

    International Nuclear Information System (INIS)

    Till, C.E.; Chang, Y.I.

    1986-01-01

    The Integral Fast Reactor (IFR) is an innovative LMR concept, being developed at Argonne National Laboratory, that exploits the inherent properties of liquid metal cooling and metallic fuel to achieve breakthroughs in economics and inherent safety. This paper describes the key features and potential advantages of the IFR concept, its technology development status, fuel cycle economics potential, and its future development path

  15. Fast-Track Teacher Recruitment.

    Science.gov (United States)

    Grant, Franklin Dean

    2001-01-01

    Schools need a Renaissance human-resources director to implement strategic staffing and fast-track teacher-recruitment plans. The HR director must attend to customer satisfaction, candidate supply, web-based recruitment possibilities, stabilization of newly hired staff, retention of veteran staff, utilization of retired employees, and latest…

  16. Fast reactor research in Switzerland

    International Nuclear Information System (INIS)

    Brogli, R.; Hudina, M.; Pelloni, S.; Sigg, B.; Stanculescu, A.

    1998-01-01

    The small Swiss research program on fast reactors serves to further understanding of the role of LMFR for energy production and to convert radioactive waste to more environmentally benign forms. These activities are on the one hand the contribution to the comparison of advanced nuclear systems and bring on the other to our physical and engineers understanding. (author)

  17. Effects of Whey, Caseinate, or Milk Protein Ingestion on Muscle Protein Synthesis after Exercise.

    Science.gov (United States)

    Kanda, Atsushi; Nakayama, Kyosuke; Sanbongi, Chiaki; Nagata, Masashi; Ikegami, Shuji; Itoh, Hiroyuki

    2016-06-03

    Whey protein (WP) is characterized as a "fast" protein and caseinate (CA) as a "slow" protein according to their digestion and absorption rates. We hypothesized that co-ingestion of milk proteins (WP and CA) may be effective for prolonging the muscle protein synthesis response compared to either protein alone. We therefore compared the effect of ingesting milk protein (MP) to either WP or CA alone on muscle protein synthesis after exercise in rats. We also compared the effects of these milk-derived proteins to a control, soy protein (SP). Male Sprague-Dawley rats swam for two hours. Immediately after exercise, one of the following four solutions was administered: WP, CA, MP, or SP. Individual rats were euthanized at designated postprandial time points and triceps muscle samples collected for measurement of the protein fractional synthesis rate (FSR). FSR tended to increase in all groups post-ingestion, although the initial peaks of FSR occurred at different times (WP, peak time = 60 min, FSR = 7.76%/day; MP, peak time = 90 min, FSR = 8.34%/day; CA, peak time = 120 min, FSR = 7.85%/day). Milk-derived proteins caused significantly greater increases (p protein synthesis to occur at different times (WP, fast; MP, intermediate; CA, slow) and the dairy proteins have a superior effect on muscle protein synthesis after exercise compared with SP.

  18. Delineation of molecular pathways that regulate hepatic PCSK9 and LDL receptor expression during fasting in normolipidemic hamsters

    Science.gov (United States)

    Wu, Minhao; Dong, Bin; Cao, Aiqin; Li, Hai; Liu, Jingwen

    2015-01-01

    Background PCSK9 has emerged as a key regulator of serum LDL-C metabolism by promoting the degradation of hepatic LDL receptor (LDLR). In this study, we investigated the effect of fasting on serum PCSK9, LDL-C, and hepatic LDLR expression in hamsters and further delineated the molecular pathways involved in fasting-induced repression of PCSK9 transcription. Results Fasting had insignificant effects on serum total cholesterol and HDL-C levels, but reduced LDL-C, triglyceride and insulin levels. The decrease in serum LDL-C was accompanied by marked reductions of hepatic PCSK9 mRNA and serum PCSK9 protein levels with concomitant increases of hepatic LDLR protein amounts. Fasting produced a profound impact on SREBP1 expression and its transactivating activity, while having modest effects on mRNA expressions of SREBP2 target genes in hamster liver. Although PPARα mRNA levels in hamster liver were elevated by fasting, ligand-induced activation of PPARα with WY14643 compound in hamster primary hepatocytes did not affect PCSK9 mRNA or protein expressions. Further investigation on HNF1α, a critical transactivator of PCSK9, revealed that fasting did not alter its mRNA expression, however, the protein abundance of HNF1α in nuclear extracts of hamster liver was markedly reduced by prolonged fasting. Conclusion Fasting lowered serum LDL-C in hamsters by increasing hepatic LDLR protein amounts via reductions of serum PCSK9 levels. Importantly, our results suggest that attenuation of SREBP1 transactivating activity owing to decreased insulin levels during fasting is primarily responsible for compromised PCSK9 gene transcription, which was further suppressed after prolonged fasting by a reduction of nuclear HNF1α protein abundance. PMID:22954675

  19. Ramadan Fasting in Kidney Transplant Recipients: A Single-Centre Retrospective Study

    Directory of Open Access Journals (Sweden)

    Ihab A. Ibrahim

    2018-01-01

    Full Text Available Background. Fasting during the lunar month of Ramadan is mandatory to all healthy adult Muslims. Renal transplant recipients are often worried about the impact of fluid and electrolyte deprivation during fasting on the function of their allograft. We aimed to examine the effect of fasting Ramadan on the graft function in renal transplant recipients. Methods. This retrospective cohort study included patients who underwent kidney transplantation in our tertiary referral center. Baseline pre-Ramadan estimated glomerular filtration rate (eGFR, mean arterial pressure (MAP, and urinary protein excretion were compared to those during and after Ramadan within and between the fasting and non-fasting groups. Results. The study population included 280 kidney transplant recipients who chose to fast during the Ramadan month (June-July 2014 and 285 recipients who did not fast. In the fasting group, baseline eGFR did not change from that during or post-Ramadan (72.6±23.7 versus 72.3±24.5 mL/min/1.73 m2, P=0.53; and 72.6±23.7 versus 72±23.2 mL/min/1.73 m2, P=0.14, respectively. Compared to baseline, there were no significant differences between the fasting and the non-fasting groups in terms of mean percent changes in eGFR, MAP, and urinary protein excretion. Conclusion. Fasting during the month of Ramadan did not have significant adverse effects on renal allograft function.

  20. Manipulating the glycosylation pathway in bacterial and lower eukaryotes for production of therapeutic proteins

    DEFF Research Database (Denmark)

    Anyaogu, Diana Chinyere; Mortensen, Uffe Hasbro

    2015-01-01

    The medical use of pharmaceutical proteins is rapidly increasing and cheap, fast and efficient production is therefore attractive. Microbial production hosts are promising candidates for development and production of pharmaceutical proteins. However, as most therapeutic proteins are secreted...... to produce proteins with humanlike glycan structures setting the stage for production of pharmaceutical proteins in bacteria, yeasts and algae....

  1. Idiopathic recurrent calcium urolithiasis (IRCU: pathophysiology evaluated in light of oxidative metabolism, without and with variation of several biomarkers in fasting urine and plasma - a comparison of stone-free and -bearing male patients, emphasizing mineral, acid-base, blood pressure and protein status*

    Directory of Open Access Journals (Sweden)

    Schwilie PO

    2011-08-01

    Full Text Available Abstract Background IRCU is traditionally considered as lifestyle disease (associations with, among others, overweight, obesity, hypertension, type-2 diabetes, arising from excess, in 24 h urine, of calcium (Ca salts (calcium oxalate (CaOx, calcium phosphate (CaPi, supersaturation of, and crystallization in, tubular fluid and urine, causing crystal-induced epithelial cell damage, proteinuria, crystal aggregation and uroliths. Methods Another picture emerges from the present uncontrolled study of 154 male adult IRCU patients (75 stone-bearing (SB and 79 age-matched stone-free (SF, in whom stone-forming and other parameters in fasting urine and plasma were contrasted with five biomarkers (see footnote of oxidative metabolism (OM, without and with variation of markers. Results 1 In SB vs. SF unstratified OM biomarkers were statistically unchanged, but the majority of patients was overweight; despite, in SB vs. SF urine pH, total and non-albumin protein concentration were elevated, fractional urinary uric acid excretion and blood bicarbonate decreased, whereas urine volume, sodium, supersaturation with CaOx and CaPi (as hydroxyapatite were unchanged; 2 upon variation of OM markers (strata below and above median numerous stone parameters differed significant!', among others urine volume, total protein, Ca/Pi ratio, pH, sodium, potassium, plasma Ca/Pi ratio and parathyroid hormone, blood pressure, renal excretion of non-albumin protein and other substances; 3 a significant shift from SF to SB patients occurred with increase of urine pH, decrease of blood bicarbonate, and increase of diastolic blood pressure, whereas increase of plasma uric acid impacted only marginally; 4 in both SF and SB patients a strong curvilinear relationship links a rise of urine Ca/Pi to urine Ca/Pi divided by plasma Ca/Pi, but in SB urine Ca/Pi failed to correlate significantly with urine hydroxyapatite supersaturation; 5 also in SB, plasma Ca/Pi and urinary nitrate were

  2. Fasting launches CRTC to facilitate long-term memory formation in Drosophila.

    Science.gov (United States)

    Hirano, Yukinori; Masuda, Tomoko; Naganos, Shintaro; Matsuno, Motomi; Ueno, Kohei; Miyashita, Tomoyuki; Horiuchi, Junjiro; Saitoe, Minoru

    2013-01-25

    Canonical aversive long-term memory (LTM) formation in Drosophila requires multiple spaced trainings, whereas appetitive LTM can be formed after a single training. Appetitive LTM requires fasting prior to training, which increases motivation for food intake. However, we found that fasting facilitated LTM formation in general; aversive LTM formation also occurred after single-cycle training when mild fasting was applied before training. Both fasting-dependent LTM (fLTM) and spaced training-dependent LTM (spLTM) required protein synthesis and cyclic adenosine monophosphate response element-binding protein (CREB) activity. However, spLTM required CREB activity in two neural populations--mushroom body and DAL neurons--whereas fLTM required CREB activity only in mushroom body neurons. fLTM uses the CREB coactivator CRTC, whereas spLTM uses the coactivator CBP. Thus, flies use distinct LTM machinery depending on their hunger state.

  3. Effects of increasing dietary protein levels on growth, feed utilization ...

    African Journals Online (AJOL)

    Yomi

    2012-01-05

    Jan 5, 2012 ... The effect of different dietary protein levels on growth performance and on feed utilization of catfish. (Heterobranchus ... (Legendre, 1991) because of its taste, fast growth rate ..... diet containing 40% protein had high growth with low food intake and feed ... protein rate (45%) combined with a bad utilization of.

  4. Ultra-fast silicon detectors

    Energy Technology Data Exchange (ETDEWEB)

    Sadrozinski, H. F.-W., E-mail: hartmut@scipp.ucsc.edu [Santa Cruz Institute for Particle Physics, UC Santa Cruz, Santa Cruz, CA 95064 (United States); Ely, S.; Fadeyev, V.; Galloway, Z.; Ngo, J.; Parker, C.; Petersen, B.; Seiden, A.; Zatserklyaniy, A. [Santa Cruz Institute for Particle Physics, UC Santa Cruz, Santa Cruz, CA 95064 (United States); Cartiglia, N.; Marchetto, F. [INFN Torino, Torino (Italy); Bruzzi, M.; Mori, R.; Scaringella, M.; Vinattieri, A. [University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, Firenze (Italy)

    2013-12-01

    We propose to develop a fast, thin silicon sensor with gain capable to concurrently measure with high precision the space (∼10 μm) and time (∼10 ps) coordinates of a particle. This will open up new application of silicon detector systems in many fields. Our analysis of detector properties indicates that it is possible to improve the timing characteristics of silicon-based tracking sensors, which already have sufficient position resolution, to achieve four-dimensional high-precision measurements. The basic sensor characteristics and the expected performance are listed, the wide field of applications are mentioned and the required R and D topics are discussed. -- Highlights: •We are proposing thin pixel silicon sensors with 10's of picoseconds time resolution. •Fast charge collection is coupled with internal charge multiplication. •The truly 4-D sensors will revolutionize imaging and particle counting in many applications.

  5. Fast light in atomic media

    International Nuclear Information System (INIS)

    Akulshin, Alexander M; McLean, Russell J

    2010-01-01

    Atomic media have played a major role in studies of fast light. One of their attractive features is the ability to manipulate experimental parameters to control the dispersive properties that determine the group velocity of a propagating light pulse. We give an overview of the experimental methods, based on both linear and nonlinear atom–light interaction, that have produced superluminal propagation in atomic media, and discuss some of the significant theoretical contributions to the issues of pulse preservation and reconciling faster-than-light propagation and the principle of causality. The comparison of storage of light, enhanced Kerr nonlinearity and efficient wave mixing processes in slow and fast light atomic media illustrates their common and distinct features. (review article)

  6. Why are idioms recognized fast?

    Science.gov (United States)

    Tabossi, Patrizia; Fanari, Rachele; Wolf, Kinou

    2009-06-01

    It is an established fact that idiomatic expressions are fast to process. However, the explanation of the phenomenon is controversial. Using a semantic judgment paradigm, where people decide whether a string is meaningful or not, the present experiment tested the predictions deriving from the three main theories of idiom recognition-the lexical representation hypothesis, the idiom decomposition hypothesis, and the configuration hypothesis. Participants were faster at judging decomposable idioms, nondecomposable idioms, and clichés than at judging their matched controls. The effect was comparable for all conventional expressions. The results were interpreted as suggesting that, as posited by the configuration hypothesis, the fact that they are known expressions, rather than idiomaticity, explains their fast recognition.

  7. Spherical Demons: Fast Surface Registration

    Science.gov (United States)

    Yeo, B.T. Thomas; Sabuncu, Mert; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, Polina

    2009-01-01

    We present the fast Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizers for the modified demons objective function can be efficiently implemented on the sphere using convolution. Based on the one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast – registration of two cortical mesh models with more than 100k nodes takes less than 5 minutes, comparable to the fastest surface registration algorithms. Moreover, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different settings: (1) parcellation in a set of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces. PMID:18979813

  8. ATLAS FTK: The Fast Tracker

    CERN Document Server

    T, Iizawa; The ATLAS collaboration

    2014-01-01

    The Fast TracKer (FTK) will perform global track reconstruction after each Level-1 trigger accept to enable the software-based High Level Trigger to have early access to tracking information. FTK is a dedicated processor based on a mixture of advanced technologies. Modern, powerful Field Programmable Gate Arrays (FPGAs) form an important part of the system architecture, and the large level of computing power required for pattern recognition is provided by incorporating standard-cell ASICs named Associative Memory (AM). FTK provides global track reconstruction in the full inner silicon detector in approximately 100 microseconds with resolution comparable to the offline algorithms. It allows a fast and precise detection of the primary and secondary vertex information. The track and vertex information is then used by the High Level Trigger algorithms, allowing highly improved trigger performance for the important signatures such as b-jets. In this paper, the architecture and the hardware development status of FT...

  9. [Preoperative fasting guidelines: an update].

    Science.gov (United States)

    López Muñoz, A C; Busto Aguirreurreta, N; Tomás Braulio, J

    2015-03-01

    Anesthesiology societies have issued various guidelines on preoperative fasting since 1990, not only to decrease the incidence of lung aspiration and anesthetic morbidity, but also to increase patient comfort prior to anesthesia. Some of these societies have been updating their guidelines, as such that, since 2010, we now have 2 evidence-based preoperative fasting guidelines available. In this article, an attempt is made to review these updated guidelines, as well as the current instructions for more controversial patients such as infants, the obese, and a particular type of ophthalmic surgery. Copyright © 2014 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

  10. Postprandial Levels of Branch Chained and Aromatic Amino Acids Associate with Fasting Glycaemia

    OpenAIRE

    Ottosson, Filip; Ericson, Ulrika; Almgren, Peter; Nilsson, Jeanette; Magnusson, Martin; Fernandez, Céline; Melander, Olle

    2016-01-01

    High fasting plasma concentrations of isoleucine, phenylalanine, and tyrosine have been associated with increased risk of hyperglycaemia and incidence of type 2 diabetes. Whether these associations are diet or metabolism driven is unknown. We examined how the dietary protein source affects the postprandial circulating profile of these three diabetes associated amino acids (DMAAs) and tested whether the postprandial DMAA profiles are associated with fasting glycaemia. We used a crossover desig...

  11. Measuring Fast Calcium Fluxes in Cardiomyocytes

    Science.gov (United States)

    Golebiewska, Urszula; Scarlata, Suzanne

    2011-01-01

    Cardiomyocytes have multiple Ca2+ fluxes of varying duration that work together to optimize function 1,2. Changes in Ca2+ activity in response to extracellular agents is predominantly regulated by the phospholipase Cβ- Gαq pathway localized on the plasma membrane which is stimulated by agents such as acetylcholine 3,4. We have recently found that plasma membrane protein domains called caveolae5,6 can entrap activated Gαq7. This entrapment has the effect of stabilizing the activated state of Gαq and resulting in prolonged Ca2+ signals in cardiomyocytes and other cell types8. We uncovered this surprising result by measuring dynamic calcium responses on a fast scale in living cardiomyocytes. Briefly, cells are loaded with a fluorescent Ca2+ indicator. In our studies, we used Ca2+ Green (Invitrogen, Inc.) which exhibits an increase in fluorescence emission intensity upon binding of calcium ions. The fluorescence intensity is then recorded for using a line-scan mode of a laser scanning confocal microscope. This method allows rapid acquisition of the time course of fluorescence intensity in pixels along a selected line, producing several hundreds of time traces on the microsecond time scale. These very fast traces are transferred into excel and then into Sigmaplot for analysis, and are compared to traces obtained for electronic noise, free dye, and other controls. To dissect Ca2+ responses of different flux rates, we performed a histogram analysis that binned pixel intensities with time. Binning allows us to group over 500 traces of scans and visualize the compiled results spatially and temporally on a single plot. Thus, the slow Ca2+ waves that are difficult to discern when the scans are overlaid due to different peak placement and noise, can be readily seen in the binned histograms. Very fast fluxes in the time scale of the measurement show a narrow distribution of intensities in the very short time bins whereas longer Ca2+ waves show binned data with a broad

  12. Fast computation of Krawtchouk moments

    Czech Academy of Sciences Publication Activity Database

    Honarvar Shakibaei Asli, B.; Flusser, Jan

    2014-01-01

    Roč. 288, č. 1 (2014), s. 73-86 ISSN 0020-0255 R&D Projects: GA ČR GAP103/11/1552 Institutional support: RVO:67985556 Keywords : Krawtchouk polynomial * Krawtchouk moment * Geometric moment * Impulse response * Fast computation * Digital filter Subject RIV: JD - Computer Applications, Robotics Impact factor: 4.038, year: 2014 http://library.utia.cas.cz/separaty/2014/ZOI/flusser-0432452.pdf

  13. Fast, low noise transimpedance preamplifier

    International Nuclear Information System (INIS)

    Parlakyan, L.K.

    1995-01-01

    A single-channel transimpedance preamplifier for fast dielectric detectors is described. The main specifications of the preamplifier are: rise time is 1,5 ns; gain is 3,5 mV/μ A (with two section- 210 mV/μ A); r.m.s input noise is 30 n A; power consumption is 22 m W. Depending on supply voltage, the parameters may vary in a wide range. 5 refs

  14. The fast slow TDPAC spectrometer

    International Nuclear Information System (INIS)

    Cekic, B.; Koicki, S.; Manasijevic, M.; Ivanovic, N.; Koteski, V.; Milosevic, Z.; Radisavljevic, I.; Cavor, J.; Novakovic, N.; Marjanovic, D.

    2001-01-01

    A 2-BaF 2 detector - fast slow time spectrometer for time differential perturbed angular correlations (TDPAC) experiments is described. This apparatus has been developed in the Group for Hyperfine Interactions in the Institute for Nuclear Sciences in VINCA. The excellent time resolution combined with high efficiency offered by these detectors enables one high counting rate performance and is operating in the wide temperature range 78-1200 K. (author)

  15. Relationship between fasting glucose, vitamin D and PTH in early postmenopausal women

    DEFF Research Database (Denmark)

    við Streym, Susanna; Rejnmark, Lars; Vestergaard, Peter

      Abstract Relationship between fasting glucose, vitamin D and PTH in early postmenopausal women Súsanna við Streym Thomsen (1), Lars Rejnmark (1), Peter Vestergaard (1), Christine Brot (2), Pia Eiken (3), Pernille Hermann (4) Leif Mosekilde (1). (1) Department of Medicine and Endocrinology C...... postmenopausal Caucasian women (n=2016) aged 45 to 58 years old. Measurements: Fasting blood glucose was measured after an overnight fast by standard laboratory methods. Serum levels of 25OHD were measured by a competitive assay using rachitic rat binding protein. The fat and lean mass was measured by DXA...... between fasting blood glucose and 25OHD and all studied indices. In a multivariate linear regression analyzing fasting blood glucose was significantly associated with BMI (b=0.038 ±0.007 (SE), 2p

  16. Non-fasting factor VII coagulant activity (FVII:C) increased by high-fat diet

    DEFF Research Database (Denmark)

    Bladbjerg, Else-Marie; Marckmann, P; Sandström, B

    1994-01-01

    :Bt/FVII:Am (a measure of FVII activation) increased from fasting levels on both diets, but most markedly on the high-fat diet. In contrast, FVII:Am (a measure of FVII protein) tended to decrease from fasting levels on both diets. FVII:C rose from fasting levels on the high-fat diet, but not on the low-fat diet....... The findings suggest that high-fat diets increase non-fasting FVII:C, and consequently may be associated with increased risk of thrombosis. Udgivelsesdato: 1994-Jun......Preliminary observations have suggested that non-fasting factor VII coagulant activity (FVII:C) may be related to the dietary fat content. To confirm this, we performed a randomised cross-over study. Seventeen young volunteers were served 2 controlled isoenergetic diets differing in fat content (20...

  17. Fast superconducting magnetic field switch

    Science.gov (United States)

    Goren, Yehuda; Mahale, Narayan K.

    1996-01-01

    The superconducting magnetic switch or fast kicker magnet is employed with electron stream or a bunch of electrons to rapidly change the direction of flow of the electron stream or bunch of electrons. The apparatus employs a beam tube which is coated with a film of superconducting material. The tube is cooled to a temperature below the superconducting transition temperature and is subjected to a constant magnetic field which is produced by an external dc magnet. The magnetic field produced by the dc magnet is less than the critical field for the superconducting material, thus, creating a Meissner Effect condition. A controllable fast electromagnet is used to provide a magnetic field which supplements that of the dc magnet so that when the fast magnet is energized the combined magnetic field is now greater that the critical field and the superconducting material returns to its normal state allowing the magnetic field to penetrate the tube. This produces an internal field which effects the direction of motion and of the electron stream or electron bunch. The switch can also operate as a switching mechanism for charged particles.

  18. The instrumentation of fast reactor

    International Nuclear Information System (INIS)

    Endo, Akira

    2003-03-01

    The author has been engaged in the development of fast reactors over the last 30 years with both an involvement with the early technology development on the experimental breeder reactor Joyo, and latterly continuing this work on the prototype breeder reactor, Monju. In order to pass on this experience to younger engineers this paper is produced to outline this experience in the sincere hope that the information given will be utilised in future educational training material. The paper discusses the wide diversity on the associated instrument technology which the fast breeder reactor requires. The first chapter outlines the fast reactor system, followed by discussions on reactor instrumentation, measurement principles, temperature dependencies, and verification response characteristics from various viewpoints, are discussed in chapters two and three. The important issues of failed fuel location detection, and sodium leak detection from steam generators are discussed in chapters 4 and 5 respectively. Appended to this report is an explanation on the methods of measuring response characteristics on instrumentation systems using error analysis, random signal theory and measuring method of response characteristic by AR (autoregressive) model on which it appears is becoming an indispensable problem for persons involved with this technology in the future. (author)

  19. Fast reactors: the industrial perspective

    International Nuclear Information System (INIS)

    Vaughan, R.D.

    1986-01-01

    Industrial participation in the development of the fast reactor is reviewed, from the construction of PFR at Dounreay to the initial steps towards collaboration in Europe. The optimum design of the fast reactor has changed considerably from the days when it was needed urgently to forestall a shortage of uranium to today when uranium is abundant and cheap. The evolution of the reactor design over this period is described. Collaboration in Europe is shown to be the only answer to high development costs and the search for a reactor which will compete with thermal reactors in today's environment. The partner countries in this collaboration are all motivated differently, and this is leading to some delays in concluding the necessary agreements. The objective on the industrial front is now to participate in the two or three demonstration fast reactors that will be built in Europe during the remainder of the century leading, it is hoped, to a competitive reactor design by the year 2000. (author)

  20. ATLAS Fast Physics Monitoring: TADA

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00375930; The ATLAS collaboration; Elsing, Markus

    2017-01-01

    The ATLAS experiment at the LHC is recording data from proton-proton collisions with 13 TeV center-of-mass energy since spring 2015. The collaboration is using a fast physics monitoring framework (TADA) to automatically perform a broad range of fast searches for early signs of new physics and to monitor the data quality across the year with the full analysis level calibrations applied to the rapidly growing data.TADA is designed to provide fast feedback directly after the collected data has been fully calibrated and processed at the Tier-0, the CERN Data Center. The system can monitor a large range of physics channels, offline data quality and physics performance quantities nearly final analysis level object calibrations. TADA output is available on a website accessible by the whole collaboration that gets updated twice a day with the data from newly processed runs. Hints of potentially interesting physics signals or performance issues identified in this way are reported to be followed up by physics or combin...

  1. ATLAS fast physics monitoring: TADA

    Science.gov (United States)

    Sabato, G.; Elsing, M.; Gumpert, C.; Kamioka, S.; Moyse, E.; Nairz, A.; Eifert, T.; ATLAS Collaboration

    2017-10-01

    The ATLAS experiment at the LHC has been recording data from proton-proton collisions with 13 TeV center-of-mass energy since spring 2015. The collaboration is using a fast physics monitoring framework (TADA) to automatically perform a broad range of fast searches for early signs of new physics and to monitor the data quality across the year with the full analysis level calibrations applied to the rapidly growing data. TADA is designed to provide fast feedback directly after the collected data has been fully calibrated and processed at the Tier-0. The system can monitor a large range of physics channels, offline data quality and physics performance quantities. TADA output is available on a website accessible by the whole collaboration. It gets updated twice a day with the data from newly processed runs. Hints of potentially interesting physics signals or performance issues identified in this way are reported to be followed up by physics or combined performance groups. The note reports as well about the technical aspects of TADA: the software structure to obtain the input TAG files, the framework workflow and structure, the webpage and its implementation.

  2. ATLAS Fast Physics Monitoring: TADA

    CERN Document Server

    Elsing, Markus; The ATLAS collaboration; Sabato, Gabriele; Kamioka, Shusei; Nairz, Armin Michael; Moyse, Edward; Gumpert, Christian

    2016-01-01

    The ATLAS Experiment at the LHC is recording data from proton-proton collisions with 13 TeV center-of-mass energy since spring 2015. The collaboration is using a fast physics monitoring framework (TADA) to automatically perform a broad range of fast searches for early signs of new physics and to monitor the data quality across the year with the full analysis level calibrations applied to the rapidly growing data. TADA is designed to provide fast feedback directly after the collected data has been fully calibrated and processed at the Tier-0. The system can monitor a large range of physics channels, offline data quality and physics performance quantities nearly final analysis level object calibrations. TADA output is available on a website accessible by the whole collaboration that gets updated twice a day with the data from newly processed runs. Hints of potentially interesting physics signals or performance issues identified in this way are reported to be followed up by physics or combined performance groups...

  3. Fast superconducting magnetic field switch

    International Nuclear Information System (INIS)

    Goren, Y.; Mahale, N.K.

    1996-01-01

    The superconducting magnetic switch or fast kicker magnet is employed with electron stream or a bunch of electrons to rapidly change the direction of flow of the electron stream or bunch of electrons. The apparatus employs a beam tube which is coated with a film of superconducting material. The tube is cooled to a temperature below the superconducting transition temperature and is subjected to a constant magnetic field which is produced by an external dc magnet. The magnetic field produced by the dc magnet is less than the critical field for the superconducting material, thus, creating a Meissner Effect condition. A controllable fast electromagnet is used to provide a magnetic field which supplements that of the dc magnet so that when the fast magnet is energized the combined magnetic field is now greater that the critical field and the superconducting material returns to its normal state allowing the magnetic field to penetrate the tube. This produces an internal field which effects the direction of motion and of the electron stream or electron bunch. The switch can also operate as a switching mechanism for charged particles. 6 figs

  4. Fast Reactors and Nuclear Nonproliferation

    International Nuclear Information System (INIS)

    Avrorina, E.N.; Chebeskovb, A.N.

    2013-01-01

    Conclusion remarks: 1. Fast reactor start-up with U-Pu fuel: – dependent on thermal reactors, – no needs in U enrichment, – needs in SNF reprocessing, – Pu is a little suitable for NED, – practically impossible gun-type NED, – difficulties for implosion-type NED: necessary tests, advanced technologies, etc. – Pu in blankets is similar to WPu by isotopic composition, – Use of blanket for production isotopes (e.g. 233 U), – Combined reprocessing of SNF: altogether blanket and core, – Blanket elimination: decrease in Pu production – No pure Pu separation. 2. Fast reactor start-up with U fuel: - Needs in both U enrichment and SNF reprocessing, - Independent of thermal reactors, - Good Pu bred in the core let alone blankets, - NED of simple gun-type design, - Increase of needs in SWU, - Increased demands in U supply. 3. Fast reactors for export: - Uranium shortage, - To replace thermal reactors in future, - No blankets (depends on the country, though), - Fuel supply and SNF take back, - International centers for rendering services of NFC. Time has come to remove from FRs and their NFC the label unfairly identifying them as the most dangerous installations of nuclear power from the standpoint of being a proliferation problem

  5. A repeating fast radio burst.

    Science.gov (United States)

    Spitler, L G; Scholz, P; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-03-10

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  6. Astrid (fast breeder nuclear reactor)

    International Nuclear Information System (INIS)

    2014-01-01

    This document presents ASTRID (Advanced Sodium Technological Reactor for Industrial Demonstration), a French project of sodium-cooled fast breeder reactor, fourth generation reactor which should be fuelled by uranium 238 rather than uranium 235, and should therefore need less extracted natural uranium to produce electricity. The operation principle of fast breeder reactors is described. They notably directly consume plutonium, allow an easier radioactive waste management as they transform long life radioactive elements into shorter life elements by transmutation. The regeneration process is briefly described, and the various operation modes are evoked (iso-generator, sub-generator, and breeder). Some peculiarities of sodium-cooled reactors are outlined. The Astrid operation principle is described, its main design innovations outlined. Various challenges are discussed regarding safety of supply and waste processing, and the safety of future reactors. Major actors are indicated: CEA, Areva, EDF, SEIV Alcen, Toshiba, Rolls Royce, and Comex. Some key data are indicated: expected lifetime, expected availability rate, cost. The projected site is Marcoule and fast breeder reactors operated or under construction in the world are indicated. The document also proposes an overview of the background and evolution of reactors of 4. generation

  7. Medical radiography with fast neutrons

    International Nuclear Information System (INIS)

    Duehmke, E.

    1980-01-01

    Neutron radiography is important in medicine for two reasons. On the one hand, macroradiographical findings are different from X-ray findings, i.e. new information may be gained on the morphology of humans and animals. On the other hand, there is a direct practical application in the radiotherapy of malignant tumours if one considers the assessment of the growth of malignant processes. Fast neutrons are required for neutron radiographies of biological objects with a diameter of more than 2 cm. In addition sensitive, two-dimensional detectors must be used which are selective for fast neutrons. The book describes the optimisation and sensitisation of a detector using the example of cellulose nitrate foil for fast reactor neutrons. Images of human spinal chords with tumours proved by pathological and anatomical examinations give a better picture of the dimensions of the tumour than comparative X-ray pictures. For examinations of living patients, neutron radiography should be applied only in those tumour-bearing parts of the bodies in which radiation treatment is required for therapeutical purposes anyway. (orig./MG) [de

  8. The Fast-Casual Conundrum: Fast-Casual Restaurant Entrées Are Higher in Calories than Fast Food.

    Science.gov (United States)

    Schoffman, Danielle E; Davidson, Charis R; Hales, Sarah B; Crimarco, Anthony E; Dahl, Alicia A; Turner-McGrievy, Gabrielle M

    2016-10-01

    Frequently eating fast food has been associated with consuming a diet high in calories, and there is a public perception that fast-casual restaurants (eg, Chipotle) are healthier than traditional fast food (eg, McDonald's). However, research has not examined whether fast-food entrées and fast-casual entrées differ in calorie content. The purpose of this study was to determine whether the caloric content of entrées at fast-food restaurants differed from that found at fast-casual restaurants. This study was a cross-sectional analysis of secondary data. Calorie information from 2014 for lunch and dinner entrées for fast-food and fast-casual restaurants was downloaded from the MenuStat database. Mean calories per entrée between fast-food restaurants and fast-casual restaurants and the proportion of restaurant entrées that fell into different calorie ranges were assessed. A t test was conducted to test the hypothesis that there was no difference between the average calories per entrée at fast-food and fast-casual restaurants. To examine the difference in distribution of entrées in different calorie ranges between fast-food and fast-casual restaurants, χ(2) tests were used. There were 34 fast-food and 28 fast-casual restaurants included in the analysis (n=3,193 entrées). Fast-casual entrées had significantly more calories per entrée (760±301 kcal) than fast-food entrées (561±268; Prestaurants to determine whether the energy content or nutrient density of full meals (ie, entrées with sides and drinks) differs between fast-casual restaurants and fast-food restaurants. Calorie-conscious consumers should consider the calorie content of entrée items before purchase, regardless of restaurant type. Copyright © 2016 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

  9. Fasting enhances TRAIL-mediated liver natural killer cell activity via HSP70 upregulation.

    Directory of Open Access Journals (Sweden)

    Vu T A Dang

    Full Text Available Acute starvation, which is frequently observed in clinical practice, sometimes augments the cytolytic activity of natural killer cells against neoplastic cells. In this study, we investigated the molecular mechanisms underlying the enhancement of natural killer cell function by fasting in mice. The total number of liver resident natural killer cells in a unit weight of liver tissue obtained from C57BL/6J mice did not change after a 3-day fast, while the proportions of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL+ and CD69+ natural killer cells were significantly elevated (n = 7, p <0.01, as determined by flow cytometric analysis. Furthermore, we found that TRAIL- natural killer cells that were adoptively transferred into Rag-2-/- γ chain-/- mice could convert into TRAIL+ natural killer cells in fasted mice at a higher proportion than in fed mice. Liver natural killer cells also showed high TRAIL-mediated antitumor function in response to 3-day fasting. Since these fasted mice highly expressed heat shock protein 70 (n = 7, p <0.05 in liver tissues, as determined by western blot, the role of this protein in natural killer cell activation was investigated. Treatment of liver lymphocytes with 50 µg/mL of recombinant heat shock protein 70 led to the upregulation of both TRAIL and CD69 in liver natural killer cells (n = 6, p <0.05. In addition, HSP70 neutralization by intraperitoneally injecting an anti- heat shock protein 70 monoclonal antibody into mice prior to fasting led to the downregulation of TRAIL expression (n = 6, p <0.05. These findings indicate that acute fasting enhances TRAIL-mediated liver natural killer cell activity against neoplastic cells through upregulation of heat shock protein 70.

  10. Status of national programmes on fast reactors

    International Nuclear Information System (INIS)

    1994-04-01

    Based on the International Working Group on Fast reactors (IWGFR) members' request, the IAEA organized a special meeting on Fast Reactor Development and the Role of the IAEA in May 1993. The purpose of the meeting was to review and discuss the status and recent development, to present major changes in fast reactor programmes and to recommend future activities on fast reactors. The IWGFR took note that in some Member States large prototypes have been built or are under construction. However, some countries, due to their current budget constraints, have reduced the level of funding for research and development programmes on fast reactors. The IWGFR noted that in this situation the international exchange of information and cooperation on the development of fast reactors is highly desirable and stressed the importance of the IAEA's programme on fast reactors. These proceedings contain important and useful information on national programmes and new developments in sodium cooled fast reactors in Member States. Refs, figs and tabs

  11. Fleet Assistance and Support Team (FAST) Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The FAST team was established by PMA-264 for introduction of multistatic ASW systems into the Fleet.FAST provides Air ASW mission planning, tactics/tactical sensor...

  12. Percentage of Fast-Track Receipts

    Data.gov (United States)

    Social Security Administration — The dataset provides the percentage of fast-track receipts by state during the reporting fiscal year. Fast-tracked cases consist of those cases identified as Quick...

  13. Gluconeogenesis and fasting in cerebral malaria

    NARCIS (Netherlands)

    van Thien, H.; Ackermans, M. T.; Weverling, G. J.; Dang Vinh, T.; Endert, E.; Kager, P. A.; Sauerwein, H. P.

    2004-01-01

    BACKGROUND: In healthy subjects after an overnight fast, glucose production is for approximately 50% derived from glycogenolysis. If the fast is prolonged, glucose production decreases due to a decline in glycogenolysis, while gluconeogenesis remains stable. In cerebral malaria, glucose production

  14. The Fast Simulation Chain for ATLAS

    CERN Document Server

    Basalaev, Artem; The ATLAS collaboration

    2016-01-01

    In order to generate the huge number of Monte Carlo events that will be required by the ATLAS experiment over the next several runs, a very fast simulation is critical. Fast detector simulation alone, however, is insufficient: with very high numbers of simultaneous proton-proton collisions expected in Run 3 and beyond, the digitization (detector response emulation) and event reconstruction time quickly become comparable to the time required for detector simulation. The ATLAS Fast Chain simulation has been developed to solve this problem. Modules are implemented for fast simulation, fast digitization, and fast track reconstruction. The application is sufficiently fast -- several orders of magnitude faster than the standard simulation -- that the simultaneous proton-proton collisions can be generated during the simulation job, so Pythia8 also runs concurrently with the rest of the algorithms. The Fast Chain has been built to be extremely modular and flexible, so that each sample can be custom-tailored to match ...

  15. Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish

    Directory of Open Access Journals (Sweden)

    Zizhen Yao

    2013-04-01

    The basic helix–loop–helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes, including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets, in particular fast-twitch muscle differentiation genes, thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast-twitch muscle-specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber-type regulator, Prdm1a, a SET-domain DNA-binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype, early and increased fast muscle differentiation, is the opposite of the Pbx-null phenotype, delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes, we used RNA-seq analysis to globally assess gene expression in zebrafish embryos with single- and double-losses-of-function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4-MO;prdm1a−/− embryos, suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However, other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus, our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program.

  16. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  17. Proteins engineering

    International Nuclear Information System (INIS)

    2000-01-01

    At the - Departement d'Ingenierie et d'etudes de proteines (Deip) of the CEA more than seventy researchers are working hard to understand the function of proteins. For that they use the molecular labelling technique (F.M.)

  18. Whey Protein

    Science.gov (United States)

    ... reliable information about the safety of taking whey protein if you are pregnant or breast feeding. Stay on the safe side and avoid use. Milk allergy: If you are allergic to cow's milk, avoid using whey protein.

  19. The digital backend of FAST

    Science.gov (United States)

    Yu, Xinying; Zhang, Xia; Duan, Ran; li, di; Hao, Jie

    2015-08-01

    The receiver system is an important part of FAST (Five-hundred-meter Aperture Spherical Radio Telescope) and plays a key role in determining the performance of the telescope.This research covers three major aspects: establishment of system synchronization and timestamps, field-programmable gate array (FPGA)-based data transmission and analysis, and the rear receiver monitoring system. We intend to combine the use of GPS and a frequency standard instrument with network access to Unix timestamps to form actual timestamps. The data are stored with timestamps that contain integer and fractional seconds to be precise and headers, which are primarily intended to distinguish the data from each other.The data analysis procedures includes converting the timestamp information to real-time information, and merging the 8 channels’ data conversion results into frequency and energy data using corresponding conversion formulae. We must develop tailored monitoring software for the FAST receiver to customize the data format and perform data transmission. Signals on the front-end and back-end of the receiver can be monitored and controlled by adjusting the parameters on the software to increase the flexibility of the receiver.Most operations are performed on FPGA board, which can be shown from the figure, including the analog-to-digital conversion (ADC), fast Fourier transform (FFT), and pulse per second (1PPS) and Unix timestamp access operations.When analog data arrive, we initialize two ADCs at a sampling rate of 3Gsps, following by 8-channel FFT parallel processing.In collaboration with the Institute of Automation, we have developed a custom FPGA board which we call "FDB"("FAST Digital Backend"). The board is integrated with two Virtex-6 and one Virtex-5 high-speed Xilinx chips. The main function of the two Virtex-6 devices is to run the FFT and PFB programs, whereas the main function of Virtex-5 is configuration of the board.This research is indispensable for realizing the

  20. Fast Weight Long Short-Term Memory

    OpenAIRE

    Keller, T. Anderson; Sridhar, Sharath Nittur; Wang, Xin

    2018-01-01

    Associative memory using fast weights is a short-term memory mechanism that substantially improves the memory capacity and time scale of recurrent neural networks (RNNs). As recent studies introduced fast weights only to regular RNNs, it is unknown whether fast weight memory is beneficial to gated RNNs. In this work, we report a significant synergy between long short-term memory (LSTM) networks and fast weight associative memories. We show that this combination, in learning associative retrie...

  1. Lysine Acetylation of CREBH Regulates Fasting-Induced Hepatic Lipid Metabolism

    Science.gov (United States)

    Kim, Hyunbae; Mendez, Roberto; Chen, Xuequn; Fang, Deyu

    2015-01-01

    Cyclic AMP-responsive element-binding protein 3-like 3, hepatocyte specific (CREBH), is a hepatic transcription factor that functions as a key regulator of energy homeostasis. Here, we defined a regulatory CREBH posttranslational modification process, namely, lysine-specific acetylation, and its functional involvement in fasting-induced hepatic lipid metabolism. Fasting induces CREBH acetylation in mouse livers in a time-dependent manner, and this event is critical for CREBH transcriptional activity in regulating hepatic lipid homeostasis. The histone acetyltransferase PCAF-mediated acetylation and the deacetylase sirtuin-1-mediated deacetylation coexist to maintain CREBH acetylation states under fasting conditions. Site-directed mutagenesis and functional analyses revealed that the lysine (K) residue at position 294 (K294) within the bZIP domain of the CREBH protein is the site where fasting-induced acetylation/deacetylation occurs. Introduction of the acetylation-deficient (K294R) or acetylation-mimicking (K294Q) mutation inhibited or enhanced CREBH transcriptional activity, respectively. Importantly, CREBH acetylation at lysine 294 was required for the interaction and synergy between CREBH and peroxisome proliferator-activated receptor α (PPARα) in activating their target genes upon fasting or glucagon stimulation. Introduction of the CREBH lysine 294 mutation in the liver leads to hepatic steatosis and hyperlipidemia in animals under prolonged fasting. In summary, our study reveals a molecular mechanism by which fasting or glucagon stimulation modulates lipid homeostasis through acetylation of CREBH. PMID:26438600

  2. Effects of fast neutrons on chromatin: dependence on chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)

    2002-07-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  3. Human skeletal muscle: transition between fast and slow fibre types.

    Science.gov (United States)

    Neunhäuserer, Daniel; Zebedin, Michaela; Obermoser, Magdalena; Moser, Gerhard; Tauber, Mark; Niebauer, Josef; Resch, Herbert; Galler, Stefan

    2011-05-01

    Human skeletal muscles consist of different fibre types: slow fibres (slow twitch or type I) containing the myosin heavy chain isoform (MHC)-I and fast fibres (fast twitch or type II) containing MHC-IIa (type IIA) or MHC-IId (type IID). The following order of decreasing kinetics is known: type IID > type IIA > type I. This order is especially based on the kinetics of stretch activation, which is the most discriminative property among fibre types. In this study we tested if hybrid fibres containing both MHC-IIa and MHC-I (type C fibres) provide a transition in kinetics between fast (type IIA) and slow fibres (type I). Our data of stretch activation kinetics suggest that type C fibres, with different ratios of MHC-IIa and MHC-I, do not provide a continuous transition. Instead, a specialized group of slow fibres, which we called "transition fibres", seems to provide a transition. Apart of their kinetics of stretch activation, which is most close to that of type IIA, the transition fibres are characterized by large cross-sectional areas and low maximal tensions. The molecular cause for the mechanical properties of the transition fibres is unknown. It is possible that the transition fibres contain an unknown slow MHC isoform, which cannot be separated by biochemical methods. Alternatively, or in addition, isoforms of myofibrillar proteins, other than MHC, and posttranslational modifications of myofibrillar proteins could play a role regarding the characteristics of the transition fibres.

  4. Effects of fast neutrons on chromatin: dependence on chromatin structure

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.

    2002-01-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  5. Protein intrinsic disorder in plants.

    Science.gov (United States)

    Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

    2013-09-12

    To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  6. Protein intrinsic disorder in plants

    Directory of Open Access Journals (Sweden)

    Florencio ePazos

    2013-09-01

    Full Text Available To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously with different partners. Similarly, they also serve as signal integrators in signalling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms can not escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  7. Fast Foods, Organic Foods, Fad Diets

    Science.gov (United States)

    There is no standard definition of fast food. Generally, fast food is eaten without cutlery, and fast-food restaurants have no wait staff. Failure to have a standardized definition makes it difficult to compare studies. Foods available outside the home tend to be high in energy and fat compared w...

  8. Introduction of the experimental fast reactor JOYO

    International Nuclear Information System (INIS)

    Matsuba, Ken-ichi; Kawahara, Hirotaka; Aoyama, Takafumi

    2006-01-01

    The experimental fast reactor JOYO at O-arai Engineering Center of Japan Nuclear Cycle Development Institute is the first liquid metal cooled fast reactor in Japan. This paper describes the plant outline, experiences on the fast reactor technology and test results accumulated through twenty eight years successful operation of JOYO. (author)

  9. Consecutive treatment with phytase and arazyme influence protein ...

    African Journals Online (AJOL)

    Jane

    2011-08-01

    Aug 1, 2011 ... accelerated livestock growth. Key words: Soybean meal, phytase, arazyme, hydrolysis. .... Fast protein liquid chromatography (FPLC) analysis. The FPLC of ..... A study on the effect of substituting soybean oil meal for imported ...

  10. Comparison of Fast-Food and Non-Fast-Food Children's Menu Items

    Science.gov (United States)

    Serrano, Elena L.; Jedda, Virginia B.

    2009-01-01

    Objective: Compare the macronutrient content of children's meals sold by fast-food restaurants (FFR) and non-fast-food restaurants (NFF). Design: All restaurants within the designated city limits were surveyed. Non-fast-food children's meals were purchased, weighed, and analyzed using nutrition software. All fast-food children's meals were…

  11. Experimental and numerical studies of the fast ions confined in TFR 600 during fast neutrals injection

    International Nuclear Information System (INIS)

    Gagey, B.

    1980-08-01

    We present a comparison between experimental fast neutrals spectrum measured with a very simple electrostatic analyzer which has been absolutely calibrated, spectrum obtained during fast neutrals injection in TFR 600, and numerical fast neutrals spectrum obtained from a modified Monte-Carlo calculation code. This comparison allows us to draw important conclusions on the fast ions behavior in the plasma

  12. Differential multiple quantum relaxation caused by chemical exchange outside the fast exchange limit

    International Nuclear Information System (INIS)

    Wang Chunyu; Palmer, Arthur G.

    2002-01-01

    Differential relaxation of multiple quantum coherences is a signature for chemical exchange processes in proteins. Previous analyses of experimental data have used theoretical descriptions applicable only in the limit of fast exchange. Theoretical expressions for differential relaxation rate constants that are accurate outside fast exchange are presented for two-spin-system subject to two-site chemical exchange. The theoretical expressions are validated using experimental results for 15 N- 1 H relaxation in basic pancreatic trypsin inhibitor. The new theoretical expression is valuable for identification and characterization of exchange processes in proteins using differential relaxation of multiple quantum coherences

  13. ATLAS FTK Fast Track Trigger

    CERN Document Server

    Iizawa, T; The ATLAS collaboration

    2014-01-01

    The Fast TracKer (FTK) will perform global track reconstruction after each Level-1 trigger accept signal to enable the software-based higher level trigger to have early access to tracking information. FTK is a dedicated processor based on a mixture of advanced technologies. Modern, powerful Field Programmable Gate Arrays (FPGAs) form an important part of the system architecture, and the large level of computing power required for pattern recognition is provided by incorporating standard-cell ASICs named Associative Memory (AM). Motivation and the architecture of the FTK system will be presented, and the status of hardware and simulation will be following.

  14. Fast feedback for linear colliders

    International Nuclear Information System (INIS)

    Hendrickson, L.; Adolphsen, C.; Allison, S.; Gromme, T.; Grossberg, P.; Himel, T.; Krauter, K.; MacKenzie, R.; Minty, M.; Sass, R.

    1995-01-01

    A fast feedback system provides beam stabilization for the SLC. As the SLC is in some sense a prototype for future linear colliders, this system may be a prototype for future feedbacks. The SLC provides a good base of experience for feedback requirements and capabilities as well as a testing ground for performance characteristics. The feedback system controls a wide variety of machine parameters throughout the SLC and associated experiments, including regulation of beam position, angle, energy, intensity and timing parameters. The design and applications of the system are described, in addition to results of recent performance studies

  15. Fast transfer of shared data

    International Nuclear Information System (INIS)

    Timmer, C.; Abbott, D.J.; Heyes, W.G.; Jostizembski, E.; MacLeod, R.W.; Wolin, E.

    2000-01-01

    The Event Transfer system enables its users to produce events (data) and share them with other users by utilizing shared memory on either Solaris or Linux-based computers. Its design emphasizes speed, reliability, ease of use, and recoverability from crashes. In addition to fast local operation, the ET system allows network transfer of events. Using multi-threaded code based on POSIX threades and mutexes, a successful implementation was developed which allowed passing events over 500 kHz on a 4 cpu Sun workstation and 150 kHz on a dual cpu PC

  16. PUC fast track nips returns

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    In the first of what it says will be annual cost-of-capital proceedings to set returns on equity and rates of return on rate base for electric utilities, the California Public Utilities Commission (PUC) lowered from 1989 levels the 1990 returns on common equity (ROE) and rates of return (ROR) for the state's four major investor-owned electric utilities. Under this fast-track procedure, by May 8 of every year, utilities will have to file an application for rate adjustments that reflect their projected costs of capital for the following year

  17. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  18. Fast-acting valve actuator

    Science.gov (United States)

    Cho, Nakwon

    1980-01-01

    A fast-acting valve actuator utilizes a spring driven pneumatically loaded piston to drive a valve gate. Rapid exhaust of pressurized gas from the pneumatically loaded side of the piston facilitates an extremely rapid piston stroke. A flexible selector diaphragm opens and closes an exhaust port in response to pressure differentials created by energizing and de-energizing a solenoid which controls the pneumatic input to the actuator as well as selectively providing a venting action to one side of the selector diaphragm.

  19. The integral fast reactor concept

    International Nuclear Information System (INIS)

    Chang, Yoon I.; Marchaterre, J.F.

    1987-01-01

    The Integral Fast Reactor (IFR) is an innovative liquid metal reactor concept being developed at Argonne National Laboratory. It seeks to specifically exploit the inherent properties of liquid metal cooling and metallic fuel in a way that leads to substantial improvements in the characteristics of the complete reactor system. The IFR concept consists of four technical features: (1) liquid sodium cooling, (2) pool-type reactor configuration, (3) metallic fuel, and (4) an integral fuel cycle, based on pyrometallurgical processing and injection-cast fuel fabrication, with the fuel cycle facility collocated with the reactor, if so desired. This paper gives a review of the IFR concept

  20. Fast processor for dilepton triggers

    International Nuclear Information System (INIS)

    Katsanevas, S.; Kostarakis, P.; Baltrusaitis, R.

    1983-01-01

    We describe a fast trigger processor, developed for and used in Fermilab experiment E-537, for selecting high-mass dimuon events produced by negative pions and anti-protons. The processor finds candidate tracks by matching hit information received from drift chambers and scintillation counters, and determines their momenta. Invariant masses are calculated for all possible pairs of tracks and an event is accepted if any invariant mass is greater than some preselectable minimum mass. The whole process, accomplished within 5 to 10 microseconds, achieves up to a ten-fold reduction in trigger rate