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Sample records for cysteine string protein

  1. Quercetin targets cysteine string protein (CSPalpha and impairs synaptic transmission.

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    Fenglian Xu

    2010-06-01

    Full Text Available Cysteine string protein (CSPalpha is a synaptic vesicle protein that displays unique anti-neurodegenerative properties. CSPalpha is a member of the conserved J protein family, also called the Hsp40 (heat shock protein of 40 kDa protein family, whose importance in protein folding has been recognized for many years. Deletion of the CSPalpha in mice results in knockout mice that are normal for the first 2-3 weeks of life followed by an unexplained presynaptic neurodegeneration and premature death. How CSPalpha prevents neurodegeneration is currently not known. As a neuroprotective synaptic vesicle protein, CSPalpha represents a promising therapeutic target for the prevention of neurodegenerative disorders.Here, we demonstrate that the flavonoid quercetin promotes formation of stable CSPalpha-CSPalpha dimers and that quercetin-induced dimerization is dependent on the unique cysteine string region. Furthermore, in primary cultures of Lymnaea neurons, quercetin induction of CSPalpha dimers correlates with an inhibition of synapse formation and synaptic transmission suggesting that quercetin interfers with CSPalpha function. Quercetin's action on CSPalpha is concentration dependent and does not promote dimerization of other synaptic proteins or other J protein family members and reduces the assembly of CSPalpha:Hsc70 units (70kDa heat shock cognate protein.Quercetin is a plant derived flavonoid and popular nutritional supplement proposed to prevent memory loss and altitude sickness among other ailments, although its precise mechanism(s of action has been unclear. In view of the therapeutic promise of upregulation of CSPalpha and the undesired consequences of CSPalpha dysfunction, our data establish an essential proof of principle that pharmaceutical agents can selectively target the neuroprotective J protein CSPalpha.

  2. Phosphomimetic mutation of cysteine string protein-α increases the rate of regulated exocytosis by modulating fusion pore dynamics in PC12 cells.

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    Ning Chiang

    Full Text Available BACKGROUND: Cysteine string protein-α (CSPα is a chaperone to ensure protein folding. Loss of CSPα function associates with many neurological diseases. However, its function in modulating regulated exocytosis remains elusive. Although cspα-knockouts exhibit impaired synaptic transmission, overexpression of CSPα in neuroendocrine cells inhibits secretion. These seemingly conflicting results lead to a hypothesis that CSPα may undergo a modification that switches its function in regulating neurotransmitter and hormone secretion. Previous studies implied that CSPα undergoes phosphorylation at Ser10 that may influence exocytosis by altering fusion pore dynamics. However, direct evidence is missing up to date. METHODOLOGY/PRINCIPAL FINDINGS: Using amperometry, we investigated how phosphorylation at Ser10 of CSPα (CSPα-Ser10 modulates regulated exocytosis and if this modulation involves regulating a specific kinetic step of fusion pore dynamics. The real-time exocytosis of single vesicles was detected in PC12 cells overexpressing control vector, wild-type CSPα (WT, the CSPα phosphodeficient mutant (S10A, or the CSPα phosphomimetic mutants (S10D and S10E. The shapes of amperometric signals were used to distinguish the full-fusion events (i.e., prespike feet followed by spikes and the kiss-and-run events (i.e., square-shaped flickers. We found that the secretion rate was significantly increased in cells overexpressing S10D or S10E compared to WT or S10A. Further analysis showed that overexpression of S10D or S10E prolonged fusion pore lifetime compared to WT or S10A. The fraction of kiss-and-run events was significantly lower but the frequency of full-fusion events was higher in cells overexpressing S10D or S10E compared to WT or S10A. Advanced kinetic analysis suggests that overexpression of S10D or S10E may stabilize open fusion pores mainly by inhibiting them from closing. CONCLUSIONS/SIGNIFICANCE: CSPα may modulate fusion pore dynamics

  3. Protein cysteine oxidation in redox signaling

    DEFF Research Database (Denmark)

    Forman, Henry Jay; Davies, Michael J; Krämer, Anna C

    2017-01-01

    Oxidation of critical signaling protein cysteines regulated by H2O2 has been considered to involve sulfenic acid (RSOH) formation. RSOH may subsequently form either a sulfenyl amide (RSNHR') with a neighboring amide, or a mixed disulfide (RSSR') with another protein cysteine or glutathione. Previ...

  4. Protein modification by acrolein: Formation and stability of cysteine adducts

    OpenAIRE

    Cai, Jian; Bhatnagar, Aruni; Pierce, William M.

    2009-01-01

    The toxicity of the ubiquitous pollutant and endogenous metabolite, acrolein, is due in part to covalent protein modifications. Acrolein reacts readily with protein nucleophiles via Michael addition and Schiff base formation. Potential acrolein targets in protein include the nucleophilic side chains of cysteine, histidine, and lysine residues as well as the free amino terminus of proteins. Although cysteine is the most acrolein-reactive residue, cysteine-acrolein adducts are difficult to iden...

  5. Overexpression of Catalase Diminishes Oxidative Cysteine Modifications of Cardiac Proteins.

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    Chunxiang Yao

    Full Text Available Reactive protein cysteine thiolates are instrumental in redox regulation. Oxidants, such as hydrogen peroxide (H2O2, react with thiolates to form oxidative post-translational modifications, enabling physiological redox signaling. Cardiac disease and aging are associated with oxidative stress which can impair redox signaling by altering essential cysteine thiolates. We previously found that cardiac-specific overexpression of catalase (Cat, an enzyme that detoxifies excess H2O2, protected from oxidative stress and delayed cardiac aging in mice. Using redox proteomics and systems biology, we sought to identify the cysteines that could play a key role in cardiac disease and aging. With a 'Tandem Mass Tag' (TMT labeling strategy and mass spectrometry, we investigated differential reversible cysteine oxidation in the cardiac proteome of wild type and Cat transgenic (Tg mice. Reversible cysteine oxidation was measured as thiol occupancy, the ratio of total available versus reversibly oxidized cysteine thiols. Catalase overexpression globally decreased thiol occupancy by ≥1.3 fold in 82 proteins, including numerous mitochondrial and contractile proteins. Systems biology analysis assigned the majority of proteins with differentially modified thiols in Cat Tg mice to pathways of aging and cardiac disease, including cellular stress response, proteostasis, and apoptosis. In addition, Cat Tg mice exhibited diminished protein glutathione adducts and decreased H2O2 production from mitochondrial complex I and II, suggesting improved function of cardiac mitochondria. In conclusion, our data suggest that catalase may alleviate cardiac disease and aging by moderating global protein cysteine thiol oxidation.

  6. Using an alignment of fragment strings for comparing protein structures

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Kolodny, Rachel

    2007-01-01

    . RESULTS: Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained...

  7. Carbon Nanotubes Facilitate Oxidation of Cysteine Residues of Proteins.

    Science.gov (United States)

    Hirano, Atsushi; Kameda, Tomoshi; Wada, Momoyo; Tanaka, Takeshi; Kataura, Hiromichi

    2017-10-19

    The adsorption of proteins onto nanoparticles such as carbon nanotubes (CNTs) governs the early stages of nanoparticle uptake into biological systems. Previous studies regarding these adsorption processes have primarily focused on the physical interactions between proteins and nanoparticles. In this study, using reduced lysozyme and intact human serum albumin in aqueous solutions, we demonstrated that CNTs interact chemically with proteins. The CNTs induce the oxidation of cysteine residues of the proteins, which is accounted for by charge transfer from the sulfhydryl groups of the cysteine residues to the CNTs. The redox reaction simultaneously suppresses the intermolecular association of proteins via disulfide bonds. These results suggest that CNTs can affect the folding and oxidation degree of proteins in biological systems such as blood and cytosol.

  8. Isolation of recombinant cysteine dioxygenase protein from Trichophyton mentagrophytes

    Czech Academy of Sciences Publication Activity Database

    Kašperová, A.; Kunert, J.; Horynová, M.; Weigl, E.; Sebela, M.; Lenobel, René; Raška, M.

    2011-01-01

    Roč. 54, č. 5 (2011), E456-E462 ISSN 0933-7407 R&D Projects: GA ČR GA301/08/1649 Institutional research plan: CEZ:AV0Z50380511 Keywords : Cysteine dioxygenase * dermatophytes * recombinant protein * keratinolytic fungi * cDNA Subject RIV: CE - Biochemistry Impact factor: 2.247, year: 2011

  9. Soft Cysteine Signaling Network: The Functional Significance of Cysteine in Protein Function and the Soft Acids/Bases Thiol Chemistry That Facilitates Cysteine Modification.

    Science.gov (United States)

    Wible, Ryan S; Sutter, Thomas R

    2017-03-20

    The unique biophysical and electronic properties of cysteine make this molecule one of the most biologically critical amino acids in the proteome. The defining sulfur atom in cysteine is much larger than the oxygen and nitrogen atoms more commonly found in the other amino acids. As a result of its size, the valence electrons of sulfur are highly polarizable. Unique protein microenvironments favor the polarization of sulfur, thus increasing the overt reactivity of cysteine. Here, we provide a brief overview of the endogenous generation of reactive oxygen and electrophilic species and specific examples of enzymes and transcription factors in which the oxidation or covalent modification of cysteine in those proteins modulates their function. The perspective concludes with a discussion of cysteine chemistry and biophysics, the hard and soft acids and bases model, and the proposal of the Soft Cysteine Signaling Network: a hypothesis proposing the existence of a complex signaling network governed by layered chemical reactivity and cross-talk in which the chemical modification of reactive cysteine in biological networks triggers the reorganization of intracellular biochemistry to mitigate spikes in endogenous or exogenous oxidative or electrophilic stress.

  10. Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

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    Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

    2013-01-01

    One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

  11. Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families

    Science.gov (United States)

    Defelipe, Lucas A.; Lanzarotti, Esteban; Gauto, Diego; Marti, Marcelo A.; Turjanski, Adrián G.

    2015-01-01

    Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function. PMID:25741692

  12. Identification and preliminary characterization of protein-cysteine farnesyltransferase

    International Nuclear Information System (INIS)

    Manne, V.; Roberts, D.; Tobin, A.; O'Rourke, E.; Barbacid, M.; De Virgilio, M.; Meyers, C.; Ahmed, N.; Kurz, B.; Resh, M.; Kung, Hsiang-Fu

    1990-01-01

    Ras proteins must be isoprenylated at a conserved cysteine residue near the carboxyl terminus in order to exert their biological activity. Previous studies indicate that an intermediate in the mevalonate pathway, most likely farnesyl pyrophosphate, is the donor of this isoprenyl group. Inhibition of mevalonate synthesis reverts the abnormal phenotypes induced by the mutant RAS2 Valendash19 gene in Saccharomyces cerevisiae and blocks the maturation of Xenopus oocytes induced by an onocogenic Ras p21 protein of human origin. These results have raised the possibility of using inhibitors of the mevalonate pathway to block the transforming properties of ras oncogenes. Unfortunately, mevalonate is a precursor of various end products essential to mammalian cells, such as dolichols, ubiquinones, heme A, and cholesterol. In this study, the authors describe an enzymatic activity(ies) capable of catalyzing the farnesylation of unprocessed Ras p21 proteins in vitro at the correct (Cys-186) residue. Gel filtration analysis of a partially purified preparation of protein farnesyltransferase revealed two peaks of activity at 250-350 kDa and 80-130 kDa. Availability of an in vitro protein farnesyltransferase assay should be useful in screening for potential inhibitors of ras oncogene function that will not interfere with other aspects of the mevalonate pathway

  13. Replication of murine coronavirus requires multiple cysteines in the endodomain of spike protein

    International Nuclear Information System (INIS)

    Yang, Jinhua; Lv, Jun; Wang, Yuyan; Gao, Shuang; Yao, Qianqian; Qu, Di; Ye, Rong

    2012-01-01

    A conserved cysteine-rich motif located between the transmembrane domain and the endodomain is essential for membrane fusion and assembly of coronavirus spike (S) protein. Here, we proved that three cysteines within the motif, but not dependent on position, are minimally required for the survival of the recombinant mouse hepatitis virus. When the carboxy termini with these mutated motifs of S proteins were respectively introduced into a heterogeneous protein, both incorporation into lipid rafts and S-palmitoylation of these recombinant proteins showed a similar quantity requirement to cysteine residues. Meanwhile, the redistribution of these proteins on cellular surface indicated that the absence of the positively charged rather than cysteine residues in the motif might lead the dramatic reduction in syncytial formation of some mutants with the deleted motifs. These results suggest that multiple cysteine as well as charged residues concurrently improves the membrane-associated functions of S protein in viral replication and cytopathogenesis.

  14. Replication of murine coronavirus requires multiple cysteines in the endodomain of spike protein

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jinhua; Lv, Jun; Wang, Yuyan; Gao, Shuang; Yao, Qianqian; Qu, Di; Ye, Rong, E-mail: yerong24@fudan.edu.cn

    2012-06-05

    A conserved cysteine-rich motif located between the transmembrane domain and the endodomain is essential for membrane fusion and assembly of coronavirus spike (S) protein. Here, we proved that three cysteines within the motif, but not dependent on position, are minimally required for the survival of the recombinant mouse hepatitis virus. When the carboxy termini with these mutated motifs of S proteins were respectively introduced into a heterogeneous protein, both incorporation into lipid rafts and S-palmitoylation of these recombinant proteins showed a similar quantity requirement to cysteine residues. Meanwhile, the redistribution of these proteins on cellular surface indicated that the absence of the positively charged rather than cysteine residues in the motif might lead the dramatic reduction in syncytial formation of some mutants with the deleted motifs. These results suggest that multiple cysteine as well as charged residues concurrently improves the membrane-associated functions of S protein in viral replication and cytopathogenesis.

  15. Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

    Science.gov (United States)

    Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

    2012-11-01

    One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

  16. Mutation choice to eliminate buried free cysteines in protein therapeutics.

    Science.gov (United States)

    Xia, Xue; Longo, Liam M; Blaber, Michael

    2015-02-01

    Buried free-cysteine (Cys) residues can contribute to an irreversible unfolding pathway that promotes protein aggregation, increases immunogenic potential, and significantly reduces protein functional half-life. Consequently, mutation of buried free-Cys residues can result in significant improvement in the storage, reconstitution, and pharmacokinetic properties of protein-based therapeutics. Mutational design to eliminate buried free-Cys residues typically follows one of two common heuristics: either substitution by Ser (polar and isosteric), or substitution by Ala or Val (hydrophobic); however, a detailed structural and thermodynamic understanding of Cys mutations is lacking. We report a comprehensive structure and stability study of Ala, Ser, Thr, and Val mutations at each of the three buried free-Cys positions (Cys16, Cys83, and Cys117) in fibroblast growth factor-1. Mutation was almost universally destabilizing, indicating a general optimization for the wild-type Cys, including van der Waals and H-bond interactions. Structural response to Cys mutation characteristically involved changes to maintain, or effectively substitute, local H-bond interactions-by either structural collapse to accommodate the smaller oxygen radius of Ser/Thr, or conversely, expansion to enable inclusion of novel H-bonding solvent. Despite the diverse structural effects, the least destabilizing average substitution at each position was Ala, and not isosteric Ser. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  17. Correlation of secreted protein acidic and rich in cysteine with diabetic nephropathy

    OpenAIRE

    Li, Lei; Song, Hai-Yan; Liu, Kai; An, Meng-Meng

    2015-01-01

    To detect the serum concentrations of secreted protein acidic and rich in cysteine (SPARC) in patients with diabetic nephropathy and SPARC mRNA and protein expressions in renal tissue of db/db mice (C57BL/KsJ, diabetic nephropathy mice), thus preliminary exploration on the role of secreted protein acidic riches in cysteine in the development of diabetic nephropathy were carried out. Serum SPARC levels in normal subjects, patients with type 2 diabetes mellitus (without diabetic nephropathy), c...

  18. Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation.

    Science.gov (United States)

    Lipton, Stuart A; Choi, Yun-Beom; Takahashi, Hiroto; Zhang, Dongxian; Li, Weizhong; Godzik, Adam; Bankston, Laurie A

    2002-09-01

    Until recently cysteine residues, especially those located extracellularly, were thought to be important for metal coordination, catalysis and protein structure by forming disulfide bonds - but they were not thought to regulate protein function. However, this is not the case. Crucial cysteine residues can be involved in modulation of protein activity and signaling events via other reactions of their thiol (sulfhydryl; -SH) groups. These reactions can take several forms, such as redox events (chemical reduction or oxidation), chelation of transition metals (chiefly Zn(2+), Mn(2+) and Cu(2+)) or S-nitrosylation [the catalyzed transfer of a nitric oxide (NO) group to a thiol group]. In several cases, these disparate reactions can compete with one another for the same thiol group on a single cysteine residue, forming a molecular switch composed of a latticework of possible redox, NO or Zn(2+) modifications to control protein function. Thiol-mediated regulation of protein function can also involve reactions of cysteine residues that affect ligand binding allosterically. This article reviews the basis for these molecular cysteine switches, drawing on the NMDA receptor as an exemplary protein, and proposes a molecular model for the action of S-nitrosylation based on recently derived crystal structures.

  19. Do cysteine residues regulate transient receptor potential canonical type 6 (TRPC6) channel protein expression?

    DEFF Research Database (Denmark)

    Thilo, Florian; Liu, Ying; Krueger, Katharina

    2012-01-01

    The regulation of calcium influx through transient receptor potential canonical type 6 channel is mandatory for the activity of human monocytes. We submit the first evidence that cysteine residues of homocysteine or acetylcysteine affect TRPC6 expression in human monocytes. We observed that patie......The regulation of calcium influx through transient receptor potential canonical type 6 channel is mandatory for the activity of human monocytes. We submit the first evidence that cysteine residues of homocysteine or acetylcysteine affect TRPC6 expression in human monocytes. We observed...... that patients with chronic renal failure had significantly elevated homocysteine levels and TRPC6 mRNA expression levels in monocytes compared to control subjects. We further observed that administration of homocysteine or acetylcysteine significantly increased TRPC6 channel protein expression compared...... to control conditions. We therefore hypothesize that cysteine residues increase TRPC6 channel protein expression in humans....

  20. The proteins of Fusobacterium spp. involved in hydrogen sulfide production from L-cysteine.

    Science.gov (United States)

    Basic, Amina; Blomqvist, Madeleine; Dahlén, Gunnar; Svensäter, Gunnel

    2017-03-14

    Hydrogen sulfide (H 2 S) is a toxic foul-smelling gas produced by subgingival biofilms in patients with periodontal disease and is suggested to be part of the pathogenesis of the disease. We studied the H 2 S-producing protein expression of bacterial strains associated with periodontal disease. Further, we examined the effect of a cysteine-rich growth environment on the synthesis of intracellular enzymes in F. nucleatum polymorphum ATCC 10953. The proteins were subjected to one-dimensional (1DE) and two-dimensional (2DE) gel electrophoresis An in-gel activity assay was used to detect the H 2 S-producing enzymes; Sulfide from H 2 S, produced by the enzymes in the gel, reacted with bismuth forming bismuth sulfide, illustrated as brown bands (1D) or spots (2D) in the gel. The discovered proteins were identified with liquid chromatography - tandem mass spectrometry (LC-MS/MS). Cysteine synthase and proteins involved in the production of the coenzyme pyridoxal 5'phosphate (that catalyzes the production of H 2 S) were frequently found among the discovered enzymes. Interestingly, a higher expression of H 2 S-producing enzymes was detected from bacteria incubated without cysteine prior to the experiment. Numerous enzymes, identified as cysteine synthase, were involved in the production of H 2 S from cysteine and the expression varied among Fusobacterium spp. and strains. No enzymes were detected with the in-gel activity assay among the other periodontitis-associated bacteria tested. The expression of the H 2 S-producing enzymes was dependent on environmental conditions such as cysteine concentration and pH but less dependent on the presence of serum and hemin.

  1. 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.

  2. Cysteine-rich intestinal protein binds zinc during transmucosal zinc transport

    International Nuclear Information System (INIS)

    Hempe, J.M.; Cousins, R.J.

    1991-01-01

    The mechanism of zinc absorption has not been delineated, but kinetic studies show that both passive and carrier-mediated processes are involved. The authors have identified a low molecular mass zinc-binding protein in the soluble fraction of rat intestinal mucosa that could function as an intracellular zinc carrier. The protein was not detected in liver or pancreas, suggesting a role specific to the intestine. The protein binds zinc during transmucosal zinc transport and shows signs of saturation at higher luminal zinc concentrations, characteristics consistent with a role in carrier-mediated zinc absorption. Microsequence analysis of the protein purified by gel-filtration HPCL and SDS/PAGE showed complete identity within the first 41 N-terminal amino acids with the deduced protein sequence of cysteine-rich intestinal protein. These investigators showed that the gene for this protein is developmentally regulated in neonates during the suckling period, conserved in many vertebrate species, and predominantly expressed in the small intestine. Cysteine-rich intestinal protein contains a recently identified conserved sequence of histidine and cysteine residues, the LIM motif, which our results suggest confers metal-binding properties that are important for zinc transport and/or functions of this micronutrient

  3. Protein redox chemistry: post-translational cysteine modifications that regulate signal transduction and drug pharmacology

    Directory of Open Access Journals (Sweden)

    Revati eWani

    2014-10-01

    Full Text Available The perception of reactive oxygen species (ROS has evolved over the past decade from agents of cellular damage to secondary messengers which modify signaling proteins in physiology and the disease state (e.g. cancer. New protein targets of specific oxidation are rapidly being identified. One emerging class of redox modification occurs to the thiol side chain of cysteine residues which can produce multiple chemically-distinct alterations to the protein (e.g. sulfenic/sulfinic/sulfonic acid, disulfides. These post-translational modifications (PTM are shown to affect the protein structure and function. Because redox-sensitive proteins can traffic between subcellular compartments that have different redox environments, cysteine oxidation enables a spatio-temporal control to signaling. Understanding ramifications of these oxidative modifications to the functions of signaling proteins is crucial for understanding cellular regulation as well as for informed-drug discovery process. The effects of EGFR oxidation of Cys797 on inhibitor pharmacology are presented to illustrate the principle. Taken together, cysteine redox PTM can impact both cell biology and drug pharmacology.

  4. STRING 8--a global view on proteins and their functional interactions in 630 organisms

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Kuhn, Michael; Stark, Manuel

    2008-01-01

    Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein-protein inter......Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein......-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set...... of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures...

  5. 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.

  6. Soluble cysteine-rich tick saliva proteins Salp15 and Iric-1 from E. coli

    OpenAIRE

    Kolb, Philipp; Vorreiter, Jolanta; Habicht, J?ri; Bentrop, Detlef; Wallich, Reinhard; Nassal, Michael

    2014-01-01

    Ticks transmit numerous pathogens, including borreliae, which cause Lyme disease. Tick saliva contains a complex mix of anti-host defense factors, including the immunosuppressive cysteine-rich secretory glycoprotein Salp15 from Ixodes scapularis ticks and orthologs like Iric-1 from Ixodes ricinus. All tick-borne microbes benefit from the immunosuppression at the tick bite site; in addition, borreliae exploit the binding of Salp15 to their outer surface protein C (OspC) for enhanced transmissi...

  7. Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation

    OpenAIRE

    Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

    2015-01-01

    This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, ...

  8. Mechanical strength of 17,134 model proteins and cysteine slipknots.

    Directory of Open Access Journals (Sweden)

    Mateusz Sikora

    2009-10-01

    Full Text Available A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17,134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids. Our previous studies have dealt with 7510 proteins of no more than 150 amino acids. The proteins are ranked according to the strength of the resistance. Most of the predicted top-strength proteins have not yet been studied experimentally. Architectures and folds which are likely to yield large forces are identified. New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. An effective energy parameter of the model is estimated by comparing the theoretical data on characteristic forces to the corresponding experimental values combined with an extrapolation of the theoretical data to the experimental pulling speeds. These studies provide guidance for future experiments on single molecule manipulation and should lead to selection of proteins for applications. A new class of proteins, involving cysteine slipknots, is identified as one that is expected to lead to the strongest force clamps known. This class is characterized through molecular dynamics simulations.

  9. Cysteine and tryptophan anomalies found when scanning all the binding sites in the Protein Data Bank.

    Science.gov (United States)

    Iván, Gábor; Szabadka, Zoltán; Grolmusz, Vince

    2010-01-01

    The Protein Data Bank (PDB) is one of the richest sources of structural biological information in the World. It started to exist as the computer-readable depository of crystallographic data complementing printed papers. The proper interpretation of the content of the individual files in the PDB still needs the detailed information found in the citing publication. An advanced graph theoretical method is presented here for automatically repairing, re-organising and re-structuring PDB data yielding the identification of all the protein-ligand complexes and all the binding sites in the PDB. As an application, we identified strong cysteine and tryptophan irregularities in the data.

  10. Plasmodium cysteine repeat modular proteins 1-4: complex proteins with roles throughout the malaria parasite life cycle.

    Science.gov (United States)

    Thompson, Joanne; Fernandez-Reyes, Delmiro; Sharling, Lisa; Moore, Sally G; Eling, Wijnand M; Kyes, Sue A; Newbold, Christopher I; Kafatos, Fotis C; Janse, Chris J; Waters, Andrew P

    2007-06-01

    The Cysteine Repeat Modular Proteins (PCRMP1-4) of Plasmodium, are encoded by a small gene family that is conserved in malaria and other Apicomplexan parasites. They are very large, predicted surface proteins with multipass transmembrane domains containing motifs that are conserved within families of cysteine-rich, predicted surface proteins in a range of unicellular eukaryotes, and a unique combination of protein-binding motifs, including a >100 kDa cysteine-rich modular region, an epidermal growth factor-like domain and a Kringle domain. PCRMP1 and 2 are expressed in life cycle stages in both the mosquito and vertebrate. They colocalize with PfEMP1 (P. falciparum Erythrocyte Membrane Antigen-1) during its export from P. falciparum blood-stage parasites and are exposed on the surface of haemolymph- and salivary gland-sporozoites in the mosquito, consistent with a role in host tissue targeting and invasion. Gene disruption of pcrmp1 and 2 in the rodent malaria model, P. berghei, demonstrated that both are essential for transmission of the parasite from the mosquito to the mouse and has established their discrete and important roles in sporozoite targeting to the mosquito salivary gland. The unprecedented expression pattern and structural features of the PCRMPs thus suggest a variety of roles mediating host-parasite interactions throughout the parasite life cycle.

  11. Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Donald Adjeroh

    2018-03-01

    Full Text Available In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI. In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences, and structure information (protein and RNA secondary structures. This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.

  12. Iron-Binding Protein Degradation by Cysteine Proteases of Naegleria fowleri

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    Moisés Martínez-Castillo

    2015-01-01

    Full Text Available Naegleria fowleri causes acute and fulminant primary amoebic meningoencephalitis. This microorganism invades its host by penetrating the olfactory mucosa and then traveling up the mesaxonal spaces and crossing the cribriform plate; finally, the trophozoites invade the olfactory bulbs. During its invasion, the protozoan obtains nutrients such as proteins, lipids, carbohydrates, and cationic ions (e.g., iron, calcium, and sodium from the host. However, the mechanism by which these ions are obtained, particularly iron, is poorly understood. In the present study, we evaluated the ability of N. fowleri to degrade iron-binding proteins, including hololactoferrin, transferrin, ferritin, and hemoglobin. Zymography assays were performed for each substrate under physiological conditions (pH 7 at 37°C employing conditioned medium (CM and total crude extracts (TCEs of N. fowleri. Different degradation patterns with CM were observed for hololactoferrin, transferrin, and hemoglobin; however, CM did not cause ferritin degradation. In contrast, the TCEs degraded only hololactoferrin and transferrin. Inhibition assays revealed that cysteine proteases were involved in this process. Based on these results, we suggest that CM and TCEs of N. fowleri degrade iron-binding proteins by employing cysteine proteases, which enables the parasite to obtain iron to survive while invading the central nervous system.

  13. Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Jicheng; Gaffrey, Matthew J.; Qian, Wei-Jun

    2017-01-01

    Protein cysteine thiols play a crucial role in redox signaling, regulation of enzymatic activity and protein function, and maintaining redox homeostasis in living systems. The unique chemical reactivity of thiol groups makes cysteine susceptible to oxidative modifications by reactive oxygen and nitrogen species to form a broad array of reversible and irreversible protein post-translational modifications (PTMs). The reversible modifications in particular are one of the major components of redox signaling and are involved in regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in health and diseases has been increasingly recognized. Herein, we review the recent advances of quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including the general considerations of sample processing, various chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for addressing specific biological questions. Although some technological limitations remain, redox proteomics is paving the way towards a better understanding of redox signaling and regulation in human health and diseases.

  14. Harvey murine sarcoma virus p21 ras protein: biological and biochemical significance of the cysteine nearest the carboxy terminus

    DEFF Research Database (Denmark)

    Willumsen, B M; Norris, K; Papageorge, A G

    1984-01-01

    localization. We have now further characterized the post-translational processing of these mutants and have also studied two C-terminal v-rasH point mutants: one encodes serine in place of cysteine-186, the other threonine for valine-187. The Thr-187 mutant was transformation-competent, and its p21 protein...... not undergo the posttranslational processing common to biologically active ras proteins: their electrophoretic migration rate did not change, they remained in the cytosol, and they failed to bind lipid. Since the cell-encoded ras proteins also contain this cysteine, we conclude that this amino acid residue...

  15. The synthesis and protein resistance of amphiphilic PDMS-b-(PDMS-g-cysteine) copolymers

    Science.gov (United States)

    Lei, Yufeng; Lin, Yaling; Zhang, Anqiang

    2017-10-01

    Zwitterionic polymers have been used to cope with nonspecific protein adsorption and bio-fouling problems for a wide range of materials, including biomedical devices, marine coatings and membrane separation. However, direct surface modification with highly water-soluble zwitterionic polymers is rather difficult due to their poor attachment to hydrophobic solid surfaces. In this work, we utilize the hydrophobic interaction to anchor zwitterionic polysiloxanes grafted with cysteine onto surfaces by adding an hydrophobic block of polydimethylsiloxanes, referred as PDMS-b-(PDMS-g-Cys)s. The synthesis involves only three steps of reactions, and the structures of each product were characterized using GPC, FT-IR and 1H NMR. The adsorption and protein resistance of PDMS-b-(PDMS-g-Cys)s on a gold surface are investigated with QCM-D. The results show that the hydrophobic interaction moieties of the additional PDMS blocks help the hydrophilic cysteine-grafted blocks stably attach and then function on the sensor. These findings suggest that the addition of hydrophobic moieties provides an effective approach to construct anti-fouling interfaces with zwitterionic polymers in aqueous solution.

  16. Regulation of basal resistance by a powdery mildew-induced cysteine-rich receptor-like protein kinase in barley

    DEFF Research Database (Denmark)

    Rayapuram, Channabasavangowda; Jensen, Michael Krogh; Maiser, Fabian

    2012-01-01

    The receptor-like protein kinases (RLKs) constitute a large and diverse group of proteins controlling numerous plant physiological processes, including development, hormone perception and stress responses. The cysteine-rich RLKs (CRKs) represent a prominent subfamily of transmembrane-anchored RLKs...

  17. Cysteine-rich secretory protein 3 is a ligand of alpha1B-glycoprotein in human plasma

    DEFF Research Database (Denmark)

    Udby, Lene; Sørensen, Ole E; Pass, Jesper

    2004-01-01

    Human cysteine-rich secretory protein 3 (CRISP-3; also known as SGP28) belongs to a family of closely related proteins found in mammals and reptiles. Some mammalian CRISPs are known to be involved in the process of reproduction, whereas some of the CRISPs from reptiles are neurotoxin...

  18. Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation.

    Science.gov (United States)

    Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

    2016-02-01

    This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, both in terms of hazing potential and total protein decrease, was significantly higher than PBR-pa, in all the seven unfined, white wines used. Among the wines tested, Sauvignon Blanc, given its total protein content as well as its very high intrinsic instability, was selected as a control wine to evaluate the effect of the treatment on wine as to its soluble protein profile, phenolic composition, mineral component, and sensory properties. The treatment in a PBR containing immobilised bromelain appeared effective in decreasing both wine hazing potential and total protein amount, while it did not significantly affect the phenol compounds, the mineral component nor the sensory quality of wine. The enzymatic treatment in PBR was shown to be a specific and mild technique for use as an alternative to bentonite fining for white wine protein stabilisation.

  19. Merging in-silico and in vitro salivary protein complex partners using the STRING database: A tutorial.

    Science.gov (United States)

    Crosara, Karla Tonelli Bicalho; Moffa, Eduardo Buozi; Xiao, Yizhi; Siqueira, Walter Luiz

    2018-01-16

    Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions. We used an in-silico approach along with the STRING database (http://string-db.org/) and successfully performed a fast simulation of a novel constructed histatin 1 protein-protein network, including both the previously known and the predicted interactors, along with our newly identified interactors. Our study highlights the advantages and importance of applying bioinformatics tools to merge in-silico tactics with experimental in vitro findings for rapid advancement of our knowledge about protein-protein interactions. Our findings also indicate that bioinformatics tools such as the STRING protein network database can help predict potential interactions between proteins and thus serve as a guide for future steps in our exploration of the Human Interactome. Our study highlights the usefulness of the STRING protein database for studying protein-protein interactions. The STRING database can collect and integrate data about known and predicted protein-protein associations from many organisms, including both direct (physical) and indirect (functional) interactions, in an easy-to-use interface. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Direct determination of the redox status of cysteine residues in proteins in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Hara, Satoshi [Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503 (Japan); Tatenaka, Yuki; Ohuchi, Yuya [Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202 (Japan); Hisabori, Toru, E-mail: thisabor@res.titech.ac.jp [Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075 (Japan)

    2015-01-02

    Highlights: • A new DNA-maleimide which is cleaved by UV irradiation, DNA-PCMal, was developed. • DNA-PCMal can be used like DNA-Mal to analyze the redox state of cysteine residues. • It is useful for detecting the thiol redox status of a protein in vivo by Western blotting method. • Thus, DNA-PCMal can be a powerful tool for redox proteomics analysis. - Abstract: The redox states of proteins in cells are key factors in many cellular processes. To determine the redox status of cysteinyl thiol groups in proteins in vivo, we developed a new maleimide reagent, a photocleavable maleimide-conjugated single stranded DNA (DNA-PCMal). The DNA moiety of DNA-PCMal is easily removed by UV-irradiation, allowing DNA-PCMal to be used in Western blotting applications. Thereby the state of thiol groups in intracellular proteins can be directly evaluated. This new maleimide compound can provide information concerning redox proteins in vivo, which is important for our understanding of redox networks in the cell.

  1. Soilborne wheat mosaic virus (SBWMV 19K protein belongs to a class of cysteine rich proteins that suppress RNA silencing

    Directory of Open Access Journals (Sweden)

    Howard Amanda

    2005-03-01

    Full Text Available Abstract Amino acid sequence analyses indicate that the Soilborne wheat mosaic virus (SBWMV 19K protein is a cysteine-rich protein (CRP and shares sequence homology with CRPs derived from furo-, hordei-, peclu- and tobraviruses. Since the hordei- and pecluvirus CRPs were shown to be pathogenesis factors and/or suppressors of RNA silencing, experiments were conducted to determine if the SBWMV 19K CRP has similar activities. The SBWMV 19K CRP was introduced into the Potato virus X (PVX viral vector and inoculated to tobacco plants. The SBWMV 19K CRP aggravated PVX-induced symptoms and restored green fluorescent protein (GFP expression to GFP silenced tissues. These observations indicate that the SBWMV 19K CRP is a pathogenicity determinant and a suppressor of RNA silencing.

  2. Soluble cysteine-rich tick saliva proteins Salp15 and Iric-1 from E. coli.

    Science.gov (United States)

    Kolb, Philipp; Vorreiter, Jolanta; Habicht, Jüri; Bentrop, Detlef; Wallich, Reinhard; Nassal, Michael

    2015-01-01

    Ticks transmit numerous pathogens, including borreliae, which cause Lyme disease. Tick saliva contains a complex mix of anti-host defense factors, including the immunosuppressive cysteine-rich secretory glycoprotein Salp15 from Ixodes scapularis ticks and orthologs like Iric-1 from Ixodes ricinus. All tick-borne microbes benefit from the immunosuppression at the tick bite site; in addition, borreliae exploit the binding of Salp15 to their outer surface protein C (OspC) for enhanced transmission. Hence, Salp15 proteins are attractive targets for anti-tick vaccines that also target borreliae. However, recombinant Salp proteins are not accessible in sufficient quantity for either vaccine manufacturing or for structural characterization. As an alternative to low-yield eukaryotic systems, we investigated cytoplasmic expression in Escherichia coli, even though this would not result in glycosylation. His-tagged Salp15 was efficiently expressed but insoluble. Among the various solubility-enhancing protein tags tested, DsbA was superior, yielding milligram amounts of soluble, monomeric Salp15 and Iric-1 fusions. Easily accessible mutants enabled epitope mapping of two monoclonal antibodies that, importantly, cross-react with glycosylated Salp15, and revealed interaction sites with OspC. Free Salp15 and Iric-1 from protease-cleavable fusions, despite limited solubility, allowed the recording of (1)H-(15)N 2D NMR spectra, suggesting partial folding of the wild-type proteins but not of Cys-free variants. Fusion to the NMR-compatible GB1 domain sufficiently enhanced solubility to reveal first secondary structure elements in (13)C/(15)N double-labeled Iric-1. Together, E. coli expression of appropriately fused Salp15 proteins may be highly valuable for the molecular characterization of the function and eventually the 3D structure of these medically relevant tick proteins.

  3. Immobilized palladium(II) ion affinity chromatography for recovery of recombinant proteins with peptide tags containing histidine and cysteine.

    Science.gov (United States)

    Kikot, Pamela; Polat, Aise; Achilli, Estefania; Fernandez Lahore, Marcelo; Grasselli, Mariano

    2014-11-01

    Fusion of peptide-based tags to recombinant proteins is currently one of the most used tools for protein production. Also, immobilized metal ion affinity chromatography (IMAC) has a huge application in protein purification, especially in research labs. The combination of expression systems of recombinant tagged proteins with this robust chromatographic system has become an efficient and rapid tool to produce milligram-range amounts of proteins. IMAC-Ni(II) columns have become the natural partners of 6xHis-tagged proteins. The Ni(II) ion is considered as the best compromise of selectivity and affinity for purification of a recombinant His-tagged protein. The palladium(II) ion is also able to bind to side chains of amino acids and form ternary complexes with iminodiacetic acid and free amino acids and other sulfur-containing molecules. In this work, we evaluated two different cysteine- and histidine-containing six amino acid tags linked to the N-terminal group of green fluorescent protein (GFP) and studied the adsorption and elution conditions using novel eluents. Both cysteine-containing tagged GFPs were able to bind to IMAC-Pd(II) matrices and eluted successfully using a low concentration of thiourea solution. The IMAC-Ni(II) system reaches less than 20% recovery of the cysteine-containing tagged GFP from a crude homogenate of recombinant Escherichia coli, meanwhile the IMAC-Pd(II) yields a recovery of 45% with a purification factor of 13. Copyright © 2014 John Wiley & Sons, Ltd.

  4. [Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

    Science.gov (United States)

    Melnik, T N; Nagibina, G S; Surin, A K; Glukhova, K A; Melnik, B S

    2018-01-01

    Studying the effect of cysteine bridges on different energy levels of multistage folding proteins will enable a better understanding of the process of folding and functioning of globular proteins. In particular, it will create prospects for directed change in the stability and rate of protein folding. In this work, using the method of differential scanning microcalorimetry, we have studied the effect of three cysteine bridges introduced in different structural elements of the green fluorescent protein on the denaturation enthalpies, activation energies, and heat-capacity increments when this protein passes from native to intermediate and transition states. The studies have allowed us to confirm that, with this protein denaturation, the process hardly damages the structure initially, but then changes occur in the protein structure in the region of 4-6 beta sheets. The cysteine bridge introduced in this region decreases the hydration of the second transition state and increases the hydration of the second intermediate state during the thermal denaturation of the green fluorescent protein.

  5. Covalent protein modification with ISG15 via a conserved cysteine in the hinge region.

    Directory of Open Access Journals (Sweden)

    Veronika N Bade

    Full Text Available The ubiquitin-like protein ISG15 (interferon-stimulated gene of 15 kDa is strongly induced by type I interferons and displays antiviral activity. As other ubiquitin-like proteins (Ubls, ISG15 is post-translationally conjugated to substrate proteins by an isopeptide bond between the C-terminal glycine of ISG15 and the side chains of lysine residues in the substrates (ISGylation. ISG15 consists of two ubiquitin-like domains that are separated by a hinge region. In many orthologs, this region contains a single highly reactive cysteine residue. Several hundred potential substrates for ISGylation have been identified but only a few of them have been rigorously verified. In order to investigate the modification of several ISG15 substrates, we have purified ISG15 conjugates from cell extracts by metal-chelate affinity purification and immunoprecipitations. We found that the levels of proteins modified by human ISG15 can be decreased by the addition of reducing agents. With the help of thiol blocking reagents, a mutational analysis and miRNA mediated knock-down of ISG15 expression, we revealed that this modification occurs in living cells via a disulphide bridge between the substrates and Cys78 in the hinge region of ISG15. While the ISG15 activating enzyme UBE1L is conjugated by ISG15 in the classical way, we show that the ubiquitin conjugating enzyme Ubc13 can either be classically conjugated by ISG15 or can form a disulphide bridge with ISG15 at the active site cysteine 87. The latter modification would interfere with its function as ubiquitin conjugating enzyme. However, we found no evidence for an ISG15 modification of the dynamin-like GTPases MxA and hGBP1. These findings indicate that the analysis of potential substrates for ISG15 conjugation must be performed with great care to distinguish between the two types of modification since many assays such as immunoprecipitation or metal-chelate affinity purification are performed with little or no

  6. Formation of S-(carboxymethyl)-cysteine in rat liver mitochondrial proteins: effects of caloric and methionine restriction.

    Science.gov (United States)

    Naudí, Alba; Jové, Mariona; Cacabelos, Daniel; Ayala, Victoria; Cabre, Rosanna; Caro, Pilar; Gomez, José; Portero-Otín, Manuel; Barja, Gustavo; Pamplona, Reinald

    2013-02-01

    Maillard reaction contributes to the chemical modification and cross-linking of proteins. This process plays a significant role in the aging process and determination of animal longevity. Oxidative conditions promote the Maillard reaction. Mitochondria are the primary site of oxidants due to the reactive molecular species production. Mitochondrial proteome cysteine residues are targets of oxidative attack due to their specific chemistry and localization. Their chemical, non-enzymatic modification leads to dysfunctional proteins, which entail cellular senescence and organismal aging. Previous studies have consistently shown that caloric and methionine restrictions, nutritional interventions that increase longevity, decrease the rate of mitochondrial oxidant production and the physiological steady-state levels of markers of oxidative damage to macromolecules. In this scenario, we have detected S-(carboxymethyl)-cysteine (CMC) as a new irreversible chemical modification in mitochondrial proteins. CMC content in mitochondrial proteins significantly correlated with that of the lysine-derived analog N (ε)-(carboxymethyl)-lysine. The concentration of CMC is, however, one order of magnitude lower compared with CML likely due in part to the lower content of cysteine with respect to lysine of the mitochondrial proteome. CMC concentrations decreases in liver mitochondrial proteins of rats subjected to 8.5 and 25 % caloric restriction, as well as in 40 and 80 % methionine restriction. This is associated with a concomitant and significant increase in the protein content of sulfhydryl groups. Data presented here evidence that CMC, a marker of Cys-AGE formation, could be candidate as a biomarker of mitochondrial damage during aging.

  7. Secreted Protein Acidic and Rich in Cysteine (SPARC) in Human Skeletal Muscle

    Science.gov (United States)

    Jørgensen, Louise H.; Petersson, Stine J.; Sellathurai, Jeeva; Andersen, Ditte C.; Thayssen, Susanne; Sant, Dorte J.; Jensen, Charlotte H.; Schrøder, Henrik D.

    2009-01-01

    Secreted protein acidic and rich in cysteine (SPARC)/osteonectin is expressed in different tissues during remodeling and repair, suggesting a function in regeneration. Several gene expression studies indicated that SPARC was expressed in response to muscle damage. Studies on myoblasts further indicated a function of SPARC in skeletal muscle. We therefore found it of interest to study SPARC expression in human skeletal muscle during development and in biopsies from Duchenne and Becker muscular dystrophy and congenital muscular dystrophy, congenital myopathy, inclusion body myositis, and polymyositis patients to analyze SPARC expression in a selected range of inherited and idiopathic muscle wasting diseases. SPARC-positive cells were observed both in fetal and neonatal muscle, and in addition, fetal myofibers were observed to express SPARC at the age of 15–16 weeks. SPARC protein was detected in the majority of analyzed muscle biopsies (23 of 24), mainly in mononuclear cells of which few were pax7 positive. Myotubes and regenerating myofibers also expressed SPARC. The expression-degree seemed to reflect the severity of the lesion. In accordance with these in vivo findings, primary human-derived satellite cells were found to express SPARC both during proliferation and differentiation in vitro. In conclusion, this study shows SPARC expression both during muscle development and in regenerating muscle. The expression is detected both in satellite cells/myoblasts and in myotubes and muscle fibers, indicating a role for SPARC in the skeletal muscle compartment. (J Histochem Cytochem 57:29–39, 2009) PMID:18796407

  8. Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein.

    Directory of Open Access Journals (Sweden)

    Berlin Londono-Renteria

    2015-10-01

    Full Text Available Dengue virus (DENV is a mosquito-borne flavivirus that causes serious human disease and mortality worldwide. There is no specific antiviral therapy or vaccine for DENV infection. Alterations in gene expression during DENV infection of the mosquito and the impact of these changes on virus infection are important events to investigate in hopes of creating new treatments and vaccines. We previously identified 203 genes that were ≥5-fold differentially upregulated during flavivirus infection of the mosquito. Here, we examined the impact of silencing 100 of the most highly upregulated gene targets on DENV infection in its mosquito vector. We identified 20 genes that reduced DENV infection by at least 60% when silenced. We focused on one gene, a putative cysteine rich venom protein (SeqID AAEL000379; CRVP379, whose silencing significantly reduced DENV infection in Aedes aegypti cells. Here, we examine the requirement for CRVP379 during DENV infection of the mosquito and investigate the mechanisms surrounding this phenomenon. We also show that blocking CRVP379 protein with either RNAi or specific antisera inhibits DENV infection in Aedes aegypti. This work identifies a novel mosquito gene target for controlling DENV infection in mosquitoes that may also be used to develop broad preventative and therapeutic measures for multiple flaviviruses.

  9. A bacterial cysteine protease effector protein interferes with photosynthesis to suppress plant innate immune responses.

    Science.gov (United States)

    Rodríguez-Herva, José J; González-Melendi, Pablo; Cuartas-Lanza, Raquel; Antúnez-Lamas, María; Río-Alvarez, Isabel; Li, Ziduo; López-Torrejón, Gema; Díaz, Isabel; Del Pozo, Juan C; Chakravarthy, Suma; Collmer, Alan; Rodríguez-Palenzuela, Pablo; López-Solanilla, Emilia

    2012-05-01

    The bacterial pathogen Pseudomonas syringae pv tomato DC3000 suppresses plant innate immunity with effector proteins injected by a type III secretion system (T3SS). The cysteine protease effector HopN1, which reduces the ability of DC3000 to elicit programmed cell death in non-host tobacco, was found to also suppress the production of defence-associated reactive oxygen species (ROS) and callose when delivered by Pseudomonas fluorescens heterologously expressing a P. syringae T3SS. Purified His(6) -tagged HopN1 was used to identify tomato PsbQ, a member of the oxygen evolving complex of photosystem II (PSII), as an interacting protein. HopN1 localized to chloroplasts and both degraded PsbQ and inhibited PSII activity in chloroplast preparations, whereas a HopN1(D299A) non-catalytic mutant lost these abilities. Gene silencing of NtPsbQ in tobacco compromised ROS production and programmed cell death by DC3000. Our data reveal PsbQ as a contributor to plant immunity responses and a target for pathogen suppression. © 2012 Blackwell Publishing Ltd.

  10. In vivo inhibition of cysteine proteases provides evidence for the involvement of 'senescence-associated vacuoles' in chloroplast protein degradation during dark-induced senescence of tobacco leaves.

    Science.gov (United States)

    Carrión, Cristian A; Costa, María Lorenza; Martínez, Dana E; Mohr, Christina; Humbeck, Klaus; Guiamet, Juan J

    2013-11-01

    Breakdown of leaf proteins, particularly chloroplast proteins, is a massive process in senescing leaves. In spite of its importance in internal N recycling, the mechanism(s) and the enzymes involved are largely unknown. Senescence-associated vacuoles (SAVs) are small, acidic vacuoles with high cysteine peptidase activity. Chloroplast-targeted proteins re-localize to SAVs during senescence, suggesting that SAVs might be involved in chloroplast protein degradation. SAVs were undetectable in mature, non-senescent tobacco leaves. Their abundance, visualized either with the acidotropic marker Lysotracker Red or by green fluorescent protein (GFP) fluorescence in a line expressing the senescence-associated cysteine protease SAG12 fused to GFP, increased during senescence induction in darkness, and peaked after 2-4 d, when chloroplast dismantling was most intense. Increased abundance of SAVs correlated with higher levels of SAG12 mRNA. Activity labelling with a biotinylated derivative of the cysteine protease inhibitor E-64 was used to detect active cysteine proteases. The two apparently most abundant cysteine proteases of senescing leaves, of 40kDa and 33kDa were detected in isolated SAVs. Rubisco degradation in isolated SAVs was completely blocked by E-64. Treatment of leaf disks with E-64 in vivo substantially reduced degradation of Rubisco and leaf proteins. Overall, these results indicate that SAVs contain most of the cysteine protease activity of senescing cells, and that SAV cysteine proteases are at least partly responsible for the degradation of stromal proteins of the chloroplast.

  11. Excessive L-cysteine induces vacuole-like cell death by activating endoplasmic reticulum stress and mitogen-activated protein kinase signaling in intestinal porcine epithelial cells.

    Science.gov (United States)

    Ji, Yun; Wu, Zhenlong; Dai, Zhaolai; Sun, Kaiji; Zhang, Qing; Wu, Guoyao

    2016-01-01

    High intake of dietary cysteine is extremely toxic to animals and the underlying mechanism remains largely unknown. This study was conducted to test the hypothesis that excessive L-cysteine induces cell death by activating endoplasmic reticulum (ER) stress and mitogen-activated protein kinase (MAPK) signaling in intestinal porcine epithelial cells. Jejunal enterocytes were cultured in the presence of 0-10 mmol/L L-cysteine. Cell viability, morphologic alterations, mRNA levels for genes involved in ER stress, protein abundances for glucose-regulated protein 78, C/EBP homologous protein (CHOP), alpha subunit of eukaryotic initiation factor-2 (eIF2α), extracellular signal-regulated kinase (ERK1/2), p38 MAPK, and c-Jun N-terminal protein kinase (JNK1/2) were determined. The results showed that L-cysteine (5-10 mmol/L) reduced cell viability (P L-cysteine were not affected by the autophagy inhibitor 3-methyladenine. The protein abundances for CHOP, phosphorylated (p)-eIF2α, p-JNK1/2, p-p38 MAPK, and the spliced form of XBP-1 mRNA were enhanced (P L-cysteine induces vacuole-like cell death via the activation of ER stress and MAPK signaling in small intestinal epithelial cells. These signaling pathways may be potential targets for developing effective strategies to prevent the toxicity of dietary cysteine.

  12. A fluorescent-based HPLC assay for quantification of cysteine and cysteamine adducts in Escherichia coli-derived proteins.

    Science.gov (United States)

    Soriano, Brian D; Tam, Lei-Ting T; Lu, Hsieng S; Valladares, Violeta G

    2012-01-01

    Recombinant proteins expressed in Escherichia coli are often produced as unfolded, inactive forms accumulated in inclusion bodies. Redox-coupled thiols are typically employed in the refolding process in order to catalyze the formation of correct disulfide bonds at maximal folding efficiency. These thiols and the recombinant proteins can form mixed disulfide bonds to generate thiol-protein adducts. In this work, we apply a fluorescent-based assay for the quantification of cysteine and cysteamine adducts as observed in E. coli-derived proteins. The thiols are released by reduction of the adducted protein, collected and labeled with a fluorescent reagent, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. The derivatized thiols are separated by reversed-phase HPLC and can be accurately quantified after method optimization. The estimated thiol content represents total amount of adducted forms present in the analyzed samples. The limit of quantification (LOQ) was established; specifically, the lowest amount of quantifiable cysteine adduction is 30 picograms and the lowest amount of quantifiable cysteamine adduction is 60 picograms. The assay is useful for quantification of adducts in final purified products as well as in-process samples from various purification steps. The assay indicates that the purification process accomplishes a decrease in cysteine adduction from 0.19 nmol adduct/nmol protein to 0.03 nmol adduct/nmol protein as well as a decrease in cysteamine adduction from 0.24 nmol adduct/nmol protein to 0.14 nmol adduct/nmol protein. Copyright © 2011. Published by Elsevier B.V.

  13. Click-PEGylation - A mobility shift approach to assess the redox state of cysteines in candidate proteins.

    Science.gov (United States)

    van Leeuwen, Lucie A G; Hinchy, Elizabeth C; Murphy, Michael P; Robb, Ellen L; Cochemé, Helena M

    2017-07-01

    The redox state of cysteine thiols is critical for protein function. Whereas cysteines play an important role in the maintenance of protein structure through the formation of internal disulfides, their nucleophilic thiol groups can become oxidatively modified in response to diverse redox challenges and thereby function in signalling and antioxidant defences. These oxidative modifications occur in response to a range of agents and stimuli, and can lead to the existence of multiple redox states for a given protein. To assess the role(s) of a protein in redox signalling and antioxidant defence, it is thus vital to be able to assess which of the multiple thiol redox states are present and to investigate how these alter under different conditions. While this can be done by a range of mass spectrometric-based methods, these are time-consuming, costly, and best suited to study abundant proteins or to perform an unbiased proteomic screen. One approach that can facilitate a targeted assessment of candidate proteins, as well as proteins that are low in abundance or proteomically challenging, is by electrophoretic mobility shift assays. Redox-modified cysteine residues are selectively tagged with a large group, such as a polyethylene glycol (PEG) polymer, and then the proteins are separated by electrophoresis followed by immunoblotting, which allows the inference of redox changes based on band shifts. However, the applicability of this method has been impaired by the difficulty of cleanly modifying protein thiols by large PEG reagents. To establish a more robust method for redox-selective PEGylation, we have utilised a Click chemistry approach, where free thiol groups are first labelled with a reagent modified to contain an alkyne moiety, which is subsequently Click-reacted with a PEG molecule containing a complementary azide function. This strategy can be adapted to study reversibly reduced or oxidised cysteines. Separation of the thiol labelling step from the PEG

  14. Mechanism of Sirt1 NAD+-dependent Protein Deacetylase Inhibition by Cysteine S-Nitrosation.

    Science.gov (United States)

    Kalous, Kelsey S; Wynia-Smith, Sarah L; Olp, Michael D; Smith, Brian C

    2016-12-02

    The sirtuin family of proteins catalyze the NAD + -dependent deacylation of acyl-lysine residues. Humans encode seven sirtuins (Sirt1-7), and recent studies have suggested that post-translational modification of Sirt1 by cysteine S-nitrosation correlates with increased acetylation of Sirt1 deacetylase substrates. However, the mechanism of Sirt1 inhibition by S-nitrosation was unknown. Here, we show that Sirt1 is transnitrosated and inhibited by the physiologically relevant nitrosothiol S-nitrosoglutathione. Steady-state kinetic analyses and binding assays were consistent with Sirt1 S-nitrosation inhibiting binding of both the NAD + and acetyl-lysine substrates. Sirt1 S-nitrosation correlated with Zn 2+ release from the conserved sirtuin Zn 2+ -tetrathiolate and a loss of α-helical structure without overall thermal destabilization of the enzyme. Molecular dynamics simulations suggested that Zn 2+ loss due to Sirt1 S-nitrosation results in repositioning of the tetrathiolate subdomain away from the rest of the catalytic domain, thereby disrupting the NAD + and acetyl-lysine-binding sites. Sirt1 S-nitrosation was reversed upon exposure to the thiol-based reducing agents, including physiologically relevant concentrations of the cellular reducing agent glutathione. Reversal of S-nitrosation resulted in full restoration of Sirt1 activity only in the presence of Zn 2+ , consistent with S-nitrosation of the Zn 2+ -tetrathiolate as the primary source of Sirt1 inhibition upon S-nitrosoglutathione treatment. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Giardia duodenalis Surface Cysteine Proteases Induce Cleavage of the Intestinal Epithelial Cytoskeletal Protein Villin via Myosin Light Chain Kinase.

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    Amol Bhargava

    Full Text Available Giardia duodenalis infections are among the most common causes of waterborne diarrhoeal disease worldwide. At the height of infection, G. duodenalis trophozoites induce multiple pathophysiological processes within intestinal epithelial cells that contribute to the development of diarrhoeal disease. To date, our understanding of pathophysiological processes in giardiasis remains incompletely understood. The present study reveals a previously unappreciated role for G. duodenalis cathepsin cysteine proteases in intestinal epithelial pathophysiological processes that occur during giardiasis. Experiments first established that Giardia trophozoites indeed produce cathepsin B and L in strain-dependent fashion. Co-incubation of G. duodenalis with human enterocytes enhanced cathepsin production by Assemblage A (NF and S2 isolates trophozoites, but not when epithelial cells were exposed to Assemblage B (GSM isolate trophozoites. Direct contact between G. duodenalis parasites and human intestinal epithelial monolayers resulted in the degradation and redistribution of the intestinal epithelial cytoskeletal protein villin; these effects were abolished when parasite cathepsin cysteine proteases were inhibited. Interestingly, inhibition of parasite proteases did not prevent degradation of the intestinal tight junction-associated protein zonula occludens 1 (ZO-1, suggesting that G. duodenalis induces multiple pathophysiological processes within intestinal epithelial cells. Finally, this study demonstrates that G. duodenalis-mediated disruption of villin is, at least, in part dependent on activation of myosin light chain kinase (MLCK. Taken together, this study indicates a novel role for parasite cathepsin cysteine proteases in the pathophysiology of G. duodenalis infections.

  16. Screening and identification of host proteins interacting with Theileria annulata cysteine proteinase (TaCP by yeast-two-hybrid system

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    Shuaiyang Zhao

    2017-10-01

    Full Text Available Abstract Background Theileria annulata can infect monocytes/macrophages and B lymphocytes and causes severe lymphoproliferative disease in ruminants. Meanwhile, infection by T. annulata leads to the permanent proliferation of cell population through regulating signaling pathways of host cells. Cysteine proteinases (CPs are one kind of protein hydrolase and usually play critical roles in parasite virulence, host invasion, nutrition and host immune response. However, the biological function of T. annulata CP (TaCP is still unclear. In this study, a yeast-two-hybrid assay was performed to screen host proteins interacting with TaCP, to provide information to help our understanding of the molecular mechanisms between T. annulata and host cells. Methods The cDNA from purified bovine B cells was inserted into pGADT7-SfiI vector (pGADT7-SfiI-BcDNA, Prey plasmid for constructing the yeast two-hybrid cDNA library. TaCP was cloned into the pGBKT7 vector (pGBKT7-TaCP and was considered as bait plasmid after evaluating the expression, auto-activation and toxicity tests in the yeast strain Y2HGold. The yeast two-hybrid screening was carried out via co-transforming bait and prey plasmids into yeast strain Y2HGold. Sequences of positive preys were analyzed using BLAST, Gene Ontology, UniProt and STRING. Results Two host proteins, CRBN (Bos taurus cereblon transcript variant X2 and Ppp4C (Bos indicus protein phosphatase 4 catalytic subunit were identified to interact with TaCP. The results of functional analysis showed that the two proteins were involved in many cellular processes, such as ubiquitylation regulation, microtubule organization, DNA repair, cell apoptosis and maturation of spliceosomal snRNPs. Conclusions This study is the first to screen the host proteins of bovine B cells interacting with TaCP, and 2 proteins, CRBN and Ppp4C, were identified using yeast two-hybrid technique. The results of functional analysis suggest that the two proteins are

  17. Irreversible Cysteine-Selective Protein Labeling Employing Modular Electrophilic Tetrafluoroethylation Reagents

    Czech Academy of Sciences Publication Activity Database

    Václavík, Jiří; Zschoche, R.; Klimánková, Iveta; Matoušek, V.; Beier, Petr; Hilvert, D.; Togni, A.

    2017-01-01

    Roč. 23, č. 27 (2017), s. 6490-6494 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GA17-00598S Institutional support: RVO:61388963 Keywords : bioconjugation * cysteine * enzymes * fluorine * fluoroalkylation * hypervalent iodine Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 5.317, year: 2016

  18. Differential processing of Arabidopsis ubiquitin-like Atg8 autophagy proteins by Atg4 cysteine proteases

    Science.gov (United States)

    Woo, Jongchan; Park, Eunsook; Dinesh-Kumar, S. P.

    2014-01-01

    Autophagy is a highly conserved biological process during which double membrane bound autophagosomes carry intracellular cargo material to the vacuole or lysosome for degradation and/or recycling. Autophagosome biogenesis requires Autophagy 4 (Atg4) cysteine protease-mediated processing of ubiquitin-like Atg8 proteins. Unlike single Atg4 and Atg8 genes in yeast, the Arabidopsis genome contains two Atg4 (AtAtg4a and AtAtg4b) and nine Atg8 (AtAtg8a–AtAtg8i) genes. However, we know very little about specificity of different AtAtg4s for processing of different AtAtg8s. Here, we describe a unique bioluminescence resonance energy transfer-based AtAtg8 synthetic substrate to assess AtAtg4 activity in vitro and in vivo. In addition, we developed a unique native gel assay of superhRLUC catalytic activity assay to monitor cleavage of AtAtg8s in vitro. Our results indicate that AtAtg4a is the predominant protease and that it processes AtAtg8a, AtAtg8c, AtAtg8d, and AtAtg8i better than AtAtg4b in vitro. In addition, kinetic analyses indicate that although both AtAtg4s have similar substrate affinity, AtAtg4a is more active than AtAtg4b in vitro. Activity of AtAtg4s is reversibly inhibited in vitro by reactive oxygen species such as H2O2. Our in vivo bioluminescence resonance energy transfer analyses in Arabidopsis transgenic plants indicate that the AtAtg8 synthetic substrate is efficiently processed and this is AtAtg4 dependent. These results indicate that the synthetic AtAtg8 substrate is used efficiently in the biogenesis of autophagosomes in vivo. Transgenic Arabidopsis plants expressing the AtAtg8 synthetic substrate will be a valuable tool to dissect autophagy processes and the role of autophagy during different biological processes in plants. PMID:24379391

  19. Advanced purification strategy for CueR, a cysteine containing copper(I) and DNA binding protein

    DEFF Research Database (Denmark)

    Balogh, Ria K.; Gyurcsik, Béla; Hunyadi-Gulyás, Éva

    2016-01-01

    . A detailed understanding of their function may be exploited in potential health, environmental and analytical applications. Members of the MerR protein family sense a broad range of mostly late transition and heavy metal ions through their cysteine thiolates. The air sensitivity of latter groups makes...... the expression and purification of such proteins challenging. Here we describe a method for the purification of the copper-regulatory CueR protein under optimized conditions. In order to avoid protein precipitation and/or eventual aggregation and to get rid of the co-purifying Escherichia coli elongation factor...... any affinity tag. Structure and functionality tests performed with mass spectrometry, circular dichroism spectroscopy and electrophoretic gel mobility shift assays approved the success of the purification procedure....

  20. 5,5'-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2

    International Nuclear Information System (INIS)

    Mi Wei; Li Lanfen; Su Xiaodong

    2008-01-01

    Structural studies of human chloride intracellular channel protein 2 (CLIC2) had been hampered by the problem of generating suitable crystals primarily due to the protein containing exposed cysteines. Several chemical reagents were used to react with the cysteines on CLIC2 in order to modify the redox state of the protein. We have obtained high quality crystals that diffracted to better than 2.5 A at a home X-ray source by treating the protein with 5,5'-dithio-bis(2-nitrobenzoic acid) (DTNB). After solving the crystal structure of CLIC2, we found that the DTNB had reacted with the Cys 114 , and made CLIC2 in a homogenous oxidized state. This study demonstrated that the DTNB modification drastically improved the crystallization of CLIC2, and it implied that this method may be useful for other proteins containing exposed cysteines in general

  1. Cysteine-rich buccal gland protein suppressed the proliferation, migration and invasion of hela cells through akt pathway.

    Science.gov (United States)

    Han, Jianmei; Liu, Yu; Jiang, Qi; Xiao, Rong

    2017-11-01

    Cysteine-rich buccal gland protein (CRBGP) as a member of cysteine-rich secretory proteins (CRISPs) superfamily was isolated from the buccal glands of Lampetra japonica, the blood suckers in the marine. Previous studies showed CRBGP could suppress angiogenesis probably due to its ion channel blocking activity. Whether CRBGP could also affect the activity of tumor cells has not been reported yet. In this study, CRBGP suppressed the proliferation of Hela cells with an IC 50 of 6.7 μM by inducing apoptosis. Both microscopic observation and Western blot indicated that CRBGP was able to induce the nuclei shrinking, downregulate the protein level of BCL2 and caspase 3 as well as upregulate the level of BAX in Hela cells, suggested that CRBGP might induce apoptosis of Hela cells in a mitochondrial-dependent pathway. Furthermore, CRBGP could disturb F-actin organization, which would finally cause the Hela cells to lose their shape and to lessen their abilities on adhesion, migration and invasion. Finally, CRBGP was shown to reduce the phosphorylation level of Akt, which indicated that CRBGP might inhibit the proliferation and metastasis of Hela cells through Akt pathway. CRBGP, as a voltage-gated sodium channel blocker, also possesses the anti-tumor abilities which provided information on the effects and action manner of the other CRISPs. © 2017 IUBMB Life, 69(11):856-866, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

  2. Effect of dietary nutrients on ileal endogenous losses of threonine, cysteine, methionine, lysine, leucine and protein in broiler chicks.

    Science.gov (United States)

    Cerrate, S; Vignale, S K; Ekmay, R; England, J; Coon, C

    2018-04-01

    An isotope dose technique was utilized (i) to determine endogenous amino acid (AA) and protein losses and (ii) to propose adjusted values for AA requirements. The endogenous flow rate was calculated from the pool of enrichment in plasma AA, assuming similitude to enrichment of endogenous AA. In experiment 1, chicks were orally administered D4-lysine at 2% of estimated lysine intake from 16 to 24 days to find the isotopic steady state of the atom percent excess (APE) of lysine for plasma and jejunal and ileal digesta. The APE of D4-lysine in plasma, jejunal digesta and ileal digesta reached the isotopic steady state at 5.5, 3.4 and 2.0 days, respectively, by using the broken-line model. It was assumed that the isotopic steady state at 5 days identified for D4-lysine is also representative for the 15N-labeled AA. In experiment 2, chicks were fed diets from 1 to 21 days with increasing levels of fat (6%, 8%, 12%, 13% extract ether), protein (26%, 28.5%, 31% CP) or fiber (14%, 16%, 18% NDF) by adding poultry fat, soybean meal, blended animal protein or barley. Chicks were orally administered 15N-threonine, 15N-cysteine, 15N-methionine, 15N-lysine and 15N-leucine at 2% of estimated daily intake for 5 days from 17 to 21 days of age. Dietary nutrients influenced endogenous losses (EL), where dietary fat stimulated EL of lysine (P=0.06), leucine and protein (P=0.07); dietary protein enhanced EL of leucine and protein; and finally the dietary fiber increased EL of leucine. Dietary nutrients also affected apparent ileal digestibility (AID). Dietary fat increased AID of cysteine but decreased AID of lysine. Dietary protein reduced AID of protein, threonine, lysine and leucine, and similarly dietary fiber decreased AID of protein, threonine, methionine, lysine and leucine. In contrast, dietary fat or protein did not affect real ileal digestibility (RID) of protein and AA except threonine and leucine. The dietary fiber reduced the RID of protein, threonine and leucine. This

  3. Lack of the matricellular protein SPARC (secreted protein, acidic and rich in cysteine attenuates liver fibrogenesis in mice.

    Directory of Open Access Journals (Sweden)

    Catalina Atorrasagasti

    Full Text Available INTRODUCTION: Secreted Protein, Acidic and Rich in Cysteine (SPARC is a matricellular protein involved in many biological processes and found over-expressed in cirrhotic livers. By mean of a genetic approach we herein provide evidence from different in vivo liver disease models suggesting a profibrogenic role for SPARC. METHODS: Two in vivo models of liver fibrosis, based on TAA administration and bile duct ligation, were developed on SPARC wild-type (SPARC(+/+ and knock-out (SPARC(-/- mice. Hepatic SPARC expression was analyzed by qPCR. Fibrosis was assessed by Sirius Red staining, and the maturation state of collagen fibers was analyzed using polarized light. Necroinflammatory activity was evaluated by applying the Knodell score and liver inflammatory infiltration was characterized by immunohistochemistry. Hepatic stellate cell activation was assessed by α-SMA immunohistochemistry. In addition, pro-fibrogenic genes and inflammatory cytokines were measured by qPCR and/or ELISA. Liver gene expression profile was analyzed in SPARC(-/- and SPARC(+/+ mice using Affymetrix Mouse Gene ST 1.0 array. RESULTS: SPARC expression was found induced in fibrotic livers of mouse and human. SPARC(-/- mice showed a reduction in the degree of inflammation, mainly CD4+ cells, and fibrosis. Consistently, collagen deposits and mRNA expression levels were decreased in SPARC(-/- mice when compared to SPARC(+/+ mice; in addition, MMP-2 expression was increased in SPARC(-/- mice. A reduction in the number of activated myofibroblasts was observed. Moreover, TGF-β1 expression levels were down-regulated in the liver as well as in the serum of TAA-treated knock-out animals. Ingenuity Pathway Analysis (IPA analysis suggested several gene networks which might involve protective mechanisms of SPARC deficiency against liver fibrogenesis and a better established machinery to repair DNA and detoxify from external chemical stimuli. CONCLUSIONS: Overall our data suggest that

  4. Cysteine Specific Targeting of the Functionally Distinct Peroxiredoxin and Glutaredoxin Proteins by the Investigational Disulfide BNP7787

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    Aulma R. Parker

    2015-03-01

    Full Text Available Glutaredoxin (Grx, peroxiredoxin (Prx, and thioredoxin (Trx are redoxin family proteins that catalyze different types of chemical reactions that impact cell growth and survival through functionally distinct intracellular pathways. Much research is focused on understanding the roles of these redoxin proteins in the development and/or progression of human diseases. Grx and Prx are overexpressed in human cancers, including human lung cancers. BNP7787 is a novel investigational agent that has been evaluated in previous clinical studies, including non-small cell lung cancer (NSCLC studies. Herein, data from activity assays, mass spectrometry analyses, and X-ray crystallographic studies indicate that BNP7787 forms mixed disulfides with select cysteine residues on Grx and Prx and modulates their function. Studies of interactions between BNP7787 and Trx have been conducted and reported separately. Despite the fact that Trx, Grx, and Prx are functionally distinct proteins that impact oxidative stress, cell proliferation and disease processes through different intracellular pathways, BNP7787 can modify each protein and appears to modulate function through mechanisms that are unique to each target protein. Tumor cells are often genomically heterogeneous containing subpopulations of cancer cells that often express different tumor-promoting proteins or that have multiple dysregulated signaling pathways modulating cell proliferation and drug resistance. A multi-targeted agent that simultaneously modulates activity of proteins important in mediating cell proliferation by functionally distinct intracellular pathways could have many potentially useful therapeutic applications.

  5. Introgression of leginsulin, a cysteine-rich protein, and high-protein trait from an Asian soybean plant introduction genotype into a North American experimental soybean line.

    Science.gov (United States)

    Krishnan, Hari B; Kim, Won-Seok; Oehrle, Nathan W; Alaswad, Alaa A; Baxter, Ivan; Wiebold, William J; Nelson, Randall L

    2015-03-25

    Soybean is an important protein source for both humans and animals. However, soybean proteins are relatively poor in the sulfur-containing amino acids, cysteine and methionine. Improving the content of endogenous proteins rich in sulfur-containing amino acids could enhance the nutritive value of soybean meal. Leginsulin, a cysteine-rich peptide, predominantly accumulates in Asian soybean accessions but not in most North American cultivars. By screening diverse soybean accessions from the USDA Soybean Germplasm Collection, we were able to identify one plant introduction, PI 427138, as a high-protein line with relatively high amounts of both elemental sulfur and leginsulin. We introgressed these desirable traits from PI 427138 into an experimental line with the aim of improving the overall protein content and quality of seed proteins. Biochemical characterization of inbred progenies from the cross of LD00-3309 with PI 427138 grown at six locations revealed stable ingression of high protein, high elemental sulfur, and high leginsulin accumulation. Comparison of soybean seed proteins resolved by high-resolution 2-D gel electrophoresis in combination with Delta2D image analysis software revealed preferential accumulation of a few glycinin subunits contributed to the increased protein content in the introgressed lines. Amino acid analysis revealed that even though the leginsulin introgressed lines had higher protein, leginsulin, and elemental sulfur, the overall concentration of sulfur-containing amino acids was not significantly altered when compared with the parental lines. The experimental soybean lines developed during this study (Leg-3, Leg-7, and Leg-8) lack A5, A4, and B3 glycinin subunits and could be utilized in breeding programs to develop high-quality tofu cultivars.

  6. Identification, Characterization and Down-Regulation of Cysteine Protease Genes in Tobacco for Use in Recombinant Protein Production.

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    Kishor Duwadi

    Full Text Available Plants are an attractive host system for pharmaceutical protein production. Many therapeutic proteins have been produced and scaled up in plants at a low cost compared to the conventional microbial and animal-based systems. The main technical challenge during this process is to produce sufficient levels of recombinant proteins in plants. Low yield is generally caused by proteolytic degradation during expression and downstream processing of recombinant proteins. The yield of human therapeutic interleukin (IL-10 produced in transgenic tobacco leaves was found to be below the critical level, and may be due to degradation by tobacco proteases. Here, we identified a total of 60 putative cysteine protease genes (CysP in tobacco. Based on their predicted expression in leaf tissue, 10 candidate CysPs (CysP1-CysP10 were selected for further characterization. The effect of CysP gene silencing on IL-10 accumulation was examined in tobacco. It was found that the recombinant protein yield in tobacco could be increased by silencing CysP6. Transient expression of CysP6 silencing construct also showed an increase in IL-10 accumulation in comparison to the control. Moreover, CysP6 localizes to the endoplasmic reticulum (ER, suggesting that ER may be the site of IL-10 degradation. Overall results suggest that CysP6 is important in determining the yield of recombinant IL-10 in tobacco leaves.

  7. MicroRNA-27a-mediated repression of cysteine-rich secretory protein 2 translation in asthenoteratozoospermic patients

    Directory of Open Access Journals (Sweden)

    Jun-Hao Zhou

    2017-01-01

    Full Text Available Cysteine-rich secretory protein 2 (CRISP2 is an important protein in spermatozoa that plays roles in modulating sperm flagellar motility, the acrosome reaction, and gamete fusion. Spermatozoa lacking CRISP2 exhibit low sperm motility and abnormal morphology. However, the molecular mechanisms underlying the reduction of CRISP2 in asthenoteratozoospermia (ATZ remain unknown. In this study, low expression of CRISP2 protein rather than its mRNA was observed in the ejaculated spermatozoa from ATZ patients as compared with normozoospermic males. Subsequently, bioinformatic prediction, luciferase reporter assays, and microRNA-27a (miR-27a transfection experiments revealed that miR-27a specifically targets CRISP2 by binding to its 3′ untranslated region (3′-UTR, suppressing CRISP2 expression posttranscriptionally. Further evidence was provided by the clinical observation of high miR-27a expression in ejaculated spermatozoa from ATZ patients and a negative correlation between miR-27a expression and CRISP2 protein expression. Finally, a retrospective follow-up study supported that both high miR-27a expression and low CRISP2 protein expression were associated with low progressive sperm motility, abnormal morphology, and infertility. This study demonstrates a novel mechanism responsible for reduced CRISP2 expression in ATZ, which may offer a potential therapeutic target for treating male infertility, or for male contraception.

  8. Antioxidant activity of protein hydrolysates from raw and heat-treated yellow string beans (Phaseolus vulgaris L.).

    Science.gov (United States)

    Karaś, Monika; Jakubczyk, Anna; Szymanowska, Urszula; Materska, Małgorzata; Zielińska, Ewelina

    2014-01-01

    Nowadays, legume plants have been considered not only a source of valuable proteins necessary for the proper functioning and growth of the body but also a source of bioactive compounds such as bioactive peptides, that may be beneficial to human health and protect against negative change in food. The aim of this study was to investigate the effect of heat treatment on the release of antioxidant peptides obtained by hydrolysis of the yellow string beans protein. The antioxidant properties of the hydrolysates were evaluated through free radical scavenging activities (DPPH and ABTS) and inhibition of iron activities (chelation of Fe2+). The results show that the heat treatment had influence on both increased peptides content and antioxidant activity after pepsin hydrolysis of string bean protein. The peptides content after protein hydrolysis derived from raw and heat treated beans were noted 2.10 and 2.50 mg·ml-1, respectively. The hydrolysates obtained from raw (PHR) and heat treated (PHT) beans showed better antioxidant properties than protein isolates (PIR and PIT). Moreover, the hydrolysates obtained from heat treated beans showed the higher ability to scavenge DPPH• (46.12%) and ABTS+• (92.32%) than obtained from raw beans (38.02% and 88.24%, correspondingly). The IC50 value for Fe2+ chelating ability for pepsin hydrolysates obtained from raw and heat treatment beans were noted 0.81 and 0.19 mg·ml-1, respectively. In conclusion, the results of this study showed that the heat treatment string beans caused increase in the antioxidant activities of peptide-rich hydrolysates.

  9. Selective Incorporation of Nitrile-Based Infrared Probes into Proteins via Cysteine Alkylation

    Science.gov (United States)

    Jo, Hyunil; Culik, Robert M.; Korendovych, Ivan V.; DeGrado, William F.; Gai, Feng

    2010-01-01

    The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction. PMID:21077670

  10. Selective Incorporation of Nitrile-Based Infrared Probes into Proteins via Cysteine Alkylation

    OpenAIRE

    Jo, Hyunil; Culik, Robert M.; Korendovych, Ivan V.; DeGrado, William F.; Gai, Feng

    2010-01-01

    The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction.

  11. The s48/45 six-cysteine proteins: mediators of interaction throughout the Plasmodium life cycle.

    Science.gov (United States)

    Arredondo, Silvia A; Kappe, Stefan H I

    2017-06-01

    During their life cycle Plasmodium parasites rely upon an arsenal of proteins that establish key interactions with the host and vector, and between the parasite sexual stages, with the purpose of ensuring infection, reproduction and proliferation. Among these is a group of secreted or membrane-anchored proteins known as the six-cysteine (6-cys) family. This is a small but important family with only 14 members thus far identified, each stage-specifically expressed during the parasite life cycle. 6-cys proteins often localise at the parasite surface or interface with the host and vector, and are conserved in different Plasmodium species. The unifying feature of the family is the s48/45 domain, presumably involved in adhesion and structurally related to Ephrins, the ligands of Eph receptors. The most prominent s48/45 members are currently under functional investigation and are being pursued as vaccine candidates. In this review, we examine what is known about the 6-cys family, their structure and function, and discuss future research directions. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  12. Cysteine residue is not essential for CPM protein thermal-stability assay.

    Science.gov (United States)

    Wang, Zhaoshuai; Ye, Cui; Zhang, Xinyi; Wei, Yinan

    2015-05-01

    A popular thermal-stability assay developed especially for the study of membrane proteins uses a thiol-specific probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). The fluorescence emission of CPM surges when it forms a covalent bond with the side chain of a free Cys, which becomes more readily accessible upon protein thermal denaturation. Interestingly, the melting temperatures of membrane proteins determined using the CPM assay in literature are closely clustered in the temperature range 45-55 °C. A thorough understanding of the mechanism behind the observed signal change is critical for the accurate interpretation of the protein unfolding. Here we used two α-helical membrane proteins, AqpZ and AcrB, as model systems to investigate the nature of the fluorescence surge in the CPM assay. We found that the transition temperatures measured using circular-dichroism (CD) spectroscopy and the CPM assay were significantly different. To eliminate potential artifact that might arise from the presence of detergent, we monitored the unfolding of two soluble proteins. We found that, contrary to current understanding, the presence of a sulfhydryl group was not a prerequisite for the CPM thermal-stability assay. The observed fluorescence increase is probably caused by binding of the fluorophore to hydrophobic patches exposed upon protein unfolding.

  13. Salivary agglutinin, which binds Streptococcus mutans and Helicobacter pylori, is the lung scavenger receptor cysteine-rich protein gp-340.

    Science.gov (United States)

    Prakobphol, A; Xu, F; Hoang, V M; Larsson, T; Bergstrom, J; Johansson, I; Frängsmyr, L; Holmskov, U; Leffler, H; Nilsson, C; Borén, T; Wright, J R; Strömberg, N; Fisher, S J

    2000-12-22

    Salivary agglutinin is a high molecular mass component of human saliva that binds Streptococcus mutans, an oral bacterium implicated in dental caries. To study its protein sequence, we isolated the agglutinin from human parotid saliva. After trypsin digestion, a portion was analyzed by matrix-assisted laser/desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), which gave the molecular mass of 14 unique peptides. The remainder of the digest was subjected to high performance liquid chromatography, and the separated peptides were analyzed by MALDI-TOF/post-source decay; the spectra gave the sequences of five peptides. The molecular mass and peptide sequence information showed that salivary agglutinin peptides were identical to sequences in lung (lavage) gp-340, a member of the scavenger receptor cysteine-rich protein family. Immunoblotting with antibodies that specifically recognized either lung gp-340 or the agglutinin confirmed that the salivary agglutinin was gp-340. Immunoblotting with an antibody specific to the sialyl Le(x) carbohydrate epitope detected expression on the salivary but not the lung glycoprotein, possible evidence of different glycoforms. The salivary agglutinin also interacted with Helicobacter pylori, implicated in gastritis and peptic ulcer disease, Streptococcus agalactiae, implicated in neonatal meningitis, and several oral commensal streptococci. These results identify the salivary agglutinin as gp-340 and suggest it binds bacteria that are important determinants of either the oral ecology or systemic diseases.

  14. Impact of Secreted Protein Acidic and Rich in Cysteine (SPARC) Expression on Prognosis After Surgical Resection for Biliary Carcinoma.

    Science.gov (United States)

    Toyota, Kazuhiro; Murakami, Yoshiaki; Kondo, Naru; Uemura, Kenichiro; Nakagawa, Naoya; Takahashi, Shinya; Sueda, Taijiro

    2017-06-01

    Secreted protein acidic and rich in cysteine (SPARC) is a matricellular protein that influences chemotherapy effectiveness and prognosis. The aim of this study was to investigate whether SPARC expression correlates with the postoperative survival of patients treated with surgical resection for biliary carcinoma. SPARC expression in resected biliary carcinoma specimens was investigated immunohistochemically in 175 patients. The relationship between SPARC expression and prognosis after surgery was evaluated using univariate and multivariate analyses. High SPARC expression in peritumoral stroma was found in 61 (35%) patients. In all patients, stromal SPARC expression was significantly associated with overall survival (OS) (P = 0.006). Multivariate analysis revealed that high stromal SPARC expression was an independent risk factor for poor OS (HR 1.81, P = 0.006). Moreover, high stromal SPARC expression was independently associated with poor prognosis in a subset of 118 patients treated with gemcitabine-based adjuvant chemotherapy (HR 2.04, P = 0.010) but not in the 57 patients who did not receive adjuvant chemotherapy (P = 0.21). Stromal SPARC expression correlated with the prognosis of patients with resectable biliary carcinoma, and its significance was enhanced in patients treated with adjuvant gemcitabine-based chemotherapy.

  15. Crovirin, a snake venom cysteine-rich secretory protein (CRISP with promising activity against Trypanosomes and Leishmania.

    Directory of Open Access Journals (Sweden)

    Camila M Adade

    2014-10-01

    Full Text Available The neglected human diseases caused by trypanosomatids are currently treated with toxic therapy with limited efficacy. In search for novel anti-trypanosomatid agents, we showed previously that the Crotalus viridis viridis (Cvv snake venom was active against infective forms of Trypanosoma cruzi. Here, we describe the purification of crovirin, a cysteine-rich secretory protein (CRISP from Cvv venom with promising activity against trypanosomes and Leishmania.Crude venom extract was loaded onto a reverse phase analytical (C8 column using a high performance liquid chromatographer. A linear gradient of water/acetonitrile with 0.1% trifluoroacetic acid was used. The peak containing the isolated protein (confirmed by SDS-PAGE and mass spectrometry was collected and its protein content was measured. T. cruzi trypomastigotes and amastigotes, L. amazonensis promastigotes and amastigotes and T. brucei rhodesiense procyclic and bloodstream trypomastigotes were challenged with crovirin, whose toxicity was tested against LLC-MK2 cells, peritoneal macrophages and isolated murine extensor digitorum longus muscle. We purified a single protein from Cvv venom corresponding, according to Nano-LC MS/MS sequencing, to a CRISP of 24,893.64 Da, henceforth referred to as crovirin. Human infective trypanosomatid forms, including intracellular amastigotes, were sensitive to crovirin, with low IC50 or LD50 values (1.10-2.38 µg/ml. A considerably higher concentration (20 µg/ml of crovirin was required to elicit only limited toxicity on mammalian cells.This is the first report of CRISP anti-protozoal activity, and suggests that other members of this family might have potential as drugs or drug leads for the development of novel agents against trypanosomatid-borne neglected diseases.

  16. Folding machineries displayed on a cation-exchanger for the concerted refolding of cysteine- or proline-rich proteins

    Directory of Open Access Journals (Sweden)

    Lee Dae-Hee

    2009-03-01

    Full Text Available Abstract Background Escherichia coli has been most widely used for the production of valuable recombinant proteins. However, over-production of heterologous proteins in E. coli frequently leads to their misfolding and aggregation yielding inclusion bodies. Previous attempts to refold the inclusion bodies into bioactive forms usually result in poor recovery and account for the major cost in industrial production of desired proteins from recombinant E. coli. Here, we describe the successful use of the immobilized folding machineries for in vitro refolding with the examples of high yield refolding of a ribonuclease A (RNase A and cyclohexanone monooxygenase (CHMO. Results We have generated refolding-facilitating media immobilized with three folding machineries, mini-chaperone (a monomeric apical domain consisting of residues 191–345 of GroEL and two foldases (DsbA and human peptidyl-prolyl cis-trans isomerase by mimicking oxidative refolding chromatography. For efficient and simple purification and immobilization simultaneously, folding machineries were fused with the positively-charged consecutive 10-arginine tag at their C-terminal. The immobilized folding machineries were fully functional when assayed in a batch mode. When the refolding-facilitating matrices were applied to the refolding of denatured and reduced RNase A and CHMO, both of which contain many cysteine and proline residues, RNase A and CHMO were recovered in 73% and 53% yield of soluble protein with full enzyme activity, respectively. Conclusion The refolding-facilitating media presented here could be a cost-efficient platform and should be applicable to refold a wide range of E. coli inclusion bodies in high yield with biological function.

  17. Secreted protein acidic and rich in cysteine (SPARC is associated with nasopharyngeal carcinoma metastasis and poor prognosis

    Directory of Open Access Journals (Sweden)

    Wang Hai-Yun

    2012-02-01

    Full Text Available Abstract Background The aim of the present study was to analyse the expression of Secreted protein acidic and rich in cysteine (SPARC in nasopharyngeal carcinoma (NPC specimens, and to evaluate its correlation with clinicopathologic features, including survival of patients with NPC Methods NPC tissue microarrays (TMAs were constructed from Sun Yat-sen University Cancer Center (SYSUCC, another three centers on mainland China, Singapore and Hong Kong. Using quantitative RT-PCR and Western-blotting techniques, we detected mRNA and protein expression of SPARC in NPC cell lines and immortalized nasopharyngeal epithelial cells (NPECs induced by Bmi-1 (NPEC2 Bmi-1. The difference of SPARC expression in the cell lines was tested using a t-test method. The relationship between the SPARC expression and clinicopathological data was assessed by chi-square. Survival analysis was estimated using the Kaplan-Meier approach with log-rank test. Univariate and multivariate analyses of clinical variables were performed using Cox proportional hazards regression models. Results The expression levels of SPARC mRNA and protein were markedly higher in NPC cell lines than in NPEC2 Bmi-1. Especially, the expression levels of SPARC mRNA and protein were much lower in the 6-10B than in the 5-8 F (P = 0.002, P = 0.001. SPARC immunostaining revealed cytoplasmic localization in NPC cells and no staining in the stroma and epithelium. In addition, high level of SPARC positively correlated with the status of distant metastasis (P = 0.001 and WHO histological classification (P = 0.023. NPC patients with high SPARC expression also had a significantly poorer prognosis than patients with low SPARC expression (log-rank test, P P P Conclusions SPARC expression is common in NPC patients. Our data shows that elevated SPARC expression is a potential unfavorable prognostic factor for patients with NPC.

  18. String theory

    International Nuclear Information System (INIS)

    Chan Hongmo.

    1987-10-01

    The paper traces the development of the String Theory, and was presented at Professor Sir Rudolf Peierls' 80sup(th) Birthday Symposium. The String theory is discussed with respect to the interaction of strings, the inclusion of both gauge theory and gravitation, inconsistencies in the theory, and the role of space-time. The physical principles underlying string theory are also outlined. (U.K.)

  19. Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Nobuhiro [Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Yamazaki, Yasuo [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Brown, R. Lane [Neurological Science Institute, Oregon Health and Science University, Beaverton, Oregon 97006 (United States); Fujimoto, Zui [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); VALWAY Technology Center, NEC Soft Ltd, Koto-ku, Tokyo 136-8627 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 (Japan); Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

    2008-10-01

    The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.

  20. Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

    International Nuclear Information System (INIS)

    Suzuki, Nobuhiro; Yamazaki, Yasuo; Brown, R. Lane; Fujimoto, Zui; Morita, Takashi; Mizuno, Hiroshi

    2008-01-01

    The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn 2+ -bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn 2+ ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn 2+ binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels

  1. Cysteine mutagenesis improves the production without abrogating antigenicity of a recombinant protein vaccine candidate for human chagas disease.

    Science.gov (United States)

    Seid, Christopher A; Jones, Kathryn M; Pollet, Jeroen; Keegan, Brian; Hudspeth, Elissa; Hammond, Molly; Wei, Junfei; McAtee, C Patrick; Versteeg, Leroy; Gutierrez, Amanda; Liu, Zhuyun; Zhan, Bin; Respress, Jonathan L; Strych, Ulrich; Bottazzi, Maria Elena; Hotez, Peter J

    2017-03-04

    A therapeutic vaccine for human Chagas disease is under development by the Sabin Vaccine Institute Product Development Partnership. The aim of the vaccine is to significantly reduce the parasite burden of Trypanosoma cruzi in humans, either as a standalone product or in combination with conventional chemotherapy. Vaccination of mice with Tc24 formulated with monophosphoryl-lipid A (MPLA) adjuvant results in a Th1 skewed immune response with elevated IgG2a and IFNγ levels and a statistically significant decrease in parasitemia following T. cruzi challenge. Tc24 was therefore selected for scale-up and further evaluation. During scale up and downstream process development, significant protein aggregation was observed due to intermolecular disulfide bond formation. To prevent protein aggregation, cysteine codons were replaced with serine codons which resulted in the production of a non-aggregated and soluble recombinant protein, Tc24-C4. No changes to the secondary structure of the modified molecule were detected by circular dichroism. Immunization of mice with wild-type Tc24 or Tc24-C4, formulated with E6020 (TLR4 agonist analog to MPLA) emulsified in a squalene-oil-in-water emulsion, resulted in IgG2a and antigen specific IFNγ production levels from splenocytes that were not significantly different, indicating that eliminating putative intermolecular disulfide bonds had no significant impact on the immunogenicity of the molecule. In addition, vaccination with either formulated wild type Tc24 or Tc24-C4 antigen also significantly increased survival and reduced cardiac parasite burden in mice. Investigations are now underway to examine the efficacy of Tc24-C4 formulated with other adjuvants to reduce parasite burden and increase survival in pre-clinical studies.

  2. Residue Modification and Mass Spectrometry for the Investigation of Structural and Metalation Properties of Metallothionein and Cysteine-Rich Proteins

    Directory of Open Access Journals (Sweden)

    Gordon W. Irvine

    2017-04-01

    Full Text Available Structural information regarding metallothioneins (MTs has been hard to come by due to its highly dynamic nature in the absence of metal-thiolate cluster formation and crystallization difficulties. Thus, typical spectroscopic methods for structural determination are limited in their usefulness when applied to MTs. Mass spectrometric methods have revolutionized our understanding of protein dynamics, structure, and folding. Recently, advances have been made in residue modification mass spectrometry in order to probe the hard-to-characterize structure of apo- and partially metalated MTs. By using different cysteine specific alkylation reagents, time dependent electrospray ionization mass spectrometry (ESI-MS, and step-wise “snapshot” ESI-MS, we are beginning to understand the dynamics of the conformers of apo-MT and related species. In this review we highlight recent papers that use these and similar techniques for structure elucidation and attempt to explain in a concise manner the data interpretations of these complex methods. We expect increasing resolution in our picture of the structural conformations of metal-free MTs as these techniques are more widely adopted and combined with other promising tools for structural elucidation.

  3. Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach

    Science.gov (United States)

    Held, Jason M.; Danielson, Steven R.; Behring, Jessica B.; Atsriku, Christian; Britton, David J.; Puckett, Rachel L.; Schilling, Birgit; Campisi, Judith; Benz, Christopher C.; Gibson, Bradford W.

    2010-01-01

    Reactive oxygen species (ROS) are both physiological intermediates in cellular signaling and mediators of oxidative stress. The cysteine-specific redox-sensitivity of proteins can shed light on how ROS are regulated and function, but low sensitivity has limited quantification of the redox state of many fundamental cellular regulators in a cellular context. Here we describe a highly sensitive and reproducible oxidation analysis approach (OxMRM) that combines protein purification, differential alkylation with stable isotopes, and multiple reaction monitoring mass spectrometry that can be applied in a targeted manner to virtually any cysteine or protein. Using this approach, we quantified the site-specific cysteine oxidation status of endogenous p53 for the first time and found that Cys182 at the dimerization interface of the DNA binding domain is particularly susceptible to diamide oxidation intracellularly. OxMRM enables analysis of sulfinic and sulfonic acid oxidation levels, which we validate by assessing the oxidation of the catalytic Cys215 of protein tyrosine phosphatase-1B under numerous oxidant conditions. OxMRM also complements unbiased redox proteomics discovery studies as a verification tool through its high sensitivity, accuracy, precision, and throughput. PMID:20233844

  4. Mitochondrial and Nucleolar Localization of Cysteine Desulfurase Nfs and the Scaffold Protein Isu in Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Julie; Horáková, Eva; Changmai, Piya; Vancová, Marie; Lukeš, Julius

    2014-01-01

    Roč. 13, č. 3 (2014), s. 353-362 ISSN 1535-9778 R&D Projects: GA ČR(CZ) GAP305/11/2179; GA MŠk LH12104; GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : transfer RNA * iron sulfur protein * blood stream forms Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.820, year: 2014

  5. Cysteine-dependent immune regulation by TRX and MIF/GIF family proteins.

    Science.gov (United States)

    Kondo, Norihiko; Ishii, Yasuyuki; Son, Aoi; Sakakura-Nishiyama, Junko; Kwon, Yong-Won; Tanito, Masaki; Nishinaka, Yumiko; Matsuo, Yoshiyuki; Nakayama, Toshinori; Taniguchi, Masaru; Yodoi, Junji

    2004-03-29

    Thioredoxin (TRX) superfamily proteins that contain a conserved redox-active site -Cys-Xa.a.-Xa.a.-Cys- includes proinflammatory cytokine, macrophage migration inhibiting factor (MIF) and the immune regulatory cytokine, glycosylation inhibiting factor (GIF) in which Cys-60 is cysteinylated. In this report, we have analyzed the functional interaction between TRX and MIF/GIF. The stable Jurkat T cell line transfected with human TRX gene (TRX-transfectant) was highly resistant to hydrogen peroxide-induced apoptosis, but not the cell line transfected with vector (mock-transfectant). The expression level of MIF/GIF protein of TRX-transfectant was lower than that of mock-transfectant. Conversely, the expression level of intracellular TRX protein in CD4(+)-T cells derived from MIF -/- mice were significantly higher than that from background BALB/c mice. These findings collectively suggest that oxidative stress-induced apoptosis on T lymphocytes might be protected by the reciprocal regulation of TRX and MIF/GIF expression.

  6. Hyperbolic strings

    International Nuclear Information System (INIS)

    Popov, A.D.

    1991-01-01

    We introduce hyperbolic strings as closed bosonic strings with the target space R d-1,1 xT q+1,1 which has an additional time-like dimension in the internal space. The Fock spaces of the q-parametric family of standard bosonic, fermionic and heterotic strings with the target spaces of dimension n≤d+q are shown to be embedded into the Fock space of hyperbolic strings. The condition of the absence of anomaly fixes d and q for all three types of strings written in a bosonized form. (orig.)

  7. STRING v10

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan

    2015-01-01

    , and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10...... into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis...

  8. The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile

    Energy Technology Data Exchange (ETDEWEB)

    Bradshaw, William J. [University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Public Health England, Porton Down, Salisbury SP4 0JG (United Kingdom); Kirby, Jonathan M. [Public Health England, Porton Down, Salisbury SP4 0JG (United Kingdom); Thiyagarajan, Nethaji [University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Chambers, Christopher J.; Davies, Abigail H. [University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Public Health England, Porton Down, Salisbury SP4 0JG (United Kingdom); Roberts, April K.; Shone, Clifford C. [Public Health England, Porton Down, Salisbury SP4 0JG (United Kingdom); Acharya, K. Ravi, E-mail: bsskra@bath.ac.uk [University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom)

    2014-07-01

    The crystal structure of Cwp84, an S-layer protein from Clostridium difficile is presented for the first time. The cathepsin L-like fold of cysteine protease domain, a newly observed ‘lectin-like’ domain and several other features are described. Clostridium difficile is a major problem as an aetiological agent for antibiotic-associated diarrhoea. The mechanism by which the bacterium colonizes the gut during infection is poorly understood, but undoubtedly involves a myriad of components present on the bacterial surface. The mechanism of C. difficile surface-layer (S-layer) biogenesis is also largely unknown but involves the post-translational cleavage of a single polypeptide (surface-layer protein A; SlpA) into low- and high-molecular-weight subunits by Cwp84, a surface-located cysteine protease. Here, the first crystal structure of the surface protein Cwp84 is described at 1.4 Å resolution and the key structural components are identified. The truncated Cwp84 active-site mutant (amino-acid residues 33–497; C116A) exhibits three regions: a cleavable propeptide and a cysteine protease domain which exhibits a cathepsin L-like fold followed by a newly identified putative carbohydrate-binding domain with a bound calcium ion, which is referred to here as a lectin-like domain. This study thus provides the first structural insights into Cwp84 and a strong base to elucidate its role in the C. difficile S-layer maturation mechanism.

  9. The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile

    International Nuclear Information System (INIS)

    Bradshaw, William J.; Kirby, Jonathan M.; Thiyagarajan, Nethaji; Chambers, Christopher J.; Davies, Abigail H.; Roberts, April K.; Shone, Clifford C.; Acharya, K. Ravi

    2014-01-01

    The crystal structure of Cwp84, an S-layer protein from Clostridium difficile is presented for the first time. The cathepsin L-like fold of cysteine protease domain, a newly observed ‘lectin-like’ domain and several other features are described. Clostridium difficile is a major problem as an aetiological agent for antibiotic-associated diarrhoea. The mechanism by which the bacterium colonizes the gut during infection is poorly understood, but undoubtedly involves a myriad of components present on the bacterial surface. The mechanism of C. difficile surface-layer (S-layer) biogenesis is also largely unknown but involves the post-translational cleavage of a single polypeptide (surface-layer protein A; SlpA) into low- and high-molecular-weight subunits by Cwp84, a surface-located cysteine protease. Here, the first crystal structure of the surface protein Cwp84 is described at 1.4 Å resolution and the key structural components are identified. The truncated Cwp84 active-site mutant (amino-acid residues 33–497; C116A) exhibits three regions: a cleavable propeptide and a cysteine protease domain which exhibits a cathepsin L-like fold followed by a newly identified putative carbohydrate-binding domain with a bound calcium ion, which is referred to here as a lectin-like domain. This study thus provides the first structural insights into Cwp84 and a strong base to elucidate its role in the C. difficile S-layer maturation mechanism

  10. Association of Cysteine-Rich Secretory Protein 3 and β-Microseminoprotein with Outcome after Radical Prostatectomy

    Science.gov (United States)

    Bjartell, Anders S.; Al-Ahmadie, Hikmat; Serio, Angel M.; Eastham, James A.; Eggener, Scott E.; Fine, Samson W.; Udby, Lene; Gerald, William L.; Vickers, Andrew J.; Lilja, Hans; Reuter, Victor E.; Scardino, Peter T.

    2009-01-01

    Purpose It has been suggested that cysteine-rich secretory protein 3 (CRISP-3) and β-microseminoprotein (MSP) are associated with outcome in prostate cancer. We investigated whether these markers are related to biochemical recurrence and whether addition of the markers improves prediction of recurring disease. Experimental Design Tissue microarrays of radical prostatectomy specimens were analyzed for CRISP-3 and MSP by immunohistochemistry. Associations between marker positivity and postprostatectomy biochemical recurrence [prostate-specific antigen (PSA) >0.2 ng/mL with a confirmatory level] were evaluated by univariate and multivariable Cox proportional hazards regression. Multivariable analyses controlled for preoperative PSA and pathologic stage and grade. Results Among 945 patients, 224 had recurrence. Median follow-up for survivors was 6.0 years. Patients positive for CRISP-3 had smaller recurrence-free probabilities, whereas MSP-positive patients had larger recurrence-free probabilities. On univariate analysis, the hazard ratio for patients positive versus negative for CRISP-3 was1.53 (P = 0.010) and for MSP was 0.63 (P = 0.004). On multivariable analysis, both CRISP-3 (P = 0.007) and MSP (P = 0.002) were associated with recurrence. The hazard ratio among CRISP-3– positive/MSP-negative patients compared with CRISP-3– negative/MSP-positive patients was 2.38. Adding CRISP-3 to a base model that included PSA and pathologic stage and grade did not enhance the prediction of recurrence, but adding MSP increased the concordance index minimally from 0.778 to 0.781. Conclusion We report evidence that CRISP-3 and MSP are independent predictors of recurrence after radical prostatectomy for localized prostate cancer. However, addition of the markers does not importantly improve the performance of existing predictive models. Further research should aim to elucidate the functions of CRISP-3 and MSP in prostate cancer cells. PMID:17634540

  11. Plasmodium Cysteine Repeat Modular Proteins 3 and 4 are essential for malaria parasite transmission from the mosquito to the host

    Directory of Open Access Journals (Sweden)

    Mota Maria M

    2011-03-01

    Full Text Available Abstract Background The Plasmodium Cysteine Repeat Modular Proteins (PCRMP are a family of four conserved proteins of malaria parasites, that contain a number of motifs implicated in host-parasite interactions. Analysis of mutants of the rodent parasite Plasmodium berghei lacking expression of PCRMP1 or 2 showed that these proteins are essential for targeting of P. berghei sporozoites to the mosquito salivary gland and, hence, for transmission from the mosquito to the mouse. Methods In this work, the role of the remaining PCRMP family members, PCRMP3 and 4, has been investigated throughout the Plasmodium life cycle by generation and analysis of P. berghei gene deletion mutants, Δpcrmp3 and Δpcrmp4. The role of PCRMP members during the transmission and hepatic stages of the Plasmodium lifecycle has been evaluated by light- and electron microscopy and by analysis of liver stage development in HEPG2 cells in vitro and by infecting mice with mutant sporozoites. In addition, mice were immunized with live Δpcrmp3 and Δpcrmp4 sporozoites to evaluate their immunization potential as a genetically-attenuated parasite-based vaccine. Results Disruption of pcrmp3 and pcrmp4 in P. berghei revealed that they are also essential for transmission of the parasite through the mosquito vector, although acting in a distinct way to pbcrmp1 and 2. Mutants lacking expression of PCRMP3 or PCRMP4 show normal blood stage development and oocyst formation in the mosquito and develop into morphologically normal sporozoites, but these have a defect in egress from oocysts and do not enter the salivary glands. Sporozoites extracted from oocysts perform gliding motility and invade and infect hepatocytes but do not undergo further development and proliferation. Furthermore, the study shows that immunization with Δcrmp3 and Δcrmp4 sporozoites does not confer protective immunity upon subsequent challenge. Conclusions PCRMP3 and 4 play multiple roles during the Plasmodium life

  12. Bowed Strings

    Science.gov (United States)

    Rossing, Thomas D.; Hanson, Roger J.

    In the next eight chapters, we consider some aspects of the science of bowed string instruments, old and new. In this chapter, we present a brief discussion of bowed strings, a subject that will be developed much more thoroughly in Chap. 16. Chapters 13-15 discuss the violin, the cello, and the double bass. Chapter 17 discusses viols and other historic string instruments, and Chap. 18 discusses the Hutchins-Schelleng violin octet.

  13. Bosonic strings

    CERN Document Server

    Jost, Jürgen

    2007-01-01

    This book presents a mathematical treatment of Bosonic string theory from the point of view of global geometry. As motivation, Jost presents the theory of point particles and Feynman path integrals. He provides detailed background material, including the geometry of Teichmüller space, the conformal and complex geometry of Riemann surfaces, and the subtleties of boundary regularity questions. The high point is the description of the partition function for Bosonic strings as a finite-dimensional integral over a moduli space of Riemann surfaces. Jost concludes with some topics related to open and closed strings and D-branes. Bosonic Strings is suitable for graduate students and researchers interested in the mathematics underlying string theory.

  14. Mutation of adjacent cysteine residues in the NSs protein of Rift Valley fever virus results in loss of virulence in mice.

    Science.gov (United States)

    Monteiro, Gaby E R; Jansen van Vuren, Petrus; Wichgers Schreur, Paul J; Odendaal, Lieza; Clift, Sarah J; Kortekaas, Jeroen; Paweska, Janusz T

    2018-04-02

    The NSs protein encoded by the S segment of Rift Valley fever virus (RVFV) is the major virulence factor, counteracting the host innate antiviral defence. It contains five highly conserved cysteine residues at positions 39, 40, 149, 178 and 194, which are thought to stabilize the tertiary and quaternary structure of the protein. Here, we report significant differences between clinical, virological, histopathological and host gene responses in BALB/c mice infected with wild-type RVFV (wtRVFV) or a genetic mutant having a double cysteine-to-serine substitution at residues 39 and 40 of the NSs protein (RVFV-C39S/C40S). Mice infected with the wtRVFV developed a fatal acute disease; characterized by high levels of viral replication, severe hepatocellular necrosis, and massive up-regulation of transcription of genes encoding type I and -II interferons (IFN) as well as pro-apoptotic and pro-inflammatory cytokines. The RVFV-C39S/C40S mutant did not cause clinical disease and its attenuated virulence was consistent with virological, histopathological and host gene expression findings in BALB/c mice. Clinical signs in mice infected with viruses containing cysteine-to-serine substitutions at positions 178 or 194 were similar to those occurring in mice infected with the wtRVFV, while a mutant containing a substitution at position 149 caused mild, non-fatal disease in mice. As mutant RVFV-C39S/C40S showed an attenuated phenotype in mice, the molecular mechanisms behind this attenuation were further investigated. The results show that two mechanisms are responsible for the attenuation; (1) loss of the IFN antagonistic propriety characteristic of the wtRVFV NSs and (2) the inability of the attenuated mutant to degrade Proteine Kinase R (PKR). Copyright © 2018. Published by Elsevier B.V.

  15. Trypanoplasma borreli cysteine proteinase activities support a conservation of function with respect to digestion of host proteins in common carp

    NARCIS (Netherlands)

    Ruszczyk, Aleksandra; Forlenza, Maria; Joerink, Maaike; Ribeiro, Carla M. S.; Jurecka, Patrycja; Wiegertjes, Geert F.

    2008-01-01

    Trypanoplasma borreli is an extracellular parasite that is transmitted by a leech vector and is naturally found in the blood of cyprinid fish. High parasitemia and associated severe anemia together with splenomegaly are typical of infection of common carp, Cyprinus carpio L. Papain-like cysteine

  16. Trypanoplasma borreli cystein proteinase activities support a conservation of function with respect to digestion of host proteins in common carp

    NARCIS (Netherlands)

    Ruszczyk, A.; Forlenza, M.; Joerink, M.; Ribeiro, C.M.S.; Jurecka, P.M.; Wiegertjes, G.F.

    2008-01-01

    Trypanoplasma borreli is an extracellular parasite that is transmitted by a leech vector and is naturally found in the blood of cyprinid fish. High parasitemia and associated severe anemia together with splenomegaly are typical of infection of common carp, Cyprinus carpio L. Papain-like cysteine

  17. Sulfone-stabilized carbanions for the reversible covalent capture of a posttranslationally-generated cysteine oxoform found in protein tyrosine phosphatase 1B (PTP1B).

    Science.gov (United States)

    Parsons, Zachary D; Ruddraraju, Kasi Viswanatharaju; Santo, Nicholas; Gates, Kent S

    2016-06-15

    Redox regulation of protein tyrosine phosphatase 1B (PTP1B) involves oxidative conversion of the active site cysteine thiolate into an electrophilic sulfenyl amide residue. Reduction of the sulfenyl amide by biological thiols regenerates the native cysteine residue. Here we explored fundamental chemical reactions that may enable covalent capture of the sulfenyl amide residue in oxidized PTP1B. Various sulfone-containing carbon acids were found to react readily with a model peptide sulfenyl amide via attack of the sulfonyl carbanion on the electrophilic sulfur center in the sulfenyl amide. Both the products and the rates of these reactions were characterized. The results suggest that capture of a peptide sulfenyl amide residue by sulfone-stabilized carbanions can slow, but not completely prevent, thiol-mediated generation of the corresponding cysteine-containing peptide. Sulfone-containing carbon acids may be useful components in the construction of agents that knock down PTP1B activity in cells via transient covalent capture of the sulfenyl amide oxoform generated during insulin signaling processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. The structure of classical swine fever virus N(pro: a novel cysteine Autoprotease and zinc-binding protein involved in subversion of type I interferon induction.

    Directory of Open Access Journals (Sweden)

    Keerthi Gottipati

    Full Text Available Pestiviruses express their genome as a single polypeptide that is subsequently cleaved into individual proteins by host- and virus-encoded proteases. The pestivirus N-terminal protease (N(pro is a cysteine autoprotease that cleaves between its own C-terminus and the N-terminus of the core protein. Due to its unique sequence and catalytic site, it forms its own cysteine protease family C53. After self-cleavage, N(pro is no longer active as a protease. The released N(pro suppresses the induction of the host's type-I interferon-α/β (IFN-α/β response. N(pro binds interferon regulatory factor-3 (IRF3, the key transcriptional activator of IFN-α/β genes, and promotes degradation of IRF3 by the proteasome, thus preventing induction of the IFN-α/β response to pestivirus infection. Here we report the crystal structures of pestivirus N(pro. N(pro is structurally distinct from other known cysteine proteases and has a novel "clam shell" fold consisting of a protease domain and a zinc-binding domain. The unique fold of N(pro allows auto-catalysis at its C-terminus and subsequently conceals the cleavage site in the active site of the protease. Although many viruses interfere with type I IFN induction by targeting the IRF3 pathway, little information is available regarding structure or mechanism of action of viral proteins that interact with IRF3. The distribution of amino acids on the surface of N(pro involved in targeting IRF3 for proteasomal degradation provides insight into the nature of N(pro's interaction with IRF3. The structures thus establish the mechanism of auto-catalysis and subsequent auto-inhibition of trans-activity of N(pro, and its role in subversion of host immune response.

  19. Multiquark strings

    International Nuclear Information System (INIS)

    Wang, F.; Chun, W.

    1985-01-01

    The use of basis states described as hadronic (or hadron-hadron) or hidden-colour (or colour-colour) for a system of quarks does not necessarily imply that connected exotic multiquark hadrons do exist. Antisymmetrization of quark wave functions tends to make these descriptions ill defined. It appears necessary to have stable collective structures called strings or bags to provide the physical connections required by quark confinement. The masses of multiquark hadrons can then be estimated by using semplified string, bag and NR potential models. The results turn out to be qualitatively similar in all these models. The stability problem for multiquark strings is briefly discussed

  20. Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct

    Directory of Open Access Journals (Sweden)

    Morten K. Grøftehauge

    2015-07-01

    Full Text Available As part of the ongoing effort to functionally and structurally characterize virulence factors in the opportunistic pathogen Pseudomonas aeruginosa, we determined the crystal structure of YcaC co-purified with the target protein at resolutions of 2.34 and 2.56 Å without a priori knowledge of the protein identity or experimental phases. The three-dimensional structure of YcaC adopts a well-known cysteine hydrolase fold with the putative active site residues conserved. The active site cysteine is covalently bound to propionamide in one crystal form, whereas the second form contains an S-mercaptocysteine. The precise biological function of YcaC is unknown; however, related prokaryotic proteins have functions in antibacterial resistance, siderophore production and NADH biosynthesis. Here, we show that YcaC is exceptionally well conserved across both bacterial and fungal species despite being non-ubiquitous. This suggests that whilst YcaC may not be part of an integral pathway, the function could confer a significant evolutionary advantage to microbial life.

  1. Cosmic strings

    International Nuclear Information System (INIS)

    Bennett, D.P.

    1988-07-01

    Cosmic strings are linear topological defects that are predicted by some grand unified theories to form during a spontaneous symmetry breaking phase transition in the early universe. They are the basis for the only theories of galaxy formation aside from quantum fluctuations from inflation that are based on fundamental physics. In contrast to inflation, they can also be observed directly through gravitational lensing and their characteristic microwave background anistropy. It has recently been discovered by F. Bouchet and myself that details of cosmic string evolution are very different from the so-called ''standard model'' that has been assumed in most of the string induced galaxy formation calculations. Therefore, the details of galaxy formation in the cosmic string models are currently very uncertain. 29 refs., 9 figs

  2. Deciphering the interplay between cysteine synthase and thiol cascade proteins in modulating Amphotericin B resistance and survival of Leishmania donovani under oxidative stress

    Directory of Open Access Journals (Sweden)

    Kuljit Singh

    2017-08-01

    Full Text Available Leishmania donovani is the causative organism of the neglected human disease known as visceral leishmaniasis which is often fatal, if left untreated. The cysteine biosynthesis pathway of Leishmania may serve as a potential drug target because it is different from human host and regulates downstream components of redox metabolism of the parasites; essential for their survival, pathogenicity and drug resistance. However, despite the apparent dependency of redox metabolism of cysteine biosynthesis pathway, the role of L. donovani cysteine synthase (LdCS in drug resistance and redox homeostasis has been unexplored. Herein, we report that over-expression of LdCS in Amphotericin B (Amp B sensitive strain (S1-OE modulates resistance towards oxidative stress and drug pressure. We observed that antioxidant enzyme activities were up-regulated in S1-OE parasites and these parasites alleviate intracellular reactive oxygen species (ROS efficiently by maintaining the reduced thiol pool. In contrast to S1-OE parasites, Amp B sensitive strain (S1 showed higher levels of ROS which was positively correlated with the protein carbonylation levels and negatively correlated with cell viability. Moreover, further investigations showed that LdCS over-expression also augments the ROS-primed induction of LdCS-GFP as well as endogenous LdCS and thiol pathway proteins (LdTryS, LdTryR and LdcTXN in L. donovani parasites; which probably aids in stress tolerance and drug resistance. In addition, the expression of LdCS was found to be up-regulated in Amp B resistant isolates and during infective stationary stages of growth and consistent with these observations, our ex vivo infectivity studies confirmed that LdCS over-expression enhances the infectivity of L. donovani parasites. Our results reveal a novel crosstalk between LdCS and thiol metabolic pathway proteins and demonstrate the crucial role of LdCS in drug resistance and redox homeostasis of Leishmania. Keywords

  3. The PR-1 domain accounts for the anti-angiogenic activity of a cysteine-rich secretory protein member from the buccal glands of Lampetra japonica.

    Science.gov (United States)

    Duan, Dandan; Wang, Hongyan; Zhou, Rong; Jiang, Qi; Xiao, Rong

    2018-02-01

    Previous studies have shown that cysteine-rich buccal gland protein (CRBGP) from buccal glands of Lampetra japonica could suppress angiogenesis in chick chorioallantoic membrane models. As CRBGP is composed of a pathogenesis-related group 1 (PR-1) domain and a cysteine-rich domain (CRD), which domain accounts for the effects of CRBGP on anti-angiogenesis? In the present study, recombinant PR-1 and CRD (rL-PR-1 and rL-CRD) were obtained. MTT assays showed rL-PR-1 inhibited the proliferation of HUVECs significantly in a dose-dependent manner with an IC 50 of 2μM, while rL-CRD had no obviously inhibitory effect on the proliferation of HUVECs, suggested that PR-1 is the main function domain on the anti-angiogenic activity of CRBGP. Similar to CRBGP, rL-PR-1 induced apoptosis in HUVECs in a mitochondrial-dependent pathway by affecting the level of BAX, BCL2 and caspase 3. Also, the cytotoxic property of rL-PR-1 might be one of the factors which suppressed the proliferation of HUVECs. Furthermore, rL-PR-1 blocked the adhesion, migration, invasion and tube formation of HUVECs by disturbing the cytoskeleton arrangement and down-regulating the level of matrix metallo-peptidase 2. In summary, rL-PR-1 has the anti-angiogenic activity which would provide the information on the functions and mechanisms of cysteine-rich secretory protein family members. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Magnetic strings

    International Nuclear Information System (INIS)

    Chaves, Max

    2006-01-01

    The conception of the magnetic string is presented as an infinitely thin bundle of magnetic flux lines. The magnetic strings are surrounded by a film of current that rotates around them, and are a solution of Maxwell's equations. The magnetic potential contains a line singularity, and its stability can be established topologically. A few comments are added on the possibility that they may exist at a cosmological scale as relics of the Big Bang. (author) [es

  5. Immunolocalization of keratin-associated beta-proteins (beta-keratins) in pad lamellae of geckos suggest that glycine-cysteine-rich proteins contribute to their flexibility and adhesiveness.

    Science.gov (United States)

    Alibardi, Lorenzo

    2013-03-01

    The epidermis of digital pads in geckos comprises superficial microornamentation from the oberhautchen layer that form long setae allowing these lizards to climb vertical surfaces. The beta-layer is reduced in pad lamellae but persists up to the apical free margin. Setae are made of different proteins including keratin-associated beta-proteins, formerly indicated as beta-keratins. In order to identify specific setal proteins the present ultrastructural study on geckos pad lamellae analyzes the immunolocalization of three beta-proteins previously found in the epidermis and adhesive setae of the green anolis. A protein rich in glycine but poor in cysteine (HgG5-like) is absent or masked in gecko pad lamellae. Another protein rich in glycine and cysteine (HgGC3-like) is weakly present in setae, oberhautchen and beta-layer. A glycine and cysteine medium rich beta-protein (HgGC10-like) is present in the lower part of the beta-layer but is absent in the oberhautchen, setae, and mesos layer. The latter two proteins may form intermolecular bonds that contribute to the flexibility of the corneous material sustaining the setae. The pliable alpha-layer present beneath the thin beta-layer and in the hinge region of the pad lamellae also contains HgGC10-like proteins. Based on the possibility that some HgGC3-like or other cys-rich beta-proteins are charged in the setae it is suggested that their charges influence the mechanism of adhesion increasing the induction of dipoles on the substrate and enhancing attractive van der Waals forces. Copyright © 2013 Wiley Periodicals, Inc.

  6. Lattice strings

    International Nuclear Information System (INIS)

    Thorn, C.B.

    1988-01-01

    The possibility of studying non-perturbative effects in string theory using a world sheet lattice is discussed. The light-cone lattice string model of Giles and Thorn is studied numerically to assess the accuracy of ''coarse lattice'' approximations. For free strings a 5 by 15 lattice seems sufficient to obtain better than 10% accuracy for the bosonic string tachyon mass squared. In addition a crude lattice model simulating string like interactions is studied to find out how easily a coarse lattice calculation can pick out effects such as bound states which would qualitatively alter the spectrum of the free theory. The role of the critical dimension in obtaining a finite continuum limit is discussed. Instead of the ''gaussian'' lattice model one could use one of the vertex models, whose continuum limit is the same as a gaussian model on a torus of any radius. Indeed, any critical 2 dimensional statistical system will have a stringy continuum limit in the absence of string interactions. 8 refs., 1 fig. , 9 tabs

  7. [Effects of redox state of disulfide bonds on the intrinsic fluorescence and denaturation of Trx-fused gibberellin-induced cysteine-rich protein from Gymnadnia conopsea].

    Science.gov (United States)

    Zhang, Teng; Feng, Juan; Li, Yang; Chen, Rui; Tang, Li-Xia; Pang, Xiao-Feng; Ren, Zheng-Long

    2010-02-01

    In the present paper, thioredoxin-fused gibberellin-induced cysteine-rich protein from Gymnadnia conopsea, desigated as Trx-GcGASA and expressed prokaryotically, was purified and identified by using Ni(2+) -NTA affinity chromatography column and SDS-PAGE, and then its intrinsic fluorescence was investigated in the absence and presence of dithiothreitol (DTT), oxidized glutathione (GSSG), peroxide and guanidine hydrochloride (GdnHCl) by means of steady-state fluorescence spectroscopic methods. It was found that (1) at the neutral pH Trx-GcGASA had maximum fluorescence emission at 305 nm following excitation at different wavelengths varying from 250 to 280 nm, which was ascribed to the fluorescence emission from tyrosine residues. (2) The reduction of disulphide bonds lead to the changes in the relative fluorescence intensity between tyrosine and tryptophan residues from 0.7 to 1.8. (3) Both Tyr and Trp residues underwent 12%-21% decrease in fluorescence intensity with the addition of 0.5 mmol x L(-1) GSSG or 5 mmol x L(-1) peroxide. The latter was roughly consistent with the antioxidative activity reported in vivo. (4) No matter whether 1 mmol x L(-1) DTT was absent or present, the fusion protein could not be fully unfolded with lambda(max) Trx-GcGASA experienced GdnHCl-induced denaturation process, and the unfolding equilibrium curve could be well fitted by using two-state model, giving the Gibbs free energy change (deltaG) of 3.7 kJ x mol(-1). However, it was not the case for reduced Trx-GcGASA protein. The aforementioned experimental results will not only provide some guides to investigate the effects of fusion partner Trx on the unfolding thermodynamics, kinetics and refolding process of Trx-GcGASA, but also will be useful for further studies on the strucuture of GA-induced cysteine-rich protein with the help of spectroscopic methods.

  8. Activation of mas-related G-protein-coupled receptors by the house dust mite cysteine protease Der p1 provides a new mechanism linking allergy and inflammation.

    Science.gov (United States)

    Reddy, Vemuri B; Lerner, Ethan A

    2017-10-20

    Cysteine and serine proteases function via protease-activated and mas-related G-protein-coupled receptors (Mrgprs) to contribute to allergy and inflammation. Der p1 is a cysteine protease and major allergen from the house dust mite and is associated with allergic rhinitis and allergic asthma. Der p1 activates protease-activated receptor 2 and induces the release of the pro-inflammatory cytokine IL-6 from cells. However, the possibility that Der p1 acts on Mrgprs has not been considered. We report here that ratiometric calcium imaging reveals that Der p1 activates the human receptor MRGPRX1 and the mouse homolog MrgprC11, implicated previously in itch. Der p1 cleavage of N-terminal receptor peptides followed by site-directed mutagenesis of the cleavage sites links receptor activation to specific amino acid residues. Der p1 also induced the release of IL-6 from heterologous cells expressing MRGPRX1. In summary, activation of Mrgprs by the allergen Der p1 may contribute to inflammation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Singleton strings

    International Nuclear Information System (INIS)

    Engquist, J.; Sundell, P.; Tamassia, L.

    2007-01-01

    The group theoretical structure underlying physics in anti de Sitter (AdS) spacetime is intrinsically different with respect to the flat case, due to the presence of special ultra-short representations, named singletons, that do not admit a flat space limit. The purpose of this collaboration is to exploit this feature in the study of string and brane dynamics in AdS spacetime, in particular while trying to establish a connection between String Theory in AdS backgrounds (in the tensionless limit) and Higher-Spin Gauge Theory. (orig.)

  10. A protein extract and a cysteine protease inhibitor enriched fraction from Jatropha curcas seed cake have in vitro anti-Toxoplasma gondii activity.

    Science.gov (United States)

    Soares, A M S; Carvalho, L P; Melo, E J T; Costa, H P S; Vasconcelos, I M; Oliveira, J T A

    2015-06-01

    Toxoplasma gondii is a parasite of great medical and veterinary importance that has worldwide distribution and causes toxoplasmosis. There are few treatments available for toxoplasmosis and the search for plant extracts and compounds with anti-Toxoplasma activity is of utmost importance for the discovery of new active drugs. The objective of this study was to investigate the action of a protein extract and a protease inhibitor enriched fraction from J. curcas seed cake on developing tachyzoites of T. gondii-infected Vero cells. The protein extract (JcCE) was obtained after solubilization of the J. curcas seed cake with 100 mM sodium borate buffer, pH 10, centrifugation and dialysis of the resulting supernatant with the extracting buffer. JcCE was used for the in vitro assays of anti-Toxoplasma activity at 0.01, 0.1, 0.5, 1.5, 3.0 and 5.0 mg/ml concentration for 24 h. The results showed that JcCE reduced the percentage of infection and the number of intracellular parasites, but had no effect on the morphology of Vero cells up to 3.0 mg/mL. The cysteine protease inhibitor enriched fraction, which was obtained after chromatography of JcCE on Sephadex G-75 and presented a unique protein band following SDS-PAGE, reduced both the number of T. gondii infected cells and intracellular parasites. These results suggest that both JcCE and the cysteine protease inhibitor enriched fraction interfere with the intracellular growth of T. gondii. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Cysteine Protease Zymography: Brief Review.

    Science.gov (United States)

    Wilkesman, Jeff

    2017-01-01

    Cysteine proteases play multiple roles in basically all aspects of physiology and development. In plants, they are involved in growth and development and in accumulation and mobilization of storage proteins. Furthermore, they are engaged in signalling pathways and in the response to biotic and abiotic stresses. In animals and also in humans, they are responsible for senescence and apoptosis, prohormone processing, and ECM remodelling. When analyzed by zymography, the enzyme must be renaturated after SDS-PAGE. SDS must be washed out and substituted by Triton X-100. Gels are then further incubated under ideal conditions for activity detection. Cysteine proteases require an acidic pH (5.0-6.0) and a reducing agent, usually DTT. When screening biological samples, there is generally no previous clue on what peptidase class will be present, neither optimal proteolysis conditions are known. Hence, it is necessary to assess several parameters, such as incubation time, pH, temperature, influence of ions or reducing agents, and finally evaluate the inhibition profile. For detection of cysteine peptidase activity, the use of specific inhibitors, such as E-64, can be used to prevent the development of cysteine peptidase activity bands and positively confirm its presence. Here four different protocols to assess cysteine protease activity from different sources are presented.

  12. String phenomenology

    CERN Document Server

    Ibáñez, Luis E

    2015-01-01

    This chapter reviews a number of topics in the field of string phenomenology, focusing on orientifold/F-theory models yielding semirealistic low-energy physics. The emphasis is on the extraction of the low-energy effective action and possible tests of specific models at the LHC.

  13. String GUTs

    International Nuclear Information System (INIS)

    Aldazabal, G.; Ibanez, L.E.; Uranga, A.M.

    1995-01-01

    Standard SUSY-GUTs such as those based on SU(5) or SO(10) lead to predictions for the values of α s and sin 2 θ W in amazing agreement with experiment. In this article we investigate how these models may be obtained from string theory, thus bringing them into the only known consistent framework for quantum gravity. String models with matter in standard GUT representations require the realization of affine Lie algebras at higher levels. We start by describing some methods to build level k=2 symmetric orbifold string models with gauge groups SU(5) or SO(10). We present several examples and identify generic features of the type of models constructed. Chiral fields appropriate to break the symmetry down to the standard model generically appear in the massless spectrum. However, unlike in standard SUSY-GUTs, they often behave as string moduli, i.e., they do not have self-couplings. We also discuss briefly the doublet-triplet Higgs splitting. We find that, in some models, built-in sliding-singlet type of couplings exist. (orig.)

  14. Cysteine proteinases regulate chloroplast protein content and composition in tobacco leaves: a model for dynamic interactions with ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) vesicular bodies.

    Science.gov (United States)

    Prins, Anneke; van Heerden, Philippus D R; Olmos, Enrique; Kunert, Karl J; Foyer, Christine H

    2008-01-01

    The roles of cysteine proteinases (CP) in leaf protein accumulation and composition were investigated in transgenic tobacco (Nicotiana tabacum L.) plants expressing the rice cystatin, OC-1. The OC-1 protein was present in the cytosol, chloroplasts, and vacuole of the leaves of OC-1 expressing (OCE) plants. Changes in leaf protein composition and turnover caused by OC-1-dependent inhibition of CP activity were assessed in 8-week-old plants using proteomic analysis. Seven hundred and sixty-five soluble proteins were detected in the controls compared to 860 proteins in the OCE leaves. A cyclophilin, a histone, a peptidyl-prolyl cis-trans isomerase, and two ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase isoforms were markedly altered in abundance in the OCE leaves. The senescence-related decline in photosynthesis and Rubisco activity was delayed in the OCE leaves. Similarly, OCE leaves maintained higher leaf Rubisco activities and protein than controls following dark chilling. Immunogold labelling studies with specific antibodies showed that Rubisco was present in Rubisco vesicular bodies (RVB) as well as in the chloroplasts of leaves from 8-week-old control and OCE plants. Western blot analysis of plants at 14 weeks after both genotypes had flowered revealed large increases in the amount of Rubisco protein in the OCE leaves compared to controls. These results demonstrate that CPs are involved in Rubisco turnover in leaves under optimal and stress conditions and that extra-plastidic RVB bodies are present even in young source leaves. Furthermore, these data form the basis for a new model of Rubisco protein turnover involving CPs and RVBs.

  15. Secreted protein acidic and rich in cysteine functions in colitis via IL17A regulation in mucosal CD4+ T cells.

    Science.gov (United States)

    Tanaka, Makoto; Takagi, Tomohisa; Naito, Yuji; Uchiyama, Kazuhiko; Hotta, Yuma; Toyokawa, Yuki; Ushiroda, Chihiro; Hirai, Yasuko; Aoi, Wataru; Higashimura, Yasuki; Mizushima, Katsura; Okayama, Tetsuya; Katada, Kazuhiro; Kamada, Kazuhiro; Ishikawa, Takeshi; Handa, Osamu; Itoh, Yoshito

    2018-03-01

    Secreted protein acidic and rich in cysteine (SPARC) is a matricellular glycol that regulates cell proliferation, tissue repair, and tumorigenesis. Despite evidence linking SPARC to inflammation, the mechanisms are unclear. Accordingly, the role of SPARC in intestinal inflammation was investigated. Colitis was induced in wild-type (WT) and SPARC knockout (KO) mice using trinitrobenzene sulfonic acid (TNBS). Colons were assessed for damage; leukocyte infiltration; Tnf, Ifng, Il17a, and Il10 mRNA expression; and histology. Cytokine profiling of colonic lamina propria mononuclear cells (LPMCs) was performed by flow cytometry. Naïve CD4 + T cells were isolated from WT and SPARC KO mouse spleens, and the effect of SPARC on Th17 cell differentiation was examined. Recombination activating gene 1 knockout (RAG1 KO) mice reconstituted with T cells from either WT or SPARC KO mice were investigated. Trinitrobenzene sulfonic acid exposure significantly reduced bodyweight and increased mucosal inflammation, leukocyte infiltration, and Il17a mRNA expression in WT relative to SPARC KO mice. The percentage of IL17A-producing CD4 + T cells among LPMCs from KO mice was lower than that in WT mice when both groups were exposed to TNBS. Th17 cell differentiation was suppressed in cells from SPARC KO mice. In the T cell transfer colitis model, RAG1 KO mice receiving T cells from WT mice were more severely affected than those reconstituted with cells from SPARC KO mice. Secreted protein acidic and rich in cysteine accelerates colonic mucosal inflammation via modulation of IL17A-producing CD4 + T cells. SPARC is a potential therapeutic target for conditions involving intestinal inflammation. © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

  16. Targeted disruption of the mouse Csrp2 gene encoding the cysteine- and glycine-rich LIM domain protein CRP2 result in subtle alteration of cardiac ultrastructure

    Directory of Open Access Journals (Sweden)

    Stoll Doris

    2008-08-01

    Full Text Available Abstract Background The cysteine and glycine rich protein 2 (CRP2 encoded by the Csrp2 gene is a LIM domain protein expressed in the vascular system, particularly in smooth muscle cells. It exhibits a bimodal subcellular distribution, accumulating at actin-based filaments in the cytosol and in the nucleus. In order to analyze the function of CRP2 in vivo, we disrupted the Csrp2 gene in mice and analysed the resulting phenotype. Results A ~17.3 kbp fragment of the murine Csrp2 gene containing exon 3 through 6 was isolated. Using this construct we confirmed the recently determined chromosomal localization (Chromosome 10, best fit location between markers D10Mit203 proximal and D10Mit150 central. A gene disruption cassette was cloned into exon 4 and a mouse strain lacking functional Csrp2 was generated. Mice lacking CRP2 are viable and fertile and have no obvious deficits in reproduction and survival. However, detailed histological and electron microscopic studies reveal that CRP2-deficient mice have subtle alterations in their cardiac ultrastructure. In these mice, the cardiomyocytes display a slight increase in their thickness, indicating moderate hypertrophy at the cellular level. Although the expression of several intercalated disc-associated proteins such as β-catenin, N-RAP and connexin-43 were not affected in these mice, the distribution of respective proteins was changed within heart tissue. Conclusion We conclude that the lack of CRP2 is associated with alterations in cardiomyocyte thickness and hypertrophy.

  17. Efficient Disk-Based Techniques for Manipulating Very Large String Databases

    KAUST Repository

    Allam, Amin

    2017-01-01

    Indexing and processing strings are very important topics in database management. Strings can be database records, DNA sequences, protein sequences, or plain text. Various string operations are required for several application categories

  18. Mutation of cysteine-88 in the Saccharomyces cerevisiae RAD6 protein abolishes its ubiquitin-conjugating activity and its various biological functions

    International Nuclear Information System (INIS)

    Sung, P.; Prakash, S.; Prakash, L.

    1990-01-01

    The RAD6 gene of Saccharomyces cerevisiae is required for DNA repair, DNA damage-induced mutagenesis, and sporulation. RAD6 protein is a ubiquitin-conjugating enzyme (E2) that has been shown to attach multiple molecules of ubiquitin to histones H2A and H2B. We have now examined whether the E2 activity of RAD6 is involved in its various biological functions. Since the formation of a thioester adduct between E2 and ubiquitin is necessary for E2 activity, the single cysteine residue (Cys-88) present in RAD6 was changed to alanine or valine. The mutant proteins were overproduced in yeast cells and purified to near homogeneity. We show that the rad6 Ala-88 and rad6 Val-88 mutant proteins lack the capacity for thioester formation with ubiquitin and, as a consequence, are totally devoid of any E2 activity. The rad6 Ala-88 and rad6 Val-88 mutations confer a defect in DNA repair, mutagenesis, and sporulation equivalent to that in the rad6 null allele. We suggest that the biological functions of RAD6 require its E2 activity. (author)

  19. Investigating possible biological targets of Bj-CRP, the first cysteine-rich secretory protein (CRISP) isolated from Bothrops jararaca snake venom.

    Science.gov (United States)

    Lodovicho, Marina E; Costa, Tássia R; Bernardes, Carolina P; Menaldo, Danilo L; Zoccal, Karina F; Carone, Sante E; Rosa, José C; Pucca, Manuela B; Cerni, Felipe A; Arantes, Eliane C; Tytgat, Jan; Faccioli, Lúcia H; Pereira-Crott, Luciana S; Sampaio, Suely V

    2017-01-04

    Cysteine-rich secretory proteins (CRISPs) are commonly described as part of the protein content of snake venoms, nevertheless, so far, little is known about their biological targets and functions. Our study describes the isolation and characterization of Bj-CRP, the first CRISP isolated from Bothrops jararaca snake venom, also aiming at the identification of possible targets for its actions. Bj-CRP was purified using three chromatographic steps (Sephacryl S-200, Source 15Q and C18) and showed to be an acidic protein of 24.6kDa with high sequence identity to other snake venom CRISPs. This CRISP was devoid of proteolytic, hemorrhagic or coagulant activities, and it did not affect the currents from 13 voltage-gated potassium channel isoforms. Conversely, Bj-CRP induced inflammatory responses characterized by increase of leukocytes, mainly neutrophils, after 1 and 4h of its injection in the peritoneal cavity of mice, also stimulating the production of IL-6. Bj-CRP also acted on the human complement system, modulating some of the activation pathways and acting directly on important components (C3 and C4), thus inducing the generation of anaphylatoxins (C3a, C4a and C5a). Therefore, our results for Bj-CRP open up prospects for better understanding this class of toxins and its biological actions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Optimal expression of a Fab-effector fusion protein in Escherichia coli by removing the cysteine residues responsible for an interchain disulfide bond of a Fab molecule.

    Science.gov (United States)

    Kang, Hyeon-Ju; Kim, Hye-Jin; Jung, Mun-Sik; Han, Jae-Kyu; Cha, Sang-Hoon

    2017-04-01

    Development of novel bi-functional or even tri-functional Fab-effector fusion proteins would have a great potential in the biomedical sciences. However, the expression of Fab-effector fusion proteins in Escherichia coli is problematic especially when a eukaryotic effector moiety is genetically linked to a Fab due to the lack of proper chaperone proteins and an inappropriate physicochemical environment intrinsic to the microbial hosts. We previously reported that a human Fab molecule, referred to as SL335, reactive to human serum albumin has a prolonged in vivo serum half-life in rats. We, herein, tested six discrete SL335-human growth hormone (hGH) fusion constructs as a model system to define an optimal Fab-effector fusion format for E. coli expression. We found that one variant, referred to as HserG/Lser, outperformed the others in terms of a soluble expression yield and functionality in that HserG/Lser has a functional hGH bioactivity and possesses an serum albumin-binding affinity comparable to SL335. Our results clearly demonstrated that the genetic linkage of an effector domain to the C-terminus of Fd (V H +C H1 ) and the removal of cysteine (Cys) residues responsible for an interchain disulfide bond (IDB) ina Fab molecule optimize the periplasmic expression of a Fab-effector fusion protein in E. coli. We believe that our approach can contribute the development of diverse bi-functional Fab-effector fusion proteins by providing a simple strategy that enables the reliable expression of a functional fusion proteins in E. coli. Copyright © 2017 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

  1. Two COWP-like cysteine rich proteins from Eimeria nieschulzi (coccidia, apicomplexa) are expressed during sporulation and involved in the sporocyst wall formation.

    Science.gov (United States)

    Jonscher, Ernst; Erdbeer, Alexander; Günther, Marie; Kurth, Michael

    2015-07-25

    The family of cysteine rich proteins of the oocyst wall (COWPs) originally described in Cryptosporidium can also be found in Toxoplasma gondii (TgOWPs) localised to the oocyst wall as well. Genome sequence analysis of Eimeria suggests that these proteins may also exist in this genus and led us to the assumption that these proteins may also play a role in oocyst wall formation. In this study, COWP-like encoding sequences had been identified in Eimeria nieschulzi. The predicted gene sequences were subsequently utilized in reporter gene assays to observe time of expression and localisation of the reporter protein in vivo. Both investigated proteins, EnOWP2 and EnOWP6, were expressed during sporulation. The EnOWP2-promoter driven mCherry was found in the cytoplasm and the EnOWP2, respectively EnOWP6, fused to mCherry was initially observed in the extracytoplasmatic space between sporoblast and oocyst wall. This, so far unnamed compartment was designated as circumplasm. Later, the mCherry reporter co-localised with the sporocyst wall of the sporulated oocysts. This observation had been confirmed by confocal microscopy, excystation experiments and IFA. Transcript analysis revealed the intron-exon structure of these genes and confirmed the expression of EnOWP2 and EnOWP6 during sporogony. Our results allow us to assume a role, of both investigated EnOWP proteins, in the sporocyst wall formation of E. nieschulzi. Data mining and sequence comparisons to T. gondii and other Eimeria species allow us to hypothesise a conserved process within the coccidia. A role in oocyst wall formation had not been observed in E. nieschulzi.

  2. A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation

    Directory of Open Access Journals (Sweden)

    Patrizia Marinelli

    2018-04-01

    Full Text Available Oxidatively modified forms of proteins accumulate during aging. Oxidized protein conformers might act as intermediates in the formation of amyloids in age-related disorders. However, it is not known whether this amyloidogenic conversion requires an extensive protein oxidative damage or it can be promoted just by a discrete, localized post-translational modification of certain residues. Here, we demonstrate that the irreversible oxidation of a single free Cys suffices to severely perturb the folding energy landscape of a stable globular protein, compromise its kinetic stability, and lead to the formation of amyloids under physiological conditions. Experiments and simulations converge to indicate that this specific oxidation-promoted protein aggregation requires only local unfolding. Indeed, a large scale analysis indicates that many cellular proteins are at risk of undergoing this kind of deleterious transition; explaining how oxidative stress can impact cell proteostasis and subsequently lead to the onset of pathological states. Keywords: Protein oxidation, Protein misfolding, Protein aggregation, Oxidative stress, Post-translational modification

  3. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines.

    Science.gov (United States)

    Kristensen, Tatjana P; Maria Cherian, Reeja; Gray, Fiona C; MacNeill, Stuart A

    2014-01-01

    The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies.

  4. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

    Full Text Available The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural

  5. D19S Mutation of the Cationic, Cysteine-Rich Protein PAF: Novel Insights into Its Structural Dynamics, Thermal Unfolding and Antifungal Function.

    Directory of Open Access Journals (Sweden)

    Christoph Sonderegger

    Full Text Available The cysteine-rich, cationic, antifungal protein PAF is abundantly secreted into the culture supernatant of the filamentous Ascomycete Penicillium chrysogenum. The five β-strands of PAF form a compact β-barrel that is stabilized by three disulphide bonds. The folding of PAF allows the formation of four surface-exposed loops and distinct charged motifs on the protein surface that might regulate the interaction of PAF with the sensitive target fungus. The growth inhibitory activity of this highly stable protein against opportunistic fungal pathogens provides great potential in antifungal drug research. To understand its mode of action, we started to investigate the surface-exposed loops of PAF and replaced one aspartic acid at position 19 in loop 2 that is potentially involved in PAF active or binding site, with a serine (Asp19 to Ser19. We analysed the overall effects, such as unfolding, electrostatic changes, sporadic conformers and antifungal activity when substituting this specific amino acid to the fairly indifferent amino acid serine. Structural analyses revealed that the overall 3D solution structure is virtually identical with that of PAF. However, PAFD19S showed slightly increased dynamics and significant differences in the surface charge distribution. Thermal unfolding identified PAFD19S to be rather a two-state folder in contrast to the three-state folder PAF. Functional comparison of PAFD19S and PAF revealed that the exchange at residue 19 caused a dramatic loss of antifungal activity: the binding and internalization of PAFD19S by target cells was reduced and the protein failed to trigger an intracellular Ca2+ response, all of which are closely linked to the antifungal toxicity of PAF. We conclude that the negatively charged residue Asp19 in loop 2 is essential for full function of the cationic protein PAF.

  6. String Gas Cosmology

    OpenAIRE

    Brandenberger, Robert H.

    2008-01-01

    String gas cosmology is a string theory-based approach to early universe cosmology which is based on making use of robust features of string theory such as the existence of new states and new symmetries. A first goal of string gas cosmology is to understand how string theory can effect the earliest moments of cosmology before the effective field theory approach which underlies standard and inflationary cosmology becomes valid. String gas cosmology may also provide an alternative to the curren...

  7. SCR96, a small cysteine-rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance.

    Science.gov (United States)

    Chen, Xiao-Ren; Li, Yan-Peng; Li, Qi-Yuan; Xing, Yu-Ping; Liu, Bei-Bei; Tong, Yun-Hui; Xu, Jing-You

    2016-05-01

    Peptides and small molecules produced by both the plant pathogen Phytophthora and host plants in the apoplastic space mediate the relationship between the interplaying organisms. Various Phytophthora apoplastic effectors, including small cysteine-rich (SCR) secretory proteins, have been identified, but their roles during interaction remain to be determined. Here, we identified an SCR effector encoded by scr96, one of three novel genes encoding SCR proteins in P. cactorum with similarity to the P. cactorum phytotoxic protein PcF. Together with the other two genes, scr96 was transcriptionally induced throughout the developmental and infection stages of the pathogen. These genes triggered plant cell death (PCD) in the Solanaceae, including Nicotiana benthamiana and tomato. The scr96 gene did not show single nucleotide polymorphisms in a collection of P. cactorum isolates from different countries and host plants, suggesting that its role is essential and non-redundant during infection. Homologues of SCR96 were identified only in oomycetes, but not in fungi and other organisms. A stable protoplast transformation protocol was adapted for P. cactorum using green fluorescent protein as a marker. The silencing of scr96 in P. cactorum caused gene-silenced transformants to lose their pathogenicity on host plants and these transformants were significantly more sensitive to oxidative stress. Transient expression of scr96 partially recovered the virulence of gene-silenced transformants on plants. Overall, our results indicate that the P. cactorum scr96 gene encodes an important virulence factor that not only causes PCD in host plants, but is also important for pathogenicity and oxidative stress tolerance. © 2015 BSPP AND JOHN WILEY & SONS LTD.

  8. Closed string field theory

    International Nuclear Information System (INIS)

    Strominger, A.

    1987-01-01

    A gauge invariant cubic action describing bosonic closed string field theory is constructed. The gauge symmetries include local spacetime diffeomorphisms. The conventional closed string spectrum and trilinear couplings are reproduced after spontaneous symmetry breaking. The action S is constructed from the usual ''open string'' field of ghost number minus one half. It is given by the associator of the string field product which is non-vanishing because of associativity anomalies. S does not describe open string propagation because open string states associate and can thereby be shifted away. A field theory of closed and open strings can be obtained by adding to S the cubic open string action. (orig.)

  9. Cysteine proteinases and cystatins

    Directory of Open Access Journals (Sweden)

    Adeliana S. Oliveira

    2003-01-01

    Full Text Available This review describeds the definition, localization, functions and examples of cysteine proteinases and their protein inhibitors in vertebrate, non-vertebrate animals and plants. These inhibitors are related with defense mechanisms of plant against pests. It also describes the factors involved in the specific cysteine proteinase-cystatin interaction and high degree of affinity and large specificity in this interaction which are not only represented by the compatibility between amino acid residues of the active site involved in catalysis, but also of all amino acid residues that participante in the enzyme-inhibitor interaction.Nesta revisão foram descritas definições, localizações, funções e exemplos de proteinases cisteínicas e suas proteinas inibidoras em animais vertebrados e invertebrados e plantas. Tratamos principalmente com aqueles inibidores que são relatados com o mecanismo de defesa da planta contra pestes. Em adição, comentamos sobre recentes trabalhos que contribuíram para uma melhor compreenção dos fatores envolvidos na interação específica proteinase cisteínica-cistatina. Por outro lado, chamamos atenção para o alto grau de afinidade e grande especificidade na interação que não são apenas representadas pela compatibilidade entre os residuos de aminoácidos do sítio ativo envolvidos na catalise, mas também de todos os resíduos de aminoácidos que participam da interação enzima-inibidor.

  10. The myeloperoxidase-derived oxidant hypothiocyanous acid inhibits protein tyrosine phosphatases via oxidation of key cysteine residues

    DEFF Research Database (Denmark)

    Cook, Naomi L.; Moeke, Cassidy H.; Fantoni, Luca I.

    2016-01-01

    Phosphorylation of protein tyrosine residues is critical to cellular processes, and is regulated by kinases and phosphatases (PTPs). PTPs contain a redox-sensitive active site Cys residue, which is readily oxidized. Myeloperoxidase, released from activated leukocytes, catalyzes thiocyanate ion (SCN...

  11. Pepper pathogenesis-related protein 4c is a plasma membrane-localized cysteine protease inhibitor that is required for plant cell death and defense signaling.

    Science.gov (United States)

    Kim, Nak Hyun; Hwang, Byung Kook

    2015-01-01

    Xanthomonas campestris pv. vesicatoria (Xcv) type III effector AvrBsT triggers programmed cell death (PCD) and activates the hypersensitive response (HR) in plants. Here, we isolated and identified the plasma membrane localized pathogenesis-related (PR) protein 4c gene (CaPR4c) from pepper (Capsicum annuum) leaves undergoing AvrBsT-triggered HR cell death. CaPR4c encodes a protein with a signal peptide and a Barwin domain. Recombinant CaPR4c protein expressed in Escherichia coli exhibited cysteine protease-inhibitor activity and ribonuclease (RNase) activity. Subcellular localization analyses revealed that CaPR4c localized to the plasma membrane in plant cells. CaPR4c expression was rapidly and specifically induced by avirulent Xcv (avrBsT) infection. Transient expression of CaPR4c caused HR cell death in pepper leaves, which was accompanied by enhanced accumulation of H2 O2 and significant induction of some defense-response genes. Deletion of the signal peptide from CaPR4c abolished the induction of HR cell death, indicating a requirement for plasma membrane localization of CaPR4c for HR cell death. CaPR4c silencing in pepper disrupted both basal and AvrBsT-triggered resistance responses, and enabled Xcv proliferation in infected leaves. H2 O2 accumulation, cell-death induction, and defense-response gene expression were distinctly reduced in CaPR4c-silenced pepper. CaPR4c overexpression in transgenic Arabidopsis plants conferred greater resistance against infection by Pseudomonas syringae pv. tomato and Hyaloperonospora arabidopsidis. These results collectively suggest that CaPR4c plays an important role in plant cell death and defense signaling. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  12. A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method

    Science.gov (United States)

    Yoshida, Norio

    2018-05-01

    A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example.

  13. Evidence for cysteine sulfinate as a neurotransmitter

    International Nuclear Information System (INIS)

    Recasens, M.; Varga, V.; Nanopoulos, D.; Saadoun, F.; Vincendon, G.; Benavides, J.

    1982-01-01

    The Na + -independent binding of L-[ 3 H]cysteine sulfinate and L-[ 3 H]cysteine sulfinate uptake were investigated in rat brain membranes and vesicles. Specific binding of L-[ 3 H]cysteine sulfinate was saturable and occurred by a single high affinity process with a Ksub(b) of 100 nM +- 9 and a capacity (Bsub(max)) of 2.4 +- 0.22 pmol/mg protein. The regional distribution of the binding of L-[ 3 H]cysteine sulfinate in the brain was found to be heterogeneous. The rate of L-[ 3 H]cysteine sulfinate uptake shows a biphasic dependence on the concentration of L-cysteine sulfinate, corresponding to a high affinity (27.2 μM) and a low affinity (398 μM) transport system. The maximum L-[ 3 H]cysteine sulfinate uptake is reached at 2min and the uptake increases as a function of the sodium concentration. Chloride and potassium ions stimulate the uptake. (Auth.)

  14. Overexpression of an Arabidopsis cysteine-rich receptor-like protein kinase, CRK5, enhances abscisic acid sensitivity and confers drought tolerance

    Science.gov (United States)

    Lu, Kai; Liang, Shan; Wu, Zhen; Bi, Chao; Yu, Yong-Tao; Wang, Xiao-Fang; Zhang, Da-Peng

    2016-01-01

    Receptor-like kinases (RLKs) have been reported to regulate many developmental and defense process, but only a few members have been functionally characterized. In the present study, our observations suggest that one of the RLKs, a membrane-localized cysteine-rich receptor-like protein kinase, CRK5, is involved in abscisic acid (ABA) signaling in Arabidopsis thaliana. Overexpression of CRK5 increases ABA sensitivity in ABA-induced early seedling growth arrest and promotion of stomatal closure and inhibition of stomatal opening. Interestingly, and importantly, overexpression of CRK5 enhances plant drought tolerance without affecting plant growth at the mature stages and plant productivity. Transgenic lines overexpressing a mutated form of CRK5, CRK5 K372E with the change of the 372nd conserved amino acid residue from lysine to glutamic acid in its kinase domain, result in wild-type ABA and drought responses, supporting the role of CRK5 in ABA signaling. The loss-of-function mutation of the CRK5 gene does not affect the ABA response, while overexpression of two homologs of CRK5, CRK4 and CRK19, confers ABA responses, suggesting that these CRK members function redundantly. We further showed that WRKY18, WRKY40 and WRKY60 transcription factors repress the expression of CRK5, and that CRK5 likely functions upstream of ABI2 in ABA signaling. These findings help in understanding the complex ABA signaling network. PMID:27406784

  15. Cysteine peroxidase activity in rat blood plasma | Razygraev ...

    African Journals Online (AJOL)

    The rat plasma found to be able to accelerate greatly the H2O2-dependent oxidation of cysteine. The activity was a characteristic of a protein fraction precipitated at 30—44% ammonium sulfate saturation, and the specific activity in protein fraction was significantly higher than in plasma. Cysteine:H2O2 oxidoreductase ...

  16. Cosmic global strings

    International Nuclear Information System (INIS)

    Sikivie, P.

    1991-01-01

    The topics are: global strings; the gravitational field of a straight global string; how do global strings behave?; the axion cosmological energy density; computer simulations of the motion and decay of global strings; electromagnetic radiation from the conversion of Nambu-Goldstone bosons in astrophysical magnetic fields. (orig.)

  17. Evidence for string substructure

    International Nuclear Information System (INIS)

    Bergman, O.

    1996-06-01

    The author argues that the behavior of string theory at high temperature and high longitudinal boosts, combined with the emergence of p-branes as necessary ingredients in various string dualities, point to a possible reformulation of strings, as well as p-branes, as composites of bits. He reviews the string-bit models, and suggests generalizations to incorporate p-branes

  18. STRING v9.1

    DEFF Research Database (Denmark)

    Franceschini, A.; Simonovic, M.; Roth, A.

    2013-01-01

    for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction...... data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein...... networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring...

  19. Heterologous expression of Hordeum vulgare cysteine protease in yeast

    DEFF Research Database (Denmark)

    Rosenkilde, Anne Lind; Dionisio, Giuseppe; Holm, Preben B

    Cysteine Proteases accounts for more than 90 % of the total proteolytic activity in the degradation of barley seed storage proteins during germination. Several Cysteine proteases have been identified in barley. One of the key enzymes, Hordeum vulgare endoprotease B2 (HvEPB2) was cloned with and w......Cysteine Proteases accounts for more than 90 % of the total proteolytic activity in the degradation of barley seed storage proteins during germination. Several Cysteine proteases have been identified in barley. One of the key enzymes, Hordeum vulgare endoprotease B2 (HvEPB2) was cloned...

  20. The Cysteine Protease–Cysteine Protease Inhibitor System Explored in Soybean Nodule Development

    Directory of Open Access Journals (Sweden)

    Marian Dorcas Quain

    2013-08-01

    Full Text Available Almost all protease families have been associated with plant development, particularly senescence, which is the final developmental stage of every organ before cell death. Proteolysis remobilizes and recycles nitrogen from senescent organs that is required, for example, seed development. Senescence-associated expression of proteases has recently been characterized using large-scale gene expression analysis seeking to identify and characterize senescence-related genes. Increasing activities of proteolytic enzymes, particularly cysteine proteases, are observed during the senescence of legume nodules, in which a symbiotic relationship between the host plant and bacteria (Rhizobia facilitate the fixation of atmospheric nitrogen. It is generally considered that cysteine proteases are compartmentalized to prevent uncontrolled proteolysis in nitrogen-fixing nodules. In addition, the activities of cysteine proteases are regulated by endogenous cysteine protease inhibitors called cystatins. These small proteins form reversible complexes with cysteine proteases, leading to inactivation. However, very little is currently known about how the cysteine protease-cysteine protease inhibitor (cystatin system is regulated during nodule development. Moreover, our current understanding of the expression and functions of proteases and protease inhibitors in nodules is fragmented. To address this issue, we have summarized the current knowledge and techniques used for studying proteases and their inhibitors including the application of “omics” tools, with a particular focus on changes in the cysteine protease-cystatin system during nodule development.

  1. Crystal Structure of Mammalian Cysteine dioxygenase: A Novel Mononuclear Iron Center for Cysteine Thiol Oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons,C.; Liu, Q.; Huang, Q.; Hao, Q.; Begley, T.; Karplus, P.; Stipanuk, M.

    2006-01-01

    Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteinesulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or to the taurine biosynthetic pathway. Cysteine dioxygenase is a member of the cupin superfamily of proteins. The crystal structure of recombinant rat cysteine dioxygenase has been determined to 1.5 Angstroms resolution, and these results confirm the canonical cupin {beta}-sandwich fold and the rare cysteinyl-tyrosine intramolecular crosslink (between Cys93 and Tyr157) seen in the recently reported murine cysteine dioxygenase structure. In contrast to the catalytically inactive mononuclear Ni(II) metallocenter present in the murine structure, crystallization of a catalytically competent preparation of rat cysteine dioxygenase revealed a novel tetrahedrally coordinated mononuclear iron center involving three histidines (His86, His88, and His140) and a water molecule. Attempts to acquire a structure with bound ligand using either co-crystallization or soaks with cysteine revealed the formation of a mixed disulfide involving Cys164 near the active site, which may explain previously observed substrate inhibition. This work provides a framework for understanding the molecular mechanisms involved in thiol dioxygenation and sets the stage for exploring the chemistry of both the novel mononuclear iron center and the catalytic role of the cysteinyl-tyrosine linkage.

  2. Reconstruction of Cysteine Biosynthesis Using Engineered Cysteine-Free and Methionine-Free Enzymes

    Science.gov (United States)

    Wang, Kendrick; Fujishima, Kosuke; Abe, Nozomi; Nakahigashi, Kenji; Endy, Drew; Rothschild, Lynn J.

    2016-01-01

    Ten of the proteinogenic amino acids can be generated abiotically while the remaining thirteen require biology for their synthesis. Paradoxically, the biosynthesis pathways observed in nature require enzymes that are made with the amino acids they produce. For example, Escherichia coli produces cysteine from serine via two enzymes that contain cysteine. Here, we substituted alternate amino acids for cysteine and also methionine, which is biosynthesized from cysteine, in serine acetyl transferase (CysE) and O-acetylserine sulfhydrylase (CysM). CysE function was rescued by cysteine-and-methionine-free enzymes and CysM function was rescued by cysteine-free enzymes. Structural modeling suggests that methionine stabilizes CysM and is present in the active site of CysM. Cysteine is not conserved among CysE and CysM protein orthologs, suggesting that cysteine is not functionally important for its own synthesis. Engineering biosynthetic enzymes that lack the amino acids being synthesized provides insights into the evolution of amino acid biosynthesis and pathways for bioengineering.

  3. L-Cysteine Metabolism and Fermentation in Microorganisms.

    Science.gov (United States)

    Takagi, Hiroshi; Ohtsu, Iwao

    L-Cysteine is an important amino acid both biologically and commercially. Although most amino acids are industrially produced by microbial fermentation, L-cysteine has been mainly produced by protein hydrolysis. Due to environmental and safety problems, synthetic or biotechnological products have been preferred in the market. Here, we reviewed L-cysteine metabolism, including biosynthesis, degradation, and transport, and biotechnological production (including both enzymatic and fermentation processes) of L-cysteine. The metabolic regulation of L-cysteine including novel sulfur metabolic pathways found in microorganisms is also discussed. Recent advancement in biochemical studies, genome sequencing, structural biology, and metabolome analysis has enabled us to use various approaches to achieve direct fermentation of L-cysteine from glucose. For example, worldwide companies began to supply L-cysteine and its derivatives produced by bacterial fermentation. These companies successfully optimized the original metabolism of their private strains. Basically, a combination of three factors should be required for improving L-cysteine fermentation: that is, (1) enhancing biosynthesis: overexpression of the altered cysE gene encoding feedback inhibition-insensitive L-serine O-acetyltransferase (SAT), (2) weakening degradation: knockout of the genes encoding L-cysteine desulfhydrases, and (3) exploiting export system: overexpression of the gene involved in L-cysteine transport. Moreover, we found that "thiosulfate" is much more effective sulfur source than commonly used "sulfate" for L-cysteine production in Escherichia coli, because thiosulfate is advantageous for saving consumption of NADPH and relating energy molecules.

  4. String driven inflation

    International Nuclear Information System (INIS)

    Turok, N.

    1987-11-01

    It is argued that, in fundamental string theories, as one traces the universe back in time a point is reached when the expansion rate is so fast that the rate of string creation due to quantum effects balances the dilution of the string density due to the expansion. One is therefore led into a phase of constant string density and an exponentially expanding universe. Fundamental strings therefore seem to lead naturally to inflation. 17 refs., 1 fig

  5. Hot String Soup

    OpenAIRE

    Lowe, D. A.; Thorlacius, L.

    1994-01-01

    Above the Hagedorn energy density closed fundamental strings form a long string phase. The dynamics of weakly interacting long strings is described by a simple Boltzmann equation which can be solved explicitly for equilibrium distributions. The average total number of long strings grows logarithmically with total energy in the microcanonical ensemble. This is consistent with calculations of the free single string density of states provided the thermodynamic limit is carefully defined. If the ...

  6. String-driven inflation

    International Nuclear Information System (INIS)

    Turok, N.

    1988-01-01

    It is argued that, in fundamental string theories, as one traces the universe back in time a point is reached when the expansion rate is so fast that the rate of string creation due to quantum effects balances the dilution of the string density due to the expansion. One is therefore led into a phase of constant string density and an exponentially expanding universe. Fundamental strings therefore seem to lead naturally to inflation

  7. The STRING database in 2017

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Morris, John H; Cook, Helen

    2017-01-01

    A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organi......A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number...... of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known...... pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer...

  8. MicroRNA-15b regulates reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression in human uterine leiomyoma.

    Science.gov (United States)

    Guan, Yichun; Guo, Lankai; Zukerberg, Lawrence; Rueda, Bo R; Styer, Aaron K

    2016-08-17

    Human uterine leiomyoma (fibroids; LYO) are the most common benign neoplasms in reproductive-aged women. Dysregulated extracellular matrix and irregular LYO reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression are thought to be mediated by aberrant microRNA (miR) expression. The relationship of miR-15b and RECK expression in LYO has not been studied. The expression levels of miR-15b and RECK were determined by quantitative RT-PCR, Western blot, and immunohistochemistry in cultures derived from commercial primary leiomyoma (cpLYO) and myometrial (cpMYO) cell lines and leiomyoma (pLYO) and myometrium (pMYO) tissue from surgical samples respectively. The relationship between miR-15b and RECK expression in cpLYO and pLYO (compared to their respective myometrial controls) was evaluated following transfection of cell cultures with either miR-15b mimic or inhibitor. Elevated levels of miR-15b were observed in cpLYO (2.82-fold; p = 0.04) and pLYO cell (1.30-fold; p = 0.0001) cultures respectively compared to corresponding MYO cell controls. Following transfection with miR-15b mimic, cpLYO cells (0.62-fold; p < 0.0001) and pLYO cells (0.68-fold; p < 0.0001) demonstrated reduced RECK protein expression. Following transfection with miR-15b inhibitor, cpLYO cells (1.20-fold; p < 0.0001) and pLYO cells (1.31-fold; p = 0.0007) demonstrated elevated RECK protein expression. RECK protein expression was reduced in pLYO tissues (0.73-fold; p < 0.0001) and pLYO (0.47-fold; p = 0.047) cells when compared to the corresponding MYO tissue controls. Our findings suggest that miR-15b negatively regulates RECK expression in LYO, and increased miR-15b and decreased RECK expression may contribute to the pathobiology of LYO. The functional significance of miR-15b and RECK expression warrants further investigation as potential therapeutic targets for the treatment of human LYO.

  9. S-nitrosylation of TRIM72 at cysteine 144 is critical for protection against oxidation-induced protein degradation and cell death.

    Science.gov (United States)

    Kohr, Mark J; Evangelista, Alicia M; Ferlito, Marcella; Steenbergen, Charles; Murphy, Elizabeth

    2014-04-01

    Oxidative stress and membrane damage following myocardial ischemia/reperfusion injury are important contributors to cardiomyocyte death and the loss of myocardial function. Our previous study identified cysteine 144 (C144) of tripartite motif-containing protein 72 (TRIM72) as a potential site for S-nitrosylation (SNO). TRIM72 is a cardioprotective membrane repair protein that can be both activated and targeted for degradation by different oxidative modifications. Consistent with the potential regulation of TRIM72 by various oxidative modifications, we found that SNO levels increased at C144 of TRIM72 with ischemic preconditioning. Therefore, to investigate the role of C144 in the regulation of TRIM72 function, we mutated C144 of TRIM72 to a serine residue (TRIM72(C144S)), and expressed either TRIM72(WT) or TRIM72(C144S) in HEK-293 cells, which lack endogenous TRIM72, in order to examine the effect of this mutation on the functional stability of TRIM72 and on cell survival. We hypothesized that SNO of TRIM72 stabilizes the protein, thus allowing for membrane repair and enhanced cell survival. Upon treatment with hydrogen peroxide (H2O2), we found that TRIM72(WT) levels were decreased, but not TRIM72(C144S) and this correlated with increased H2O2-induced cell death in TRIM72(WT) cells. Additionally, we found that treatment with the cardioprotective S-nitrosylating agent S-nitrosoglutathione (GSNO), was able to preserve TRIM72(WT) protein levels and enhance TRIM72(WT)-mediated cell survival, but had no effect on TRIM72(C144S) levels. Consistent with our hypothesis, GSNO was also found to increase SNO levels and inhibit H2O2-induced irreversible oxidation for TRIM72(WT) without affecting TRIM72(C144S). In further support of our hypothesis, GSNO blocked the ischemia/reperfusion-induced decrease in TRIM72 levels and reduced infarct size in a Langendorff-perfused heart model. The results of these studies have important implications for cardioprotection and suggest that

  10. The heterotic string

    International Nuclear Information System (INIS)

    Gross, D.J.

    1986-01-01

    Traditional string theories, either bosonic or supersymmetric, came in two varieties, closed string theories and open string theories. Closed string are neutral objects which describe at low energies gravity or supergravity. Open strings have geometrically invariant ends to which charge can be attached, thereby obtaining, in addition to gravity, Yang-Mills gauge interactions. Recently a new kind of string theory was discovered--the heterotic string, which is a chiral hybrid of the closed superstring and the closed bosonic string, and which produces by an internal dynamical mechanism gauge interactions of a totally specified kind. Although this theory is found in an attempt to produce a superstring theory which would yield a low energy E/sub 8/xE/sub 8/ supersymmetric, anomaly free, gauge theory, as suggested by the anomaly cancellation mechanism of Green and Schwarz, it fits naturally into the general framework of consistent string theories

  11. Overexpression of an Arabidopsis cysteine-rich receptor-like protein kinase, CRK5, enhances abscisic acid sensitivity and confers drought tolerance.

    Science.gov (United States)

    Lu, Kai; Liang, Shan; Wu, Zhen; Bi, Chao; Yu, Yong-Tao; Wang, Xiao-Fang; Zhang, Da-Peng

    2016-09-01

    Receptor-like kinases (RLKs) have been reported to regulate many developmental and defense process, but only a few members have been functionally characterized. In the present study, our observations suggest that one of the RLKs, a membrane-localized cysteine-rich receptor-like protein kinase, CRK5, is involved in abscisic acid (ABA) signaling in Arabidopsis thaliana Overexpression of CRK5 increases ABA sensitivity in ABA-induced early seedling growth arrest and promotion of stomatal closure and inhibition of stomatal opening. Interestingly, and importantly, overexpression of CRK5 enhances plant drought tolerance without affecting plant growth at the mature stages and plant productivity. Transgenic lines overexpressing a mutated form of CRK5, CRK5 (K372E) with the change of the 372nd conserved amino acid residue from lysine to glutamic acid in its kinase domain, result in wild-type ABA and drought responses, supporting the role of CRK5 in ABA signaling. The loss-of-function mutation of the CRK5 gene does not affect the ABA response, while overexpression of two homologs of CRK5, CRK4 and CRK19, confers ABA responses, suggesting that these CRK members function redundantly. We further showed that WRKY18, WRKY40 and WRKY60 transcription factors repress the expression of CRK5, and that CRK5 likely functions upstream of ABI2 in ABA signaling. These findings help in understanding the complex ABA signaling network. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  12. Relativistic classical strings. II

    International Nuclear Information System (INIS)

    Galvao, C.A.P.

    1985-01-01

    The interactions of strings with electromagnetic and gravitational fields are extensively discussed. Some concepts of differential geometry are reviewed. Strings in Kaluza-Klein manifolds are studied. (L.C.) [pt

  13. Inflationary string theory?

    Indian Academy of Sciences (India)

    strongly motivate a detailed search for inflation within string theory, although it has ... between string theory and observations provides a strong incentive for ..... sonably be expected to arise for any system having very many degrees of freedom.

  14. Strings in the Sun?

    International Nuclear Information System (INIS)

    Chudnovsky, E.; Vilenkin, A.

    1988-01-01

    If light superconducting strings were formed in the early Universe, then it is very likely that now they exist in abundance in the interstellar plasma and in stars. The dynamics of such strings can be dominated by friction, so that they are ''frozen'' into the plasma. Turbulence of the plasma twists and stretches the strings, forming a stochastic string network. Such networks must generate particles and magnetic fields, and may play an important role in the physics of stars and of the Galaxy

  15. Why string theory?

    CERN Document Server

    Conlon, Joseph

    2016-01-01

    Is string theory a fraud or one of the great scientific advances? Why do so many physicists work on string theory if it cannot be tested? This book provides insight into why such a theory, with little direct experimental support, plays such a prominent role in theoretical physics. The book gives a modern and accurate account of string theory and science, explaining what string theory is, why it is regarded as so promising, and why it is hard to test.

  16. Site-specific O-Glycosylation on the MUC2 Mucin Protein Inhibits Cleavage by the Porphyromonas gingivalis Secreted Cysteine Protease (RgpB)

    DEFF Research Database (Denmark)

    van der Post, Sjoerd; Subramani, Durai B; Bäckström, Malin

    2013-01-01

    that are protease-resistant and has cysteine-rich N and C termini responsible for polymerization. Culture supernatants of Porphyromonas gingivalis, a bacterium that secretes proteases responsible for periodontitis, cleaved the MUC2 C-terminal region, whereas the N-terminal region was unaffected. The active enzyme...

  17. Introduction to string theory and string compactifications

    International Nuclear Information System (INIS)

    GarcIa-Compean, Hugo

    2005-01-01

    Basics of some topics on perturbative and non-perturbative string theory are reviewed. After a mathematical survey of the Standard Model of particle physics and GUTs, the bosonic string kinematics for the free case and with interaction is described. The effective action of the bosonic string and the spectrum is also discussed. T-duality in closed and open strings and the definition of D-brane are surveyed. Five perturbative superstring theories and their spectra is briefly outlined. Calabi-Yau three-fold compactifications of heterotic strings and their relation to some four-dimensional physics are given. Finally, non-perturbative issues like S-duality, M-theory and F-theory are also reviewed

  18. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz

    2013-02-28

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  19. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz; Vá zquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

    2013-01-01

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  20. Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

    Directory of Open Access Journals (Sweden)

    Uldaeliz Trujillo

    Full Text Available The polyunsaturated fatty acid (PUFA synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect and in structural stabilization of the multidomain protein (synergistic effect. While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of

  1. Random surfaces and strings

    International Nuclear Information System (INIS)

    Ambjoern, J.

    1987-08-01

    The theory of strings is the theory of random surfaces. I review the present attempts to regularize the world sheet of the string by triangulation. The corresponding statistical theory of triangulated random surfaces has a surprising rich structure, but the connection to conventional string theory seems non-trivial. (orig.)

  2. Dynamics of Carroll strings

    Energy Technology Data Exchange (ETDEWEB)

    Cardona, Biel [Departament d’Estructura i Constituents de la Matèriaand Institut de Ciències del Cosmos (ICCUB) Facultat de Física, Universitat de Barcelona,Diagonal 647, E-08028 Barcelona, Catalonia (Spain); Gomis, Joaquim [Departament d’Estructura i Constituents de la Matèriaand Institut de Ciències del Cosmos (ICCUB) Facultat de Física, Universitat de Barcelona,Diagonal 647, E-08028 Barcelona, Catalonia (Spain); Department of Physics, Faculty of Science, Chulalongkorn University,Bangkok 10330 (Thailand); Pons, Josep M. [Departament d’Estructura i Constituents de la Matèriaand Institut de Ciències del Cosmos (ICCUB) Facultat de Física, Universitat de Barcelona,Diagonal 647, E-08028 Barcelona, Catalonia (Spain)

    2016-07-11

    We construct the canonical action of a Carroll string doing the Carroll limit of a canonical relativistic string. We also study the Killing symmetries of the Carroll string, which close under an infinite dimensional algebra. The tensionless limit and the Carroll p-brane action are also discussed.

  3. String Math 2017

    CERN Document Server

    The series of String-Math conferences has developed into a central event on the interface between mathematics and physics related to string theory, quantum field theory and neighboring subjects. The conference will take place from July 24-28 in the main building of Hamburg university. The String-Math conference is organised by the University of Hamburg jointly with DESY Hamburg.

  4. Cosmic strings and inflation

    International Nuclear Information System (INIS)

    Vishniac, E.T.

    1987-01-01

    We examine the compatibility of inflation with the cosmic string theory for galaxy formation. There is a general conflict between having sufficient string tension to effect galaxy formation, and reheating after inflation to a high enough temperature that strings may form in a thermal phase transition. To escape this conflict, we propose a class of models where the inflation is coupled to the string-producing field. The strings are formed late in inflation as the inflaton rolls towards its zero-temperature value. A large subset of these models have a novel large-scale distribution of galaxies that is fractal, displays biasing without dynamics or feedback mechanisms, and contains voids. (orig.)

  5. Minimal open strings

    International Nuclear Information System (INIS)

    Hosomichi, Kazuo

    2008-01-01

    We study FZZT-branes and open string amplitudes in (p, q) minimal string theory. We focus on the simplest boundary changing operators in two-matrix models, and identify the corresponding operators in worldsheet theory through the comparison of amplitudes. Along the way, we find a novel linear relation among FZZT boundary states in minimal string theory. We also show that the boundary ground ring is realized on physical open string operators in a very simple manner, and discuss its use for perturbative computation of higher open string amplitudes.

  6. Metal binding proteins and antifreeze proteins in the beetle Tenebrio molitor: a study on possible competition for the semi-essential amino acid cysteine

    OpenAIRE

    Pedersen, Sindre Andre

    2007-01-01

    In their natural environment animals are confronted by both physical (eg. extreme temperatures, desiccation) and chemical stressors (e.g. pollutants). Stress may be defined as a condition that is evoked in an organism by one or more environmental factors that bring the organism near to or over the edges of its ecological niche (van Straalen 2003). Various defence systems exist to cope with different forms of stress and restore homeostasis. Often, production of various proteins or enzymes are ...

  7. Cysteine Biosynthesis Controls Serratia marcescens Phospholipase Activity.

    Science.gov (United States)

    Anderson, Mark T; Mitchell, Lindsay A; Mobley, Harry L T

    2017-08-15

    Serratia marcescens causes health care-associated opportunistic infections that can be difficult to treat due to a high incidence of antibiotic resistance. One of the many secreted proteins of S. marcescens is the PhlA phospholipase enzyme. Genes involved in the production and secretion of PhlA were identified by screening a transposon insertion library for phospholipase-deficient mutants on phosphatidylcholine-containing medium. Mutations were identified in four genes ( cyaA , crp , fliJ , and fliP ) that are involved in the flagellum-dependent PhlA secretion pathway. An additional phospholipase-deficient isolate harbored a transposon insertion in the cysE gene encoding a predicted serine O -acetyltransferase required for cysteine biosynthesis. The cysE requirement for extracellular phospholipase activity was confirmed using a fluorogenic phospholipase substrate. Phospholipase activity was restored to the cysE mutant by the addition of exogenous l-cysteine or O -acetylserine to the culture medium and by genetic complementation. Additionally, phlA transcript levels were decreased 6-fold in bacteria lacking cysE and were restored with added cysteine, indicating a role for cysteine-dependent transcriptional regulation of S. marcescens phospholipase activity. S. marcescens cysE mutants also exhibited a defect in swarming motility that was correlated with reduced levels of flhD and fliA flagellar regulator gene transcription. Together, these findings suggest a model in which cysteine is required for the regulation of both extracellular phospholipase activity and surface motility in S. marcescens IMPORTANCE Serratia marcescens is known to secrete multiple extracellular enzymes, but PhlA is unusual in that this protein is thought to be exported by the flagellar transport apparatus. In this study, we demonstrate that both extracellular phospholipase activity and flagellar function are dependent on the cysteine biosynthesis pathway. Furthermore, a disruption of cysteine

  8. Lysosomal cysteine peptidases - Molecules signaling tumor cell death and survival.

    Science.gov (United States)

    Pišlar, Anja; Perišić Nanut, Milica; Kos, Janko

    2015-12-01

    Lysosomal cysteine peptidases - cysteine cathepsins - are general intracellular protein-degrading enzymes that control also a variety of specific physiological processes. They can trigger irreversible events leading to signal transduction and activation of signaling pathways, resulting in cell survival and proliferation or cell death. In cancer cells, lysosomal cysteine peptidases are involved in multiple processes during malignant progression. Their translocation from the endosomal/lysosomal pathway to nucleus, cytoplasm, plasma membrane and extracellular space enables the activation and remodeling of a variety of tumor promoting proteins. Thus, lysosomal cysteine peptidases interfere with cytokine/chemokine signaling, regulate cell adhesion and migration and endocytosis, are involved in the antitumor immune response and apoptosis, and promote cell invasion, angiogenesis and metastasis. Further, lysosomal cysteine peptidases modify growth factors and receptors involved in tyrosine kinase dependent pathways such as MAPK, Akt and JNK, thus representing key signaling tools for the activation of tumor cell growth and proliferation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Closed Strings From Nothing

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, Albion

    2001-07-25

    We study the physics of open strings in bosonic and type II string theories in the presence of unstable D-branes. When the potential energy of the open string tachyon is at its minimum, Sen has argued that only closed strings remain in the perturbative spectrum. We explore the scenario of Yi and of Bergman, Hori and Yi, who argue that the open string degrees of freedom are strongly coupled and disappear through confinement. We discuss arguments using open string field theory and worldsheet boundary RG flows, which seem to indicate otherwise. We then describe a solitonic excitation of the open string tachyon and gauge field with the charge and tension of a fundamental closed string. This requires a double scaling limit where the tachyon is taken to its minimal value and the electric field is taken to its maximum value. The resulting flux tube has an unconstrained spatial profile; and for large fundamental string charge, it appears to have light, weakly coupled open strings living in the core. We argue that the flux tube acquires a size or order {alpha}' through sigma model and string coupling effects; and we argue that confinement effects make the light degrees of freedom heavy and strongly interacting.

  10. Closed Strings From Nothing

    International Nuclear Information System (INIS)

    Lawrence, Albion

    2001-01-01

    We study the physics of open strings in bosonic and type II string theories in the presence of unstable D-branes. When the potential energy of the open string tachyon is at its minimum, Sen has argued that only closed strings remain in the perturbative spectrum. We explore the scenario of Yi and of Bergman, Hori and Yi, who argue that the open string degrees of freedom are strongly coupled and disappear through confinement. We discuss arguments using open string field theory and worldsheet boundary RG flows, which seem to indicate otherwise. We then describe a solitonic excitation of the open string tachyon and gauge field with the charge and tension of a fundamental closed string. This requires a double scaling limit where the tachyon is taken to its minimal value and the electric field is taken to its maximum value. The resulting flux tube has an unconstrained spatial profile; and for large fundamental string charge, it appears to have light, weakly coupled open strings living in the core. We argue that the flux tube acquires a size or order α' through sigma model and string coupling effects; and we argue that confinement effects make the light degrees of freedom heavy and strongly interacting

  11. The arithmetic of strings

    International Nuclear Information System (INIS)

    Freund, P.G.O.

    1988-01-01

    According to the author nobody has succeeded as yet in extracting any new numbers from string theory. This paper discusses how if one cannot get new numbers from string theory, maybe one can get new strings out of number theory. Number theory is generally regarded as the purest form of mathematics. So how can it conceivably make contact with physics which aims at describing nature? The author discusses how the connecting link of these two disciplines is provided by the compact Riemann surfaces. These appear as world sheets of interacting strings. For instance, string-string scattering at the three-loop level involves the four external strings attaching themselves to a genus three compact surface

  12. π-Clamp-mediated cysteine conjugation

    Science.gov (United States)

    Zhang, Chi; Welborn, Matthew; Zhu, Tianyu; Yang, Nicole J.; Santos, Michael S.; van Voorhis, Troy; Pentelute, Bradley L.

    2016-02-01

    Site-selective functionalization of complex molecules is one of the most significant challenges in chemistry. Typically, protecting groups or catalysts must be used to enable the selective modification of one site among many that are similarly reactive, and general strategies that selectively tune the local chemical environment around a target site are rare. Here, we show a four-amino-acid sequence (Phe-Cys-Pro-Phe), which we call the ‘π-clamp’, that tunes the reactivity of its cysteine thiol for site-selective conjugation with perfluoroaromatic reagents. We use the π-clamp to selectively modify one cysteine site in proteins containing multiple endogenous cysteine residues. These examples include antibodies and cysteine-based enzymes that would be difficult to modify selectively using standard cysteine-based methods. Antibodies modified using the π-clamp retained binding affinity to their targets, enabling the synthesis of site-specific antibody-drug conjugates for selective killing of HER2-positive breast cancer cells. The π-clamp is an unexpected approach to mediate site-selective chemistry and provides new avenues to modify biomolecules for research and therapeutics.

  13. BRST invariant mixed string vertex for the bosonic string

    International Nuclear Information System (INIS)

    Clarizia, A.; Pezzella, F.

    1987-09-01

    We construct a BRST invariant (N+M)-string vertex including both open and closed string states. When we saturate it with N open string and M closed string physical states it reproduces their corresponding scattering amplitude. As a particular case we obtain BRST invariant vertex for the open-closed string transition. (orig.)

  14. Open-closed string correspondence in open string field theory

    International Nuclear Information System (INIS)

    Baumgartl, M.; Sachs, I.

    2008-01-01

    We address the problem of describing different closed string backgrounds in background independent open string field theory: A shift in the closed string background corresponds to a collective excitation of open strings. As an illustration we apply the formalism to the case where the closed string background is a group manifold. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

  15. Strings, texture, and inflation

    International Nuclear Information System (INIS)

    Hodges, H.M.; Primack, J.R.

    1991-01-01

    We examine mechanisms, several of which are proposed here, to generate structure formation, or to just add large-scale features, through either gauged or global cosmic strings or global texture, within the framework of inflation. We first explore the possibility that strings or texture form if there is no coupling between the topological theory and the inflaton or spacetime curvature, via (1) quantum creation, and (2) a sufficiently high reheat temperature. In addition, we examine the prospects for the inflaton field itself to generate strings or texture. Then, models with the string/texture field coupled to the curvature, and an equivalent model with coupling to the inflaton field, are considered in detail. The requirement that inflationary density fluctuations are not so large as to conflict with observations leads to a number of constraints on model parameters. We find that strings of relevance for structure formation can form in the absence of coupling to the inflaton or curvature through the process of quantum creation, but only if the strings are strongly type I, or if they are global strings. If formed after reheating, naturalness suggests that gauged cosmic strings correspond to a type-I superconductor. Similarly, gauged strings formed during inflation via conformal coupling ξ=1/6 to the spacetime curvature (in a model suggested by Yokoyama in order to evade the millisecond pulsar constraint on cosmic strings) are expected to be strongly type I

  16. Barley (Hordeum vulgare L.) cysteine proteases: heterologous expression, purification and characterization

    DEFF Research Database (Denmark)

    Rosenkilde, Anne Lind; Dionisio, Giuseppe; Holm, Preben Bach

    2011-01-01

    During germination of barley seeds, mobilization of protein is essential and cysteine proteases accounts for more than 90 % of the total proteolytic activity in the degradation of barley seed storage proteins. Cysteine proteases exist as pro-enzyme and is activated through reduction of the active...... site cysteines and by removal of the pro-domain. The complement of cysteine proteases is comprehensive and for detailed studies of the individual components of this complement, a fast and efficient eukaryotic expression platform is highly desirable. A cDNA clone of the barley key cysteine endoprotease...

  17. Electrostatic influence of local cysteine environments on disulfide exchange kinetics.

    Science.gov (United States)

    Snyder, G H; Cennerazzo, M J; Karalis, A J; Field, D

    1981-11-10

    The ionic strength dependence of the bimolecular rate constant for reaction of the negative disulfide 5,5'-dithiobis (2-nitrobenzoic acid) with cysteines in fragments of naturally occurring proteins was determined by stopped-flow spectroscopy. The Debye-Hückel relationship was applied to determine the effective charge at the cysteine and thereby determine the extent to which nearby neighbors in the primary sequence influence the kinetics. Corrections for the secondary salt effect on cysteine pKs were determined by direct spectrometric pH titration of sulfhydryl groups or by observation of the ionic strength dependence of kinetics of cysteine reaction with the neutral disulfide 2,2'-dithiodipyridine. Quantitative expressions was verified by model studies with N-acetyl-cystein. At ionic strengths equal to or greater than 20 mM, the net charge at the polypeptide cysteine site is the sum of the single negative charge of the thiolate anion and the charges of the amino acids immediately preceding and following the cysteine in the primary sequence. At lower ionic strengths, more distant residues influence kinetics. At pH 7.0, 23 degree C, and an ionic strength of 20 mM, rate constants for reaction of the negative disulfide with a cysteine having two positive neighbors, one positive and one neutral neighbor, or two neutral neighbors are 132000, 3350, and 367 s-1 M-1, respectively. This corresponds to a contribution to the activation energy of 0.65- 1.1 kcal/mol per ion pair involved in collision between the cysteine and disulfide regions. The results permit the estimation that cysteine local environments may provide a means of achieving a 10(6)-fold range in rate constants in disulfide exchange reactions in random-coil proteins. This range may prove useful in developing strategies for directing disulfide pairing in synthetic proteins.

  18. Topics in string theory

    International Nuclear Information System (INIS)

    Neveu, A.

    1986-01-01

    There exist several string models. In the first lecture, the simplest one, the open bosonic string, which turns out to live most naturally in 26 dimensions will be described in some detail. In the second lecture, the closed bosonic strings, and the open and closed 10-dimensional strings (superstrings) are reviewed. In the third lecture, various compactification schemes which have been proposed to deal with the extra space dimensions, from 4 to 10 or 26 are dealt with; in particular, the Frenkel-Kac construction which builds non-Abelian internal symmetry groups out of the compactified dimensions, and the resulting heterotic string are described. Finally, in the fourth lecture, the important problem of the second quantization of string theories, and of the underlying gauge invariance which is responsible for the possibility of dealing, in a consistent fashion, with interacting high-spin states without negative metric is addressed. 41 references, 8 figures

  19. Strings and quantum gravity

    International Nuclear Information System (INIS)

    Vega, H.J. de

    1990-01-01

    One of the main challenges in theoretical physics today is the unification of all interactions including gravity. At present, string theories appear as the most promising candidates to achieve such a unification. However, gravity has not completely been incorporated in string theory, many technical and conceptual problems remain and a full quantum theory of gravity is still non-existent. Our aim is to properly understand strings in the context of quantum gravity. Attempts towards this are reviewed. (author)

  20. 6d string chains

    Science.gov (United States)

    Gadde, Abhijit; Haghighat, Babak; Kim, Joonho; Kim, Seok; Lockhart, Guglielmo; Vafa, Cumrun

    2018-02-01

    We consider bound states of strings which arise in 6d (1,0) SCFTs that are realized in F-theory in terms of linear chains of spheres with negative self-intersections 1,2, and 4. These include the strings associated to N small E 8 instantons, as well as the ones associated to M5 branes probing A and D type singularities in M-theory or D5 branes probing ADE singularities in Type IIB string theory. We find that these bound states of strings admit (0,4) supersymmetric quiver descriptions and show how one can compute their elliptic genera.

  1. QCD and string theories

    International Nuclear Information System (INIS)

    Cohen-Tannoudji, G.

    1990-01-01

    This paper is devoted to a review of the connections between quantumchromodynamics (QCD) and string theories. One reviews the phenomenological models leading to string pictures in non perturbative QCD and the string effects, related to soft gluon coherence, which arise in perturbative QCD. One tries to build a string theory which goes to QCD at the zero slope limit. A specific model, based on superstring theories is shown to agree with QCD four point amplitudes at the Born approximation and with one loop corrections. One shows how this approach can provide a theoretical framework to account for the phenomenological property of parton-hadron duality

  2. Thermodynamics of quantum strings

    CERN Document Server

    Morgan, M J

    1994-01-01

    A statistical mechanical analysis of an ideal gas of non-relativistic quantum strings is presented, in which the thermodynamic properties of the string gas are calculated from a canonical partition function. This toy model enables students to gain insight into the thermodynamics of a simple 'quantum field' theory, and provides a useful pedagogical introduction to the more complicated relativistic string theories. A review is also given of the thermodynamics of the open bosonic string gas and the type I (open) superstring gas. (author)

  3. Interpolating string field theories

    International Nuclear Information System (INIS)

    Zwiebach, B.

    1992-01-01

    This paper reports that a minimal area problem imposing different length conditions on open and closed curves is shown to define a one-parameter family of covariant open-closed quantum string field theories. These interpolate from a recently proposed factorizable open-closed theory up to an extended version of Witten's open string field theory capable of incorporating on shell closed strings. The string diagrams of the latter define a new decomposition of the moduli spaces of Riemann surfaces with punctures and boundaries based on quadratic differentials with both first order and second order poles

  4. Heterotic cosmic strings

    International Nuclear Information System (INIS)

    Becker, Katrin; Becker, Melanie; Krause, Axel

    2006-01-01

    We show that all three conditions for the cosmological relevance of heterotic cosmic strings, the right tension, stability and a production mechanism at the end of inflation, can be met in the strongly coupled M-theory regime. Whereas cosmic strings generated from weakly coupled heterotic strings have the well-known problems posed by Witten in 1985, we show that strings arising from M5-branes wrapped around 4-cycles (divisors) of a Calabi-Yau in heterotic M-theory compactifications solve these problems in an elegant fashion

  5. Stretching cosmic strings

    International Nuclear Information System (INIS)

    Turok, N.; Bhattacharjee, P.

    1984-01-01

    The evolution of a network of strings produced at a grand-unification phase transition in an expanding universe is discussed, with particular reference to the processes of energy exchange between the strings and the rest of the universe. This is supported by numerical calculations simulating the behavior of strings in an expanding universe. It is found that in order that the energy density of the strings does not come to dominate the total energy density there must be an efficient mechanism for energy loss: the only plausible one being the production of closed loops and their subsequent decay via gravitational radiation

  6. QCD and hadronic strings

    International Nuclear Information System (INIS)

    Cohen-Tannoudji, G.

    1989-01-01

    This series of lectures is devoted to review ot he connections between QCD and string theories. One reviews the phenomenological models leading to string pictures in non perturbative QCD and the string effects, related to soft gluon coherence, which arise in perturbative QCD. One tries to build a string theory which goes to QCD at the zero slope limit. A specific model, based on superstring theories is shown to agree with QCD four point amplitudes at the Born approximation and with one loop corrections. One shows how this approach can provide a theoretical framework to account for the phenomenological property of parton-hadron duality.(author)

  7. Semilocal and electroweak strings

    NARCIS (Netherlands)

    Achucarro, A; Vachaspati, T

    We review a class of non-topological defects in the standard electroweak model, and their implications. Starting with the semilocal string, which provides a counterexample to many well-known properties of topological vortices, we discuss electroweak strings and their stability with and without

  8. Disordered chaotic strings

    DEFF Research Database (Denmark)

    Schäfer, Mirko; Greiner, Martin

    2011-01-01

    to chaotic strings. Inhomogeneous coupling weights as well as small-world perturbations of the ring-network structure are discussed. It is found that certain combinations of coupling and network disorder preserve the empirical relationship between chaotic strings and the weak and strong sector...

  9. A rotating string

    International Nuclear Information System (INIS)

    Jensen, B.

    1993-06-01

    The author presents a global solution of Einstein's equations which represents a rotating cosmic string with a finite coreradius. The importance of pressure for the generation of closed timelike curves outside the coreregion of such strings is clearly displayed in this model due to the simplicity of the source. 10 refs

  10. Derandomizing from random strings

    NARCIS (Netherlands)

    Buhrman, H.; Fortnow, L.; Koucký, M.; Loff, B.

    2010-01-01

    In this paper we show that BPP is truth-table reducible to the set of Kolmogorov random strings R(K). It was previously known that PSPACE, and hence BPP is Turing-reducible to R(K). The earlier proof relied on the adaptivity of the Turing-reduction to find a Kolmogorov-random string of polynomial

  11. Unification of string dualities

    International Nuclear Information System (INIS)

    Sen, A.

    1997-01-01

    We argue that all conjectured dualities involving various string, M- and F-theory compactifications can be 'derived' from the conjectured duality between type I and SO(32) heterotic string theory, T-dualities and the definition of M-and F-theories. (orig.)

  12. Optimal Packed String Matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2011-01-01

    In the packed string matching problem, each machine word accommodates – characters, thus an n-character text occupies n/– memory words. We extend the Crochemore-Perrin constantspace O(n)-time string matching algorithm to run in optimal O(n/–) time and even in real-time, achieving a factor – speed...

  13. Introduction to string theory

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit

    2002-01-01

    I will present a simple and non-technical overview of string theory, aimed for non-experts who like to get some idea what string theory is about. Besides introductory material, I intend to cover also some of the more recent developments.

  14. StringForce

    DEFF Research Database (Denmark)

    Barendregt, Wolmet; Börjesson, Peter; Eriksson, Eva

    2017-01-01

    In this paper, we present the forced collaborative interaction game StringForce. StringForce is developed for a special education context to support training of collaboration skills, using readily available technologies and avoiding the creation of a "mobile bubble". In order to play String......Force two or four physically collocated tablets are required. These tablets are connected to form one large shared game area. The game can only be played by collaborating. StringForce extends previous work, both technologically and regarding social-emotional training. We believe String......Force to be an interesting demo for the IDC community, as it intertwines several relevant research fields, such as mobile interaction and collaborative gaming in the special education context....

  15. String-Math 2015

    CERN Document Server

    2015-01-01

    Welcome to String-Math 2015 at Sanya. The conference will be opened in December 31, 2015- January 4, 2016. String theory plays a central role in theoretical physics as a candidate for the quantum theory unifying gravity with other interactions. It has profound connections with broad branches of modern mathematics ever since the birth. In the last decades, the prosperous interaction, built upon the joint efforts from both mathematicians and physicists, has given rise to marvelous deep results in supersymmetric gauge theory, topological string, M-theory and duality on the physics side as well as in algebraic geometry, differential geometry, algebraic topology, representation theory and number theory on the mathematics side. The interplay is two-fold. The mathematics has provided powerful tools to fulfill the physical interconnection of ideas and clarify physical structures to understand the nature of string theory. On the other hand, ideas from string theory and quantum field theory have been a source of sign...

  16. Open string model building

    International Nuclear Information System (INIS)

    Ishibashi, Nobuyuki; Onogi, Tetsuya

    1989-01-01

    Consistency conditions of open string theories, which can be a powerful tool in open string model building, are proposed. By making use of these conditions and assuming a simple prescription for the Chan-Paton factors, open string theories in several backgrounds are studied. We show that 1. there exist a large number of consistent bosonic open string theories on Z 2 orbifolds, 2. SO(32) type I superstring is the unique consistent model among fermionic string theories on the ten-dimensional flat Minkowski space, and 3. with our prescription for the Chan-Paton factors, there exist no consistent open superstring theories on (six-dimensional Minkowski space-time) x (Z 2 orbifold). (orig.)

  17. Rethinking Cysteine Protective Groups: S-Alkylsulfonyl-l-Cysteines for Chemoselective Disulfide Formation.

    Science.gov (United States)

    Schäfer, Olga; Huesmann, David; Muhl, Christian; Barz, Matthias

    2016-12-12

    The ability to reversibly cross-link proteins and peptides grants the amino acid cysteine its unique role in nature as well as in peptide chemistry. We report a novel class of S-alkylsulfonyl-l-cysteines and N-carboxy anhydrides (NCA) thereof for peptide synthesis. The S-alkylsulfonyl group is stable against amines and thus enables its use under Fmoc chemistry conditions and the controlled polymerization of the corresponding NCAs yielding well-defined homo- as well as block co-polymers. Yet, thiols react immediately with the S-alkylsulfonyl group forming asymmetric disulfides. Therefore, we introduce the first reactive cysteine derivative for efficient and chemoselective disulfide formation in synthetic polypeptides, thus bypassing additional protective group cleavage steps. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. A reduced covariant string model for the extrinsic string

    International Nuclear Information System (INIS)

    Botelho, L.C.L.

    1989-01-01

    It is studied a reduced covariant string model for the extrinsic string by using Polyakov's path integral formalism. On the basis of this reduced model it is suggested that the extrinsic string has its critical dimension given by 13. Additionally, it is calculated in a simple way Poliakov's renormalization group law for the string rigidity coupling constants. (A.C.A.S.) [pt

  19. Maximum margin classifier working in a set of strings.

    Science.gov (United States)

    Koyano, Hitoshi; Hayashida, Morihiro; Akutsu, Tatsuya

    2016-03-01

    Numbers and numerical vectors account for a large portion of data. However, recently, the amount of string data generated has increased dramatically. Consequently, classifying string data is a common problem in many fields. The most widely used approach to this problem is to convert strings into numerical vectors using string kernels and subsequently apply a support vector machine that works in a numerical vector space. However, this non-one-to-one conversion involves a loss of information and makes it impossible to evaluate, using probability theory, the generalization error of a learning machine, considering that the given data to train and test the machine are strings generated according to probability laws. In this study, we approach this classification problem by constructing a classifier that works in a set of strings. To evaluate the generalization error of such a classifier theoretically, probability theory for strings is required. Therefore, we first extend a limit theorem for a consensus sequence of strings demonstrated by one of the authors and co-workers in a previous study. Using the obtained result, we then demonstrate that our learning machine classifies strings in an asymptotically optimal manner. Furthermore, we demonstrate the usefulness of our machine in practical data analysis by applying it to predicting protein-protein interactions using amino acid sequences and classifying RNAs by the secondary structure using nucleotide sequences.

  20. Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles

    DEFF Research Database (Denmark)

    Serafimova, Iana M; Pufall, Miles A; Krishnan, Shyam

    2012-01-01

    Targeting noncatalytic cysteine residues with irreversible acrylamide-based inhibitors is a powerful approach for enhancing pharmacological potency and selectivity. Nevertheless, concerns about off-target modification motivate the development of reversible cysteine-targeting strategies. Here we...... of these electrophiles into a noncovalent kinase-recognition scaffold produced slowly dissociating, covalent inhibitors of the p90 ribosomal protein S6 kinase RSK2. A cocrystal structure revealed specific noncovalent interactions that stabilize the complex by positioning the electrophilic carbon near the targeted...

  1. String field theory

    International Nuclear Information System (INIS)

    Kaku, M.

    1987-01-01

    In this article, the authors summarize the rapid progress in constructing string field theory actions, such as the development of the covariant BRST theory. They also present the newer geometric formulation of string field theory, from which the BRST theory and the older light cone theory can be derived from first principles. This geometric formulation allows us to derive the complete field theory of strings from two geometric principles, in the same way that general relativity and Yang-Mills theory can be derived from two principles based on global and local symmetry. The geometric formalism therefore reduces string field theory to a problem of finding an invariant under a new local gauge group they call the universal string group (USG). Thus, string field theory is the gauge theory of the universal string group in much the same way that Yang-Mills theory is the gauge theory of SU(N). The geometric formulation places superstring theory on the same rigorous group theoretical level as general relativity and gauge theory

  2. Duality relation between charged elastic strings and superconducting cosmic strings

    International Nuclear Information System (INIS)

    Carter, B.

    1989-01-01

    The mechanical properties of macroscopic electromagnetically coupled string models in a flat or curved background are treated using a covariant formalism allowing the construction of a duality transformation that relates the category of uniform ''electric'' string models, constructed as the (nonconducting) charged generalisation of ordinary uncoupled (violin type) elastic strings, to a category of ''magnetic'' string models comprising recently discussed varieties of ''superconducting cosmic strings''. (orig.)

  3. Lattice gravity and strings

    International Nuclear Information System (INIS)

    Jevicki, A.; Ninomiya, M.

    1985-01-01

    We are concerned with applications of the simplicial discretization method (Regge calculus) to two-dimensional quantum gravity with emphasis on the physically relevant string model. Beginning with the discretization of gravity and matter we exhibit a discrete version of the conformal trace anomaly. Proceeding to the string problem we show how the direct approach of (finite difference) discretization based on Nambu action corresponds to unsatisfactory treatment of gravitational degrees. Based on the Regge approach we then propose a discretization corresponding to the Polyakov string. In this context we are led to a natural geometric version of the associated Liouville model and two-dimensional gravity. (orig.)

  4. Superconducting cosmic strings

    International Nuclear Information System (INIS)

    Chudnovsky, E.M.; Field, G.B.; Spergel, D.N.; Vilenkin, A.

    1986-01-01

    Superconducting loops of string formed in the early Universe, if they are relatively light, can be an important source of relativistic particles in the Galaxy. They can be observed as sources of synchrotron radiation at centimeter wavelengths. We propose a string model for two recently discovered radio sources, the ''thread'' in the galactic center and the source G357.7-0.1, and predict that the filaments in these sources should move at relativistic speeds. We also consider superheavy superconducting strings, and the possibility that they be observed as extragalactic radio sources

  5. Final Report: "Strings 2014"

    Energy Technology Data Exchange (ETDEWEB)

    Witten, Edward

    2015-10-21

    The Strings 2014 meeting was held at Princeton University June 23-27, 2014, co-sponsored by Princeton University and the Institute for Advanced Study. The goal of the meeting was to provide a stimulating and up-to-date overview of research in string theory and its relations to other areas of physics and mathematics, ranging from geometry to quantum field theory, condensed matter physics, and more. This brief report lists committee members and speakers but contains no scientific information. Note that the talks at Strings 2014 were videotaped and are available on the conference website: http://physics.princeton.edustrings2014/Talk_titles.shtml.

  6. A disintegrating cosmic string

    International Nuclear Information System (INIS)

    Griffiths, J B; Docherty, P

    2002-01-01

    We present a simple sandwich gravitational wave of the Robinson-Trautman family. This is interpreted as representing a shock wave with a spherical wavefront which propagates into a Minkowski background minus a wedge (i.e. the background contains a cosmic string). The deficit angle (the tension) of the string decreases through the gravitational wave, which then ceases. This leaves an expanding spherical region of Minkowski space behind it. The decay of the cosmic string over a finite interval of retarded time may be considered to generate the gravitational wave. (letter to the editor)

  7. Baryon string model

    International Nuclear Information System (INIS)

    Klimenko, S.V.; Kochin, V.N.; Plyushchaj, M.S.; Pron'ko, G.P.; Razumov, A.V.; Samarin, A.V.

    1985-01-01

    Partial solutions to classical equations of three-string motion are considered. Simplest solutions, when three-string center moving with high velocity, are co nsidered. Single-mode solutions are studied. Explicit form of their parametrization is obtained and three-string dynamics visualization is made. Means of graphic packet ''Atom'' were used for visualization. A set of processes for graphic representation of multiparametric functions is developed. Peculiarity of these processes is a wide class of functions, which are represented by parametric, coordinate and functional isolines

  8. Exceptional groups from open strings

    International Nuclear Information System (INIS)

    Gaberdiel, M.R.; Zwiebach, B.

    1998-01-01

    We consider type IIB theory compactified on a two-sphere in the presence of mutually non-local 7-branes. The BPS states associated with the gauge vectors of exceptional groups are seen to arise from open strings connecting the 7-branes, and multi-pronged open strings capable of ending on more than two 7-branes. These multi-pronged strings are built from open string junctions that arise naturally when strings cross 7-branes. The different string configurations can be multiplied as traditional open strings, and are shown to generate the structure of exceptional groups. (orig.)

  9. L-Cysteine metabolism and its nutritional implications.

    Science.gov (United States)

    Yin, Jie; Ren, Wenkai; Yang, Guan; Duan, Jielin; Huang, Xingguo; Fang, Rejun; Li, Chongyong; Li, Tiejun; Yin, Yulong; Hou, Yongqing; Kim, Sung Woo; Wu, Guoyao

    2016-01-01

    L-Cysteine is a nutritionally semiessential amino acid and is present mainly in the form of L-cystine in the extracellular space. With the help of a transport system, extracellular L-cystine crosses the plasma membrane and is reduced to L-cysteine within cells by thioredoxin and reduced glutathione (GSH). Intracellular L-cysteine plays an important role in cellular homeostasis as a precursor for protein synthesis, and for production of GSH, hydrogen sulfide (H(2)S), and taurine. L-Cysteine-dependent synthesis of GSH has been investigated in many pathological conditions, while the pathway for L-cysteine metabolism to form H(2)S has received little attention with regard to prevention and treatment of disease in humans. The main objective of this review is to highlight the metabolic pathways of L-cysteine catabolism to GSH, H(2)S, and taurine, with special emphasis on therapeutic and nutritional use of L-cysteine to improve the health and well-being of animals and humans. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Efficient Disk-Based Techniques for Manipulating Very Large String Databases

    KAUST Repository

    Allam, Amin

    2017-05-18

    Indexing and processing strings are very important topics in database management. Strings can be database records, DNA sequences, protein sequences, or plain text. Various string operations are required for several application categories, such as bioinformatics and entity resolution. When the string count or sizes become very large, several state-of-the-art techniques for indexing and processing such strings may fail or behave very inefficiently. Modifying an existing technique to overcome these issues is not usually straightforward or even possible. A category of string operations can be facilitated by the suffix tree data structure, which basically indexes a long string to enable efficient finding of any substring of the indexed string, and can be used in other operations as well, such as approximate string matching. In this document, we introduce a novel efficient method to construct the suffix tree index for very long strings using parallel architectures, which is a major challenge in this category. Another category of string operations require clustering similar strings in order to perform application-specific processing on the resulting possibly-overlapping clusters. In this document, based on clustering similar strings, we introduce a novel efficient technique for record linkage and entity resolution, and a novel method for correcting errors in a large number of small strings (read sequences) generated by the DNA sequencing machines.

  11. Cosmic strings and cosmic structure

    International Nuclear Information System (INIS)

    Albrecht, A.; Brandenberger, R.; Turok, N.

    1987-01-01

    The paper concerns the application of the theory of cosmic strings to explain the structure of the Universe. The formation of cosmic strings in the early Universe is outlined, along with the Big Bang theory, Grand Unified theories, and the first three minutes after the Big Bang. A description is given of the shaping of the Universe by cosmic strings, including the evolution of the string. The possibility for direct observation of cosmic strings is discussed. (U.K.)

  12. International conference on string theory

    CERN Document Server

    2017-01-01

    The Strings 2017 conference is part of the "Strings" series of annual conferences, that bring the entire string theory community together. It will include reviews of major developments in the field, and specialized talks on specific topics. There will also be several public lectures given by conference participants, a pre-Strings school at the Technion, and a post-Strings workshop at the Weizmann Institute.

  13. String-math 2012

    CERN Document Server

    Katz, Sheldon; Klemm, Albrecht; Morrison, David R

    2015-01-01

    This volume contains the proceedings of the conference String-Math 2012, which was held July 16-21, 2012, at the Hausdorff Center for Mathematics, Universitat Bonn. This was the second in a series of annual large meetings devoted to the interface of mathematics and string theory. These meetings have rapidly become the flagship conferences in the field. Topics include super Riemann surfaces and their super moduli, generalized moonshine and K3 surfaces, the latest developments in supersymmetric and topological field theory, localization techniques, applications to knot theory, and many more. The contributors include many leaders in the field, such as Sergio Cecotti, Matthias Gaberdiel, Rahul Pandharipande, Albert Schwarz, Anne Taormina, Johannes Walcher, Katrin Wendland, and Edward Witten. This book will be essential reading for researchers and students in this area and for all mathematicians and string theorists who want to update themselves on developments in the math-string interface.

  14. Hydroball string sensing system

    International Nuclear Information System (INIS)

    Hurwitz, M.J.; Ekeroth, D.E.; Squarer, D.

    1991-01-01

    This patent describes a hydroball string sensing system for a nuclear reactor having a core containing a fluid at a fluid pressure. It comprises a tube connectable to the nuclear reactor so that the fluid can flow within the tube at a fluid pressure that is substantially the same as the fluid pressure of the nuclear reactor core; a hydroball string including - a string member having objects positioned therealong with a specified spacing, the object including a plurality of hydroballs, and bullet members positioned at opposing ends of the string member; first sensor means, positioned outside a first segment of the tube, for sensing one of the objects being positioned within the first segment, and for providing a sensing signal responsive to the sensing of the first sensing means

  15. The QCD Effective String

    International Nuclear Information System (INIS)

    Espriu, D.

    2003-01-01

    QCD can be described in a certain kinematical regime by an effective string theory. This string must couple to background chiral fields in a chirally invariant manner, thus taking into account the true chirally non-invariant QCD vacuum. By requiring conformal symmetry of the string and the unitarity constraint on chiral fields we reconstruct the equations of motion for the latter ones. These provide a consistent background for the propagation of the string. By further requiring locality of the effective action we recover the Lagrangian of non-linear sigma model of pion interactions. The prediction is unambiguous and parameter-free. The estimated chiral structural constants of Gasser and Leutwyler fit very well the phenomenological values. (author)

  16. Field theory of strings

    International Nuclear Information System (INIS)

    Ramond, P.

    1987-01-01

    We review the construction of the free equations of motion for open and closed strings in 26 dimensions, using the methods of the Florida Group. Differing from previous treatments, we argue that the constraint L 0 -anti L 0 =0 should not be imposed on all the fields of the closed string in the gauge invariant formalism; we show that it can be incorporated in the gauge invariant formalism at the price of being unable to extract the equations of motion from a Langrangian. We then describe our purely algebraic method to introduce interactions, which works equally well for open and closed strings. Quartic interactions are absent except in the Physical Gauge. Finally, we speculate on the role of the measure of the open string path functional. (orig.)

  17. String Theory Rocks!

    CERN Multimedia

    2008-01-01

    String Theory supporters argue that the universe we live in has eleven dimensions, out of which three spacial dimensions and a temporal one, which define the void and the space-time environment we experience daily.

  18. Nonrelativistic closed string theory

    International Nuclear Information System (INIS)

    Gomis, Jaume; Ooguri, Hirosi

    2001-01-01

    We construct a Galilean invariant nongravitational closed string theory whose excitations satisfy a nonrelativistic dispersion relation. This theory can be obtained by taking a consistent low energy limit of any of the conventional string theories, including the heterotic string. We give a finite first order worldsheet Hamiltonian for this theory and show that this string theory has a sensible perturbative expansion, interesting high energy behavior of scattering amplitudes and a Hagedorn transition of the thermal ensemble. The strong coupling duals of the Galilean superstring theories are considered and are shown to be described by an eleven-dimensional Galilean invariant theory of light membrane fluctuations. A new class of Galilean invariant nongravitational theories of light-brane excitations are obtained. We exhibit dual formulations of the strong coupling limits of these Galilean invariant theories and show that they exhibit many of the conventional dualities of M theory in a nonrelativistic setting

  19. String theory compactifications

    CERN Document Server

    Graña, Mariana

    2017-01-01

    The lectures in this book provide graduate students and non-specialist researchers with a concise introduction to the concepts and formalism required to reduce the ten-dimensional string theories to the observable four-dimensional space-time - a procedure called string compactification. The text starts with a very brief introduction to string theory, first working out its massless spectrum and showing how the condition on the number of dimensions arises. It then dwells on the different possible internal manifolds, from the simplest to the most relevant phenomenologically, thereby showing that the most elegant description is through an extension of ordinary Riemannian geometry termed generalized geometry, which was first introduced by Hitchin. Last but not least, the authors review open problems in string phenomenology, such as the embedding of the Standard Model and obtaining de Sitter solutions.

  20. L-cysteine suppresses ghrelin and reduces appetite in rodents and humans.

    Science.gov (United States)

    McGavigan, A K; O'Hara, H C; Amin, A; Kinsey-Jones, J; Spreckley, E; Alamshah, A; Agahi, A; Banks, K; France, R; Hyberg, G; Wong, C; Bewick, G A; Gardiner, J V; Lehmann, A; Martin, N M; Ghatei, M A; Bloom, S R; Murphy, K G

    2015-03-01

    High-protein diets promote weight loss and subsequent weight maintenance, but are difficult to adhere to. The mechanisms by which protein exerts these effects remain unclear. However, the amino acids produced by protein digestion may have a role in driving protein-induced satiety. We tested the effects of a range of amino acids on food intake in rodents and identified l-cysteine as the most anorexigenic. Using rodents we further studied the effect of l-cysteine on food intake, behaviour and energy expenditure. We proceeded to investigate its effect on neuronal activation in the hypothalamus and brainstem before investigating its effect on gastric emptying and gut hormone release. The effect of l-cysteine on appetite scores and gut hormone release was then investigated in humans. l-Cysteine dose-dependently decreased food intake in both rats and mice following oral gavage and intraperitoneal administration. This effect did not appear to be secondary to behavioural or aversive side effects. l-Cysteine increased neuronal activation in the area postrema and delayed gastric emptying. It suppressed plasma acyl ghrelin levels and did not reduce food intake in transgenic ghrelin-overexpressing mice. Repeated l-cysteine administration decreased food intake in rats and obese mice. l-Cysteine reduced hunger and plasma acyl ghrelin levels in humans. Further work is required to determine the chronic effect of l-cysteine in rodents and humans on appetite and body weight, and whether l-cysteine contributes towards protein-induced satiety.

  1. Heterotic string construction

    International Nuclear Information System (INIS)

    Schellekens, A.N.

    1989-01-01

    In this paper an elementary introduction to the principles of four-dimensional string construction will be given. Although the emphasis is on lattice constructions, almost all results have further, and often quite straightforward generalizations to other constructions. Since heterotic strings look phenomenologically more promising than type-II theories the authors only consider the former, although everything can easily be generalized to type-II theories. Some additional aspects of lattice constructions are discussed, and an extensive review can be found

  2. Confusing the heterotic string

    International Nuclear Information System (INIS)

    Benett, D.L.; Mizrachi, L.

    1986-01-01

    A confusion mechanism is proposed as a global modification of the heterotic string model. It envolves a confusion hypersurface across which the two E 8 's of the heterotic string are permuted. A remarkable numerical coincidence is found which prevents an inconsistency in the model. The low energy limit of this theory (after compactification) is typically invariant under one E 8 only, thereby removing the shadow world from the original model. (orig.)

  3. Confusing the heterotic string

    Science.gov (United States)

    Benett, D.; Brene, N.; Mizrachi, Leah; Nielsen, H. B.

    1986-10-01

    A confusion mechanism is proposed as a global modification of the heterotic string model. It envolves a confusion hypersurface across which the two E 8's of the heterotic string are permuted. A remarkable numerical coincidence is found which prevents an inconsistency in the model. The low energy limit of this theory (after compactification) is typically invariant under one E 8 only, thereby removing the shadow world from the original model.

  4. Confusing the heterotic string

    Energy Technology Data Exchange (ETDEWEB)

    Benett, D.L.; Brene, N.; Nielsen, H.B.; Mizrachi, L.

    1986-10-02

    A confusion mechanism is proposed as a global modification of the heterotic string model. It envolves a confusion hypersurface across which the two E/sub 8/'s of the heterotic string are permuted. A remarkable numerical coincidence is found which prevents an inconsistency in the model. The low energy limit of this theory (after compactification) is typically invariant under one E/sub 8/ only, thereby removing the shadow world from the original model.

  5. Lectures on string theory

    International Nuclear Information System (INIS)

    Thorn, C.B.

    1988-01-01

    Several topics are discussed in string theory presented as three lectures to the Spring School on Superstrings at the ICTP at Trieste, Italy, in April, 1988. The first lecture is devoted to some general aspects of conformal invariance and duality. The second sketches methods for carrying out perturbative calculations in string field theory. The final lecture presents an alternative lattice approach to a nonperturbative formulation of the sum over world surfaces. 35 refs., 12 figs

  6. String dynamics in QCD

    International Nuclear Information System (INIS)

    Gervais, J.L.; Neveu, A.

    1980-01-01

    Recent works of the authors on string interpretation of the Wilson loop operators in QCD are reviewed in a self-contained fashion. Although most of the results habe already appeared in print, some new material is presented in renormalization of the Wilson loop operator and on the use of light-cone expansion to derive a linear string-like equation in light-cone formalism. (orig.)

  7. Matrix String Theory

    CERN Document Server

    Dijkgraaf, R; Verlinde, Herman L

    1997-01-01

    Via compactification on a circle, the matrix model of M-theory proposed by Banks et al suggests a concrete identification between the large N limit of two-dimensional N=8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states.

  8. Manipulating Strings in Python

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available This lesson is a brief introduction to string manipulation techniques in Python. Knowing how to manipulate strings plays a crucial role in most text processing tasks. If you’d like to experiment with the following lessons, you can write and execute short programs as we’ve been doing, or you can open up a Python shell / Terminal to try them out on the command line.

  9. Protein-stabilized fluorescent nanocrystals consisting of a gold core and a silver shell for detecting the total amount of cysteine and homocysteine

    International Nuclear Information System (INIS)

    Gui, Rijun; Wang, Yanfeng; Sun, Jie

    2014-01-01

    We report on a simple and sensitive method for the determination of the total amount of cysteine (Cys) and homocysteine (hCys), [Cys plus hCys], by exploiting the effect of Cys and hCys on the photoluminescence of human serum albumin-stabilized gold-core silver-shell nanocrystals (NCs). If Cys (or hCys) are added to these NCs, Cys (or hCys) will be adsorbed on the surface due to ligand exchange with human serum albumin, and this results in the quenching of the luminescence of the NCs. The addition of mixtures of Cys and hCys in different molar ratios also induces a decrease in luminescence whose intensity is linearly related to the concentration of [Cys plus hCys] in the range from 0.1 – 5.0 μM, with a correlation coefficient (R 2 ) of 0.9953 and a detection limit of 15 nM. The method is highly selective and sensitive over other α-amino acids, water-soluble thiols, and biomolecules. It has been successfully applied to the determination of the concentration of [Cys plus hCys] in spiked solutions of biomolecules and in real biological samples (author)

  10. Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis.

    Directory of Open Access Journals (Sweden)

    Hui-Yeng Y Yap

    Full Text Available Lignosus rhinocerotis (Cooke Ryvarden (tiger milk mushroom has long been known for its nutritional and medicinal benefits among the local communities in Southeast Asia. However, the molecular and genetic basis of its medicinal and nutraceutical properties at transcriptional level have not been investigated. In this study, the transcriptome of L. rhinocerotis sclerotium, the part with medicinal value, was analyzed using high-throughput Illumina HiSeqTM platform with good sequencing quality and alignment results. A total of 3,673, 117, and 59,649 events of alternative splicing, novel transcripts, and SNP variation were found to enrich its current genome database. A large number of transcripts were expressed and involved in the processing of gene information and carbohydrate metabolism. A few highly expressed genes encoding the cysteine-rich cerato-platanin, hydrophobins, and sugar-binding lectins were identified and their possible roles in L. rhinocerotis were discussed. Genes encoding enzymes involved in the biosynthesis of glucans, six gene clusters encoding four terpene synthases and one each of non-ribosomal peptide synthetase and polyketide synthase, and 109 transcribed cytochrome P450 sequences were also identified in the transcriptome. The data from this study forms a valuable foundation for future research in the exploitation of this mushroom in pharmacological and industrial applications.

  11. L-Cysteine supplementation increases adiponectin synthesis and secretion, and GLUT4 and glucose utilization by upregulating disulfide bond A-like protein expression mediated by MCP-1 inhibition in 3T3-L1 adipocytes exposed to high glucose.

    Science.gov (United States)

    Achari, Arunkumar Elumalai; Jain, Sushil K

    2016-03-01

    Adiponectin is an anti-diabetic and anti-atherogenic adipokine; its plasma levels are decreased in obesity, insulin resistance, and type 2 diabetes. An adiponectin-interacting protein named disulfide bond A-like protein (DsbA-L) plays an important role in the assembly of adiponectin. This study examined the hypothesis that L-cysteine (LC) regulates glucose homeostasis through the DsbA-L upregulation and synthesis and secretion of adiponectin in diabetes. 3T3L1 adipocytes were treated with LC (250 and 500 µM, 2 h) and high glucose (HG, 25 mM, 20 h). Results showed that LC supplementation significantly (p L, adiponectin, and GLUT-4 protein expression and glucose utilization in HG-treated adipocytes. LC supplementation significantly (p L expression and adiponectin levels in 3T3-L1 cells. Treatment with LC prevented the decrease in DsbA-L, adiponectin, and GLUT-4 expression in 3T3L1 adipocyte cells exposed to MCP-1. Thus, this study demonstrates that DsbA-L and adiponectin upregulation mediates the beneficial effects of LC on glucose utilization by inhibiting MCP-1 secretion in adipocytes and provides a novel mechanism by which LC supplementation can improve insulin sensitivity in diabetes.

  12. Deterministic indexing for packed strings

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Skjoldjensen, Frederik Rye

    2017-01-01

    Given a string S of length n, the classic string indexing problem is to preprocess S into a compact data structure that supports efficient subsequent pattern queries. In the deterministic variant the goal is to solve the string indexing problem without any randomization (at preprocessing time...... or query time). In the packed variant the strings are stored with several character in a single word, giving us the opportunity to read multiple characters simultaneously. Our main result is a new string index in the deterministic and packed setting. Given a packed string S of length n over an alphabet σ...

  13. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

    Science.gov (United States)

    Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

    2016-03-01

    A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

  14. Windings of twisted strings

    Science.gov (United States)

    Casali, Eduardo; Tourkine, Piotr

    2018-03-01

    Twistor string models have been known for more than a decade now but have come back under the spotlight recently with the advent of the scattering equation formalism which has greatly generalized the scope of these models. A striking ubiquitous feature of these models has always been that, contrary to usual string theory, they do not admit vibrational modes and thus describe only conventional field theory. In this paper we report on the surprising discovery of a whole new sector of one of these theories which we call "twisted strings," when spacetime has compact directions. We find that the spectrum is enhanced from a finite number of states to an infinite number of interacting higher spin massive states. We describe both bosonic and world sheet supersymmetric models, their spectra and scattering amplitudes. These models have distinctive features of both string and field theory, for example they are invariant under stringy T-duality but have the high energy behavior typical of field theory. Therefore they describe a new kind of field theories in target space, sitting on their own halfway between string and field theory.

  15. Strings and fundamental physics

    International Nuclear Information System (INIS)

    Baumgartl, Marco; Brunner, Ilka; Haack, Michael

    2012-01-01

    The basic idea, simple and revolutionary at the same time, to replace the concept of a point particle with a one-dimensional string, has opened up a whole new field of research. Even today, four decades later, its multifaceted consequences are still not fully conceivable. Up to now string theory has offered a new way to view particles as different excitations of the same fundamental object. It has celebrated success in discovering the graviton in its spectrum, and it has naturally led scientists to posit space-times with more than four dimensions - which in turn has triggered numerous interesting developments in fields as varied as condensed matter physics and pure mathematics. This book collects pedagogical lectures by leading experts in string theory, introducing the non-specialist reader to some of the newest developments in the field. The carefully selected topics are at the cutting edge of research in string theory and include new developments in topological strings, AdS/CFT dualities, as well as newly emerging subfields such as doubled field theory and holography in the hydrodynamic regime. The contributions to this book have been selected and arranged in such a way as to form a self-contained, graduate level textbook. (orig.)

  16. Strings and fundamental physics

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartl, Marco [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Brunner, Ilka; Haack, Michael (eds.) [Muenchen Univ. (Germany). Fakultaet fuer Physik

    2012-07-01

    The basic idea, simple and revolutionary at the same time, to replace the concept of a point particle with a one-dimensional string, has opened up a whole new field of research. Even today, four decades later, its multifaceted consequences are still not fully conceivable. Up to now string theory has offered a new way to view particles as different excitations of the same fundamental object. It has celebrated success in discovering the graviton in its spectrum, and it has naturally led scientists to posit space-times with more than four dimensions - which in turn has triggered numerous interesting developments in fields as varied as condensed matter physics and pure mathematics. This book collects pedagogical lectures by leading experts in string theory, introducing the non-specialist reader to some of the newest developments in the field. The carefully selected topics are at the cutting edge of research in string theory and include new developments in topological strings, AdS/CFT dualities, as well as newly emerging subfields such as doubled field theory and holography in the hydrodynamic regime. The contributions to this book have been selected and arranged in such a way as to form a self-contained, graduate level textbook. (orig.)

  17. Perspectives on string phenomenology

    CERN Document Server

    Kane, Gordon; Kumar, Piyush

    2015-01-01

    The remarkable recent discovery of the Higgs boson at the CERN Large Hadron Collider completed the Standard Model of particle physics and has paved the way for understanding the physics which may lie beyond it. String/M theory has emerged as a broad framework for describing a plethora of diverse physical systems, which includes condensed matter systems, gravitational systems as well as elementary particle physics interactions. If string/M theory is to be considered as a candidate theory of Nature, it must contain an effectively four-dimensional universe among its solutions that is indistinguishable from our own. In these solutions, the extra dimensions of string/M Theory are “compactified” on tiny scales which are often comparable to the Planck length. String phenomenology is the branch of string/M theory that studies such solutions, relates their properties to data, and aims to answer many of the outstanding questions of particle physics beyond the Standard Model. This book contains perspectives on stri...

  18. Crystallization and preliminary X-ray diffraction analyses of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels

    International Nuclear Information System (INIS)

    Suzuki, Nobuhiro; Yamazaki, Yasuo; Fujimoto, Zui; Morita, Takashi; Mizuno, Hiroshi

    2005-01-01

    Crystals of pseudechetoxin and pseudecin, potent peptidic inhibitors of cyclic nucleotide-gated ion channels, have been prepared and X-ray diffraction data have been collected to 2.25 and 1.90 Å resolution, respectively. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction of retinal and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins are structurally classified as cysteine-rich secretory proteins and exhibit structural features that are quite distinct from those of other known small peptidic channel blockers. This article describes the crystallization and preliminary X-ray diffraction analyses of these toxins. Crystals of PsTx belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 60.30, b = 61.59, c = 251.69 Å, and diffraction data were collected to 2.25 Å resolution. Crystals of Pdc also belonged to space group P2 1 2 1 2 1 , with similar unit-cell parameters a = 60.71, b = 61.67, c = 251.22 Å, and diffraction data were collected to 1.90 Å resolution

  19. Coulomb string tension, asymptotic string tension, and the gluon chain

    OpenAIRE

    Greensite, Jeff; Szczepaniak, Adam P.

    2014-01-01

    We compute, via numerical simulations, the non-perturbative Coulomb potential of pure SU(3) gauge theory in Coulomb gauge. We find that that the Coulomb potential scales nicely in accordance with asymptotic freedom, that the Coulomb potential is linear in the infrared, and that the Coulomb string tension is about four times larger than the asymptotic string tension. We explain how it is possible that the asymptotic string tension can be lower than the Coulomb string tension by a factor of four.

  20. Assay of cysteine dioxygenase activity

    International Nuclear Information System (INIS)

    Bagley, P.J.; Stipanuk, M.H.

    1990-01-01

    It has been proposed that rat liver contains two cysteine dioxygenase enzymes which convert cysteine to cysteinesulfinic acid, one which is stimulated by NAD + and has a pH optimum of 6.8 and one which is not stimulated by NAD + and has a pH optimum of 9.0. This led the authors to reinvestigate assay conditions for measuring cysteine dioxygenase activity in rat liver homogenate. An HPLC method, using an anion exchange column (Dionex Amino-Pac trademark PA1 (4x250 mm)) was used to separate the [ 35 S]cysteinesulfinic acid produced from [ 35 S]cysteine in the incubation mixture. They demonstrated that inclusion of hydroxylamine prevented further metabolism of cysteinesulfinic acid. which occurred rapidly in the absence of hydroxylamine

  1. Interacting-string picture of the fermionic string

    International Nuclear Information System (INIS)

    Mandelstam, S.

    1986-01-01

    This report gives a review of the interacting-string picture of the Bose string. In the present lecture, the author outlines a similar treatment of the Fermionic string. The quantization of the free Fermionic string is carried out to the degrees of freedom x, representing the displacement of the string. Also presented are Grassman degrees of freedom S distributed along the string. The report pictures the fermionic string as a string of dipoles. The general picture of the interaction of such strings by joining and splitting is the same as for the Bose string. The author does not at present have the simplest formula for fermion string scattering amplitudes. A less detailed treatment is given than for the Bose string. The report sets up the functional-integration formalism, derives the analog mode, and indicates in general, terms how the conformal transformation to the z-plane may be performed. The paper concludes by stating without proof the formula for the N-article tree amplitude in the manifestly supersymmetric formalism

  2. String field theory solution for any open string background

    Czech Academy of Sciences Publication Activity Database

    Erler, T.; Maccaferri, Carlo

    2014-01-01

    Roč. 10, Oct (2014), 1-37 ISSN 1029-8479 R&D Projects: GA ČR GBP201/12/G028 Institutional support: RVO:68378271 Keywords : tachyon condensation * string field theory * conformal field models in string theory * bosonic strings Subject RIV: BE - Theoretical Physics Impact factor: 6.111, year: 2014

  3. Are Stopped Strings Preferred in Sad Music?

    OpenAIRE

    David Huron; Caitlyn Trevor

    2017-01-01

    String instruments may be played either with open strings (where the string vibrates between the bridge and a hard wooden nut) or with stopped strings (where the string vibrates between the bridge and a performer's finger pressed against the fingerboard). Compared with open strings, stopped strings permit the use of vibrato and exhibit a darker timbre. Inspired by research on the timbre of sad speech, we test whether there is a tendency to use stopped strings in nominally sad music. Specifica...

  4. Strings for quantumchromodynamics

    International Nuclear Information System (INIS)

    Schomerus, V.

    2007-04-01

    During the last decade, intriguing dualities between gauge and string theory have been found and explored. they provide a novel window on strongly couplde gauge physics, including QCD-like models. Based on a short historical review of modern string theory, we explain how so-called AdS/CFT dualities emerged at the end of the 1990s. Some of their concrete implications and remarkable recent progress are then illustrated for the simplest example, namely the multicolor limit of N=4 SYM theory in four dimensions. We end with a few comments on existing extensions to more realistic models and applications, in particular to the sQGP. This text is meant as a non-technical introduction to gauge/string dualities for (particle) physicists. (orig.)

  5. The confining trailing string

    CERN Document Server

    Kiritsis, E; Nitti, F

    2014-01-01

    We extend the holographic trailing string picture of a heavy quark to the case of a bulk geometry dual to a confining gauge theory. We compute the classical trailing confining string solution for a static as well as a uniformly moving quark. The trailing string is infinitely extended and approaches a confining horizon, situated at a critical value of the radial coordinate, along one of the space-time directions, breaking boundary rotational invariance. We compute the equations for the fluctuations around the classical solutions, which are used to obtain boundary force correlators controlling the Langevin dynamics of the quark. The imaginary part of the correlators has a non-trivial low-frequency limit, which gives rise to a viscous friction coefficient induced by the confining vacuum. The vacuum correlators are used to define finite-temperature dressed Langevin correlators with an appropriate high-frequency behavior.

  6. Strings for quantumchromodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schomerus, V.

    2007-04-15

    During the last decade, intriguing dualities between gauge and string theory have been found and explored. they provide a novel window on strongly couplde gauge physics, including QCD-like models. Based on a short historical review of modern string theory, we explain how so-called AdS/CFT dualities emerged at the end of the 1990s. Some of their concrete implications and remarkable recent progress are then illustrated for the simplest example, namely the multicolor limit of N=4 SYM theory in four dimensions. We end with a few comments on existing extensions to more realistic models and applications, in particular to the sQGP. This text is meant as a non-technical introduction to gauge/string dualities for (particle) physicists. (orig.)

  7. Quark potential of spontaneous strings

    International Nuclear Information System (INIS)

    German, G.; Kleinert, H.

    1989-01-01

    The authors present some recent developments in string models with an extrinsic curvature term in action. Particular emphasis is placed upon the static quark potential and on the thermal deconfinement properties of spontaneous strings

  8. Cosmic strings and galaxy formation

    International Nuclear Information System (INIS)

    Bertschinger, E.

    1989-01-01

    Cosmic strings have become increasingly popular candidates as seeds for the formation of structure in the universe. This scenario, remains a serious cosmogonical model despite close scrutiny. In constrast, magnetic monopoles and domain walls - relic topological defects as are cosmic strings - are disastrous for cosmology if they are left over from the early universe. The production of heavy cosmic strings is speculative, as it depends on the details of ultrahigh energy physics. Fortunately, speculation about cosmic strings is not entirely idle because, if they exist and are heavy enough to seed galaxy formation, cosmic strings can be detected astronomically. Failure to detect cosmic strings would impose some constraints on grand unified theories (GUTs); their discovery would have exciting consequences for high energy physics and cosmology. This article reviews the basic physics of nonsuperconducting cosmic strings, highlighting the field theory aspects, and provides a progress report on calculations of structure formation with cosmic strings

  9. Proceedings of strings, 89

    International Nuclear Information System (INIS)

    Arnowitt, R.; Bryan, R.; Duff, M.J.; Nanopoulos, D.; Pope, C.N.

    1990-01-01

    Does string theory provide us with a consistent quantum theory of gravity? Is it that Holy Grail of elementary particle physics, a Theory of Everything with embraces all the forces and particles of Nature? Even if it is, can we extract concrete predictions about our low-energy world that can be tested experimentally at the SSC and other particle accelerators? What does it have to say about the origin of the Universe and the thorny problem of the cosmological constant? Are superstring theories unique, or might the eleven-dimensional supermembrane prove equally consistent? These are just some of the question posed and debated at Strings '89

  10. Strings draw theorists together

    International Nuclear Information System (INIS)

    Green, Michael

    2000-01-01

    Theorists are confident that they are closer than ever to finding a quantum theory that unites gravity with the three other fundamental forces in nature. Many of the leading figures in the world of string theory met at the California Institute of Technology in January to discuss recent progress in the field and to reflect on the state of the theory. The enthusiastic mood of the gathering was based on the fact that string theory provides an elegant framework for a unified theory of all the forces and particles in nature, and also gives a consistent quantum-mechanical description of general relativity. String theory, and more precisely superstring theory, describes the assortment of elementary particles such as quarks and leptons, and the gauge bosons responsible for mediating forces in a unified manner as different modes of vibration of a single extended string. This version of the theory also embodies supersymmetry a conjectured symmetry that unifies fermions and bosons. Furthermore, the fact that the string has a fundamental length scale - the ''string length'' - apparently cures the short-distance problems of uniting general relativity with quantum theory. The main problem with the early formulations of superstring theory was that they emphasized the ''perturbative'' point of view, an approximation that describes string-like quantum-mechanical particles moving through classical (that is non quantum-mechanical) space-time. However, very general arguments require that any quantum theory of gravity should also describe space-time geometry in a quantum-mechanical manner. The classical geometry of space-time should then emerge as an approximate description at distance scales much larger than the so-called Planck scale of 10 -33 m. This requires an understanding of the theory beyond the perturbative approximation. It is the quest for this more fundamental description of string theory that has provided the main challenge for string theorists over the past decade. Much

  11. Introduction to string theory

    International Nuclear Information System (INIS)

    Randjbar-Daemi, S.; Strathdee, J.

    1987-10-01

    These notes are based on a set of six introductory lectures given jointly by the authors. After developing the canonical methods we discuss the covariant quantization of the bosonic as well as the fermionic string. Conformal field theory methods are also introduced and used to calculate the anomaly coefficient, c, as well as the critical dimensions for bosonic and superstrings. We briefly sketch the BRS quantization and then offer an elementary derivation of the anomaly in the ghost number current. Finally, we address the one-loop partition function of the bosonic string and the question of SL(2,Z) invariance. (author). 15 refs

  12. Matrix string partition function

    CERN Document Server

    Kostov, Ivan K; Kostov, Ivan K.; Vanhove, Pierre

    1998-01-01

    We evaluate quasiclassically the Ramond partition function of Euclidean D=10 U(N) super Yang-Mills theory reduced to a two-dimensional torus. The result can be interpreted in terms of free strings wrapping the space-time torus, as expected from the point of view of Matrix string theory. We demonstrate that, when extrapolated to the ultraviolet limit (small area of the torus), the quasiclassical expressions reproduce exactly the recently obtained expression for the partition of the completely reduced SYM theory, including the overall numerical factor. This is an evidence that our quasiclassical calculation might be exact.

  13. Deriving the four-string and open-closed string interactions from geometric string field theory

    International Nuclear Information System (INIS)

    Kaku, M.

    1990-01-01

    One of the questions concerning the covariant open string field theory is why there are two distinct BRST theories and why the four-string interaction appears in one version but not the other. The authors solve this mystery by showing that both theories are gauge-fixed versions of a higher gauge theory, called the geometric string field theory, with a new field, a string verbein e μσ νρ , which allows us to gauge the string length and σ parametrization. By fixing the gauge, the authors can derive the endpoint gauge (the covariantized light cone gauge), the midpoint gauge of Witten, or the interpolating gauge with arbitrary string length. The authors show explicitly that the four-string interaction is a gauge artifact of the geometric theory (the counterpart of the four-fermion instantaneous Coulomb term of QED). By choosing the interpolating gauge, they produce a new class of four-string interactions which smoothly interpolate between the endpoint gauge and the midpoint gauge (where it vanishes). Similarly, they can extract the closed string as a bound state of the open string, which appears in the endpoint gauge but vanishes in the midpoint gauge. Thus, the four-string and open-closed string interactions do not have to be added to the action as long as the string vierbein is included

  14. Determination of free and total cyst(e)ine in plasma of dogs and cats.

    Science.gov (United States)

    Tôrres, Cristina L; Miller, Joshua W; Rogers, Quinton R

    2004-01-01

    In human blood, the amino acid cysteine forms disulfide bonds with itself and with other sulfhydryl compounds in their free form and with sulfhydryls in protein. Protein-bound cysteine is lost when plasma proteins are removed before amino acid analysis. The purpose of this study was to assess the time course and extent of cyst(e)ine (cysteine + half-cystine) loss in dog and cat plasma. An equal volume of 6% sulfosalicylic acid was added to plasma aliquots at 0, 2, 4, 10, 16, 24, 36, 48, 60, and 72 hours after separation of blood cells. Tris-2-carboxyethyl-phosphine hydrochloride (TCEP - HCl), a reducing agent, was used to regenerate total plasma cyst(e)ine after 3 months of sample storage (-20 degrees C). Initial free cyst(e)ine concentrations (mean +/- SEM) were higher in canine plasma (77 +/- 4 micromol/L) than in feline plasma (37 +/- 3 micromol/L). Free plasma cyst(e)ine concentrations in dogs and cats decreased after first-order kinetics, with a half-life of 23 and 69 hours, respectively. Total plasma cysteine after TCEP - HCl treatment was similar for dogs (290 micromol/L) and cats (296 micromol/L), but the percentage of free cysteine was higher (P = .02) in dogs (27%) than in cats (13%). Over half of the cyst(e)ine, homocysteine, cysteinylglycine, and glutathione were bound in vivo to plasma proteins. These results emphasize the importance of removing plasma proteins within 1 hour after blood collection for reliable assay of free plasma cyst(e)ine.

  15. Racetrack inflation and cosmic strings

    Energy Technology Data Exchange (ETDEWEB)

    Brax, P. [CEA-Saclay, Gif sur Yvette (France). CEA/DSM/SPhT, Unite de Recherche Associee au CNRS, Service de Physique Theorique; Bruck, C. van de [Sheffield Univ. (United Kingdom). Dept. of Applied Mathematics; Davis, A.C.; Davis, S.C. [Cambridge Univ. (United Kingdom). DAMTP, Centre for Mathematical Sciences; Jeannerot, R. [Instituut-Lorentz for Theoretical Physics, Leiden (Netherlands); Postma, M. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)]|[Nationaal Inst. voor Kernfysica en Hoge-Energiefysica (NIKHEF), Amsterdam (Netherlands)

    2008-05-15

    We consider the coupling of racetrack inflation to matter fields as realised in the D3/D7 brane system. In particular, we investigate the possibility of cosmic string formation in this system. We find that string formation before or at the onset of racetrack inflation is possible, but they are then inflated away. Furthermore, string formation at the end of inflation is prevented by the presence of the moduli sector. As a consequence, no strings survive racetrack inflation. (orig.)

  16. String theory in four dimensions

    International Nuclear Information System (INIS)

    Dine, M.

    1988-01-01

    A representative sample of current ideas about how one might develop a string phenomenology is presented. Some of the obstacles which lie in between string theory and contact with experiment are described. It is hoped that this volume will provide the reader with ways of thinking about string theory in four dimensions and provide tools for asking questions about string theory and ordinary physics. 102 refs

  17. The STRING database in 2011

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Franceschini, Andrea; Kuhn, Michael

    2011-01-01

    present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score...... models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org....

  18. Instability of colliding metastable strings

    Energy Technology Data Exchange (ETDEWEB)

    Hiramatsu, Takashi [Kyoto Univ. (Japan). Yukawa Inst. for Theoretical Physics; Eto, Minoru [Yamagata Univ. (Japan). Dept. of Physics; Kamada, Kohei [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Kobayashi, Tatsuo [Kyoto Univ. (Japan). Dept. of Physics; Ookouchi, Yutaka [Kyoto Univ. (Japan). Dept. of Physics; Kyoto Univ. (Japan). The Hakubi Center for Advanced Research

    2013-04-15

    We investigate the collision dynamics of two metastable strings which can be viewed as tube-like domain walls with winding numbers interpolating a false vacuum and a true vacuum. We find that depending on the relative angle and speed of two strings, instability of strings increases and the false vacuum is filled out by rapid expansion of the strings or of a remnant of the collision.

  19. Cosmic strings and galaxy formation

    Science.gov (United States)

    Bertschinger, Edmund

    1989-01-01

    The cosmogonical model proposed by Zel'dovich and Vilenkin (1981), in which superconducting cosmic strings act as seeds for the origin of structure in the universe, is discussed, summarizing the results of recent theoretical investigations. Consideration is given to the formation of cosmic strings, the microscopic structure of strings, gravitational effects, cosmic string evolution, and the formation of galaxies and large-scale structure. Simulation results are presented in graphs, and several outstanding issues are listed and briefly characterized.

  20. Instability of colliding metastable strings

    International Nuclear Information System (INIS)

    Hiramatsu, Takashi; Kobayashi, Tatsuo; Ookouchi, Yutaka; Kyoto Univ.

    2013-04-01

    We investigate the collision dynamics of two metastable strings which can be viewed as tube-like domain walls with winding numbers interpolating a false vacuum and a true vacuum. We find that depending on the relative angle and speed of two strings, instability of strings increases and the false vacuum is filled out by rapid expansion of the strings or of a remnant of the collision.

  1. Racetrack inflation and cosmic strings

    International Nuclear Information System (INIS)

    Brax, P.; Postma, M.

    2008-05-01

    We consider the coupling of racetrack inflation to matter fields as realised in the D3/D7 brane system. In particular, we investigate the possibility of cosmic string formation in this system. We find that string formation before or at the onset of racetrack inflation is possible, but they are then inflated away. Furthermore, string formation at the end of inflation is prevented by the presence of the moduli sector. As a consequence, no strings survive racetrack inflation. (orig.)

  2. Identification of thioredoxin h-reducible disulphides in proteornes by differential labelling of cysteines: Insight into recognition and regulation of proteins in barley seeds by thioredoxin h

    DEFF Research Database (Denmark)

    Maeda, Kenji; Finnie, Christine; Svensson, Birte

    2005-01-01

    alpha-amylase/subtilisin inhibitor (BASI) by barley thioredoxin h isoform 1 was analysed. Furthermore, the method was coupled with two-dimensional electrophoresis for convenient thioredoxin h-reducible disulphide identification in barley seed extracts without the need for protein purification...... or production of recombinant proteins. Mass shifts of 15 peptides, induced by treatment with thioredoxin h and differential alkylation, identified specific reduction of nine disulphides in BASI, four alpha-amylase/trypsin inhibitors and a protein of unknown function. Two specific disulphides, located...... structurally close to the alpha-amylase binding surfaces of BASI and alpha-amylase inhibitor BMAI-1 were demonstrated to be reduced to a particularly high extent. For the first time, specificity of thioredoxin h for particular disulphide bonds is demonstrated, providing a basis to study structural aspects...

  3. iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.

    Directory of Open Access Journals (Sweden)

    Yan Xu

    Full Text Available Posttranslational modifications (PTMs of proteins are responsible for sensing and transducing signals to regulate various cellular functions and signaling events. S-nitrosylation (SNO is one of the most important and universal PTMs. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for timely identifying the exact SNO sites in proteins because this kind of information is very useful for both basic research and drug development. Here, a new predictor, called iSNO-PseAAC, was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP into the general form of pseudo amino acid composition (PseAAC. The predictor was implemented using the conditional random field (CRF algorithm. As a demonstration, a benchmark dataset was constructed that contains 731 SNO sites and 810 non-SNO sites. To reduce the homology bias, none of these sites were derived from the proteins that had [Formula: see text] pairwise sequence identity to any other. It was observed that the overall cross-validation success rate achieved by iSNO-PseAAC in identifying nitrosylated proteins on an independent dataset was over 90%, indicating that the new predictor is quite promising. Furthermore, a user-friendly web-server for iSNO-PseAAC was established at http://app.aporc.org/iSNO-PseAAC/, by which users can easily obtain the desired results without the need to follow the mathematical equations involved during the process of developing the prediction method. It is anticipated that iSNO-PseAAC may become a useful high throughput tool for identifying the SNO sites, or at the very least play a complementary role to the existing methods in this area.

  4. String theory and quark confinement

    International Nuclear Information System (INIS)

    Polyakov, A.M.

    1998-01-01

    This article is based on a talk given at the ''Strings '97'' conference. It discusses the search for the universality class of confining strings. The key ingredients include the loop equations, the zigzag symmetry, the non-linear renormalization group. Some new tests for the equivalence between gauge fields and strings are proposed. (orig.)

  5. String theory in four dimensions

    CERN Document Server

    1988-01-01

    ``String Theory in Four Dimensions'' contains a representative collection of papers dealing with various aspects of string phenomenology, including compactifications on smooth manifolds and more general conformal field theories. Together with the lucid introduction by M. Dine, this material gives the reader a good working knowledge of our present ideas for connecting string theory to nature.

  6. Cysteine-containing peptides having antioxidant properties

    Science.gov (United States)

    Bielicki, John K [Castro Valley, CA

    2008-10-21

    Cysteine containing amphipathic alpha helices of the exchangeable apolipoproteins, as exemplified by apolipoprotein (apo) A-I.sub.Milano (R173C) and apoA-I.sub.Paris, (R151C) were found to exhibit potent antioxidant activity on phospholipid surfaces. The addition of a free thiol, at the hydrophobic/hydrophilic interface of an amphipathic alpha helix of synthetic peptides that mimic HDL-related proteins, imparts a unique antioxidant activity to these peptides which inhibits lipid peroxidation and protects phospholipids from water-soluble free radical initiators. These peptides can be used as therapeutic agents to combat cardiovascular disease, ischemia, bone disease and other inflammatory related diseases.

  7. String necklaces and primordial black holes from type IIB strings

    International Nuclear Information System (INIS)

    Lake, Matthew; Thomas, Steve; Ward, John

    2009-01-01

    We consider a model of static cosmic string loops in type IIB string theory, where the strings wrap cycles within the internal space. The strings are not topologically stabilised, however the presence of a lifting potential traps the windings giving rise to kinky cycloops. We find that PBH formation occurs at early times in a small window, whilst at late times we observe the formation of dark matter relics in the scaling regime. This is in stark contrast to previous predictions based on field theoretic models. We also consider the PBH contribution to the mass density of the universe, and use the experimental data to impose bounds on the string theory parameters.

  8. Cysteine-rich whey protein isolate (Immunocal®) ameliorates deficits in the GFAP.HMOX1 mouse model of schizophrenia.

    Science.gov (United States)

    Song, Wei; Tavitian, Ayda; Cressatti, Marisa; Galindez, Carmela; Liberman, Adrienne; Schipper, Hyman M

    2017-09-01

    Schizophrenia is a neuropsychiatric disorder that features neural oxidative stress and glutathione (GSH) deficits. Oxidative stress is augmented in brain tissue of GFAP.HMOX1 transgenic mice which exhibit schizophrenia-relevant characteristics. The whey protein isolate, Immunocal® serves as a GSH precursor upon oral administration. In this study, we treated GFAP.HMOX1 transgenic mice daily with either Immunocal (33mg/ml drinking water) or equivalent concentrations of casein (control) between the ages of 5 and 6.5 months. Immunocal attenuated many of the behavioral, neurochemical and redox abnormalities observed in GFAP.HMOX1 mice. In addition to restoring GSH homeostasis in the CNS of the transgenic mice, the whey protein isolate augmented GSH reserves in the brains of wild-type animals. These results demonstrate that consumption of whey protein isolate augments GSH stores and antioxidant defenses in the healthy and diseased mammalian brain. Whey protein isolate supplementation (Immunocal) may constitute a safe and effective modality for the management of schizophrenia, an unmet clinical imperative. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Measuring site occupancy: a new perspective on cysteine oxidation.

    Science.gov (United States)

    Rogowska-Wrzesinska, Adelina; Wojdyla, Katarzyna; Williamson, James; Roepstorff, Peter

    2014-10-01

    Site occupancy is an extremely important aspect of quantification of protein modifications. Knowing the degree of modification of each oxidised cysteine residue is critical to understanding the biological role of these modifications. Yet modification site occupancy is very often overlooked, in part because there are very few analytical tools that allow such measurements. Here we present a new strategy, which provides quantitative analysis of cysteine S-nitrosylation (SNO) and S-sulfenylation (SOH) simultaneously at the resolution of single cysteine and allows for determination of relative oxidation occupancy of the modification site. We show that, on one hand, heavily modified cysteines are not necessarily involved in the response to oxidative stress. On the other hand residues with low modification level can be dramatically affected by mild oxidative imbalance. We make use of high resolution mass spectrometry. The method relies on differential reduction of "total" cysteines, SNO cysteines and SOH cysteines with TCEP, sodium ascorbate and sodium arsenite respectively followed by iodoTMT(TM) alkylation. Enrichment of iodoTMT(TM)-containing peptides is performed using anti-TMT antibody. In vivo model of mild oxidative stress in Escherichia coli is used. To induce endogenous SNO bacteria were grown anaerobically in minimal media supplemented with fumarate or nitrate. Short-term treatment with submilimolar levels of hydrogen peroxide were used to induce SOH. We have quantified 114 SNO/SOH modified peptides corresponding to 90 proteins. Only 6 modified peptides changed significantly under mild oxidative stress. Quantitative information allowed us to determine relative modification site occupancy of each identified modified residue and pin point heavily modified ones. The method proved to be precise and sensitive enough to detect and quantify endogenous levels of oxidative stress on proteome-wide scale and brings a new perspective on the role of the modification site

  10. SUPERCOLLIDER: String test success

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    On 14 August at the Superconducting Supercollider (SSC) Laboratory in Ellis County, Texas, the Accelerator Systems String Test (ASST) successfully met its objective by operating a half-cell of five collider dipole magnets, one quadrupole magnet, and two spool pieces at the design current of 6500 amperes

  11. Help from the strings

    CERN Multimedia

    2007-01-01

    "How can the nature of basic particles be defined beyond the mechanisms presiding over their creation? Besides the standard model of particle physics - resulting from the postulations of quantum mechanics - contemporary science has pinned its hopes on the totally new unifying notion provided by the highly mathematical string theory."(2 pages)

  12. New Z3 strings

    Directory of Open Access Journals (Sweden)

    Marco A.C. Kneipp

    2016-12-01

    Full Text Available We consider a Yang–Mills–Higgs theory with the gauge group SU(3 broken to its center Z3 by two scalar fields in the adjoint representation and obtain new Z3 strings asymptotic configurations with the gauge field and magnetic field in the direction of the step operators.

  13. On exceptional instanton strings

    NARCIS (Netherlands)

    Del Zotto, M.; Lockhart, G.

    According to a recent classification of 6d (1, 0) theories within F-theory there are only six “pure” 6d gauge theories which have a UV superconformal fixed point. The corresponding gauge groups are SU(3), SO(8), F4, E6, E7, and E8. These exceptional models have BPS strings which are also instantons

  14. String perturbation theory diverges

    International Nuclear Information System (INIS)

    Gross, D.J.; Periwal, V.

    1988-01-01

    We prove that perturbation theory for the bosonic string diverges for arbitrary values of the coupling constant and is not Borel summable. This divergence is independent of the existence of the infinities that occur in the theory due to the presence of tachyons and dilaton tadpoles. We discuss the physical implications of such a divergence

  15. Transversally extended string

    International Nuclear Information System (INIS)

    Akama, Keiichi

    1988-01-01

    Starting with the space-time action of the transversally extended string, we derive its world-sheet action, which is that of a gravitational and gauge theory with matter fields on the world-sheet, with additional effects of the second fundamental quantity. (author)

  16. Lectures on strings and dualities

    International Nuclear Information System (INIS)

    Vafa, C.

    1997-01-01

    In this set of lectures I review recent developments in string theory emphasizing their non-perturbative aspects and their recently discovered duality symmetries. The goal of the lectures is to make the recent exciting developments in string theory accessible to those with no previous background in string theory who wish to join the research effort in this area. Topics covered include a brief review of string theory, its compactifications, solitons and D-branes, black hole entropy and wed of string dualities. (author)

  17. Macroscopic fundamental strings in cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Aharonov, Y; Englert, F; Orloff, J

    1987-12-24

    We show that, when D greater than or equal to 4, theories of closed strings of closed strings in D, non-compact space-time dimensions exhibit a phase transition. The high-temperature phase is characterized by a condensate of arbitrarily long strings with Hausdorff dimension two (area filling curves). We suggest that this stringy phase is the ancestor of the adiabatic era. Fundamental strings could then both drive the inflation and seed, in a way reminiscent of the cosmic string mechanism, the large structures in the universe.

  18. Strings draw theorists together

    Energy Technology Data Exchange (ETDEWEB)

    Green, Michael [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge (United Kingdom)

    2000-03-01

    Theorists are confident that they are closer than ever to finding a quantum theory that unites gravity with the three other fundamental forces in nature. Many of the leading figures in the world of string theory met at the California Institute of Technology in January to discuss recent progress in the field and to reflect on the state of the theory. The enthusiastic mood of the gathering was based on the fact that string theory provides an elegant framework for a unified theory of all the forces and particles in nature, and also gives a consistent quantum-mechanical description of general relativity. String theory, and more precisely superstring theory, describes the assortment of elementary particles such as quarks and leptons, and the gauge bosons responsible for mediating forces in a unified manner as different modes of vibration of a single extended string. This version of the theory also embodies supersymmetry a conjectured symmetry that unifies fermions and bosons. Furthermore, the fact that the string has a fundamental length scale - the ''string length'' - apparently cures the short-distance problems of uniting general relativity with quantum theory. The main problem with the early formulations of superstring theory was that they emphasized the ''perturbative'' point of view, an approximation that describes string-like quantum-mechanical particles moving through classical (that is non quantum-mechanical) space-time. However, very general arguments require that any quantum theory of gravity should also describe space-time geometry in a quantum-mechanical manner. The classical geometry of space-time should then emerge as an approximate description at distance scales much larger than the so-called Planck scale of 10{sup -33} m. This requires an understanding of the theory beyond the perturbative approximation. It is the quest for this more fundamental description of string theory that has provided the main challenge for

  19. Retaining in-gel zymographic activity of cysteine proteases via a cysteine-supplemented running buffer.

    Science.gov (United States)

    Vootukuri Reddy, Sreekanth; Philpott, Mike P; Trigiante, Giuseppe

    2016-10-01

    Zymography is a powerful technique to separate and identify different enzymatic activities on a standard acrylamide gel. For oxidation prone enzymes such as cysteine proteases however, the oxidizing species generated by electrolysis of the gel running buffer may result in partial or complete inactivation, thus compromising the final readout. This can be only partially remedied by subsequent treatment of the gel with reducing agents. We demonstrate the generation of reactive oxidizing species during electrophoresis and discovered that supplementation of the gel running buffer with a minimum of 5 mM cysteine prevents enzyme inactivation and allows retention of proteolytic activity as measured by zymography on model substrate N α-benzoyl-l-arginine p-nitroanilide, without at the same time altering the mobilities of the gel proteins. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Gravitational effects of global strings

    International Nuclear Information System (INIS)

    Aryal, M.; Everett, A.E.

    1986-01-01

    We have obtained the gravitational field, in the weak-field approximation, of cosmic strings formed in a phase transition in which a global symmetry is broken (global strings). The effect of this field on light rays passing a global string is found, and the resulting formation of double images and production of discontinuities in the microwave background temperature compared with the corresponding results for gauge strings. There are some differences in the case of global strings, reflecting the fact that the space surrounding such strings is not purely conical. However, the differences between gauge and global strings with masses suitable to explain galaxy formation are small, and the task of distinguishing them observationally appears difficult at best

  1. Device for balancing parallel strings

    Science.gov (United States)

    Mashikian, Matthew S.

    1985-01-01

    A battery plant is described which features magnetic circuit means in association with each of the battery strings in the battery plant for balancing the electrical current flow through the battery strings by equalizing the voltage across each of the battery strings. Each of the magnetic circuit means generally comprises means for sensing the electrical current flow through one of the battery strings, and a saturable reactor having a main winding connected electrically in series with the battery string, a bias winding connected to a source of alternating current and a control winding connected to a variable source of direct current controlled by the sensing means. Each of the battery strings is formed by a plurality of batteries connected electrically in series, and these battery strings are connected electrically in parallel across common bus conductors.

  2. Activation of the Nrf2/ARE pathway via S-alkylation of cysteine 151 in the chemopreventive agent-sensor Keap1 protein by falcarindiol, a conjugated diacetylene compound

    International Nuclear Information System (INIS)

    Ohnuma, Tomokazu; Nakayama, Shinji; Anan, Eisaburo; Nishiyama, Takahito; Ogura, Kenichiro; Hiratsuka, Akira

    2010-01-01

    Under basal conditions, the interaction of the cytosolic protein Kelch-like ECH-associated protein 1 (Keap1) with the transcription factor nuclear factor-E2-related factor 2 (Nrf2) results in a low level of expression of cytoprotective genes whose promoter region contains the antioxidant response element (ARE). In response to oxidants and electrophiles, Nrf2 is stabilized and accumulates in the nucleus. The mechanism for this effect has been proposed to involve thiol-dependent modulation of Keap1, leading to loss of its ability to negatively regulate Nrf2. We previously reported that falcarindiol (heptadeca-1,9(Z)-diene-4,6-diyne-3,8-diol), which occurs in Apiaceae and the closely related Araliaceae plants, causes nuclear accumulation of Nrf2 and induces ARE-regulated enzymes. Here, we report the mechanism of Nrf2 induction by falcarindiol. NMR analysis revealed that the conjugated diacetylene carbons of falcarindiol acted as electrophilic moieties to form adducts with a cysteine (Cys) thiol. In addition, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and circular dichroism spectroscopy, it was demonstrated that falcarindiol alkylated Cys residues in Keap1 and altered the Keap1 secondary structure. Transfection studies using the purified Keap1 protein, a luciferase reporter construct, and an Nrf2-expressing plasmid indicated that the intact Keap1 protein suppressed Nrf2-mediated ARE-luciferase activity. On the other hand, the falcarindiol-alkylated Keap1 protein did not suppress such activity. Treatment of HEK293 cells overexpressing Keap1 with falcarindiol generated a high molecular weight (HMW) form of Keap1. Furthermore, the Cys151 residue in Keap1 was found to be uniquely required for not only the formation of HMW Keap1 but also an increase in ARE-luciferase activity by falcarindiol. Our results demonstrate that falcarindiol having conjugated diacetylene carbons covalently modifies the Cys151 residue in Keap1 and that the

  3. Silencing of reversion-inducing cysteine-rich protein with Kazal motifs stimulates hyperplastic phenotypes through activation of epidermal growth factor receptor and hypoxia-inducible factor-2α.

    Directory of Open Access Journals (Sweden)

    You Mie Lee

    Full Text Available Reversion-inducing cysteine-rich protein with Kazal motifs (RECK, a tumor suppressor is down-regulated by the oncogenic signals and hypoxia, but the biological function of RECK in early tumorigenic hyperplastic phenotypes is largely unknown. Knockdown of RECK by small interfering RNA (siRECK or hypoxia significantly promoted cell proliferation in various normal epithelial cells. Hypoxia as well as knockdown of RECK by siRNA increased the cell cycle progression, the levels of cyclin D1 and c-Myc, and the phosphorylation of Rb protein (p-pRb, but decreased the expression of p21(cip1, p27(kip1, and p16(ink4A. HIF-2α was upregulated by knockdown of RECK, indicating HIF-2α is a downstream target of RECK. As knockdown of RECK induced the activation of epidermal growth factor receptor (EGFR and treatment of an EGFR kinase inhibitor, gefitinib, suppressed HIF-2α expression induced by the silencing of RECK, we can suggest that the RECK silenicng-EGFR-HIF-2α axis might be a key molecular mechanism to induce hyperplastic phenotype of epithelial cells. It was also found that shRNA of RECK induced larger and more numerous colonies than control cells in an anchorage-independent colony formation assay. Using a xenograft assay, epithelial cells with stably transfected with shRNA of RECK formed a solid mass earlier and larger than those with control cells in nude mice. In conclusion, the suppression of RECK may promote the development of early tumorigenic hyperplastic characteristics in hypoxic stress.

  4. Optimal shapes of compact strings

    International Nuclear Information System (INIS)

    Maritan, A.; Micheletti, C.; Trovato, A.; Banavar, J.R.

    2000-07-01

    Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest packing fraction; only recently has it been proved that the answer for infinite systems is a face-centred-cubic lattice. This simply stated problem has had a profound impact in many areas, ranging from the crystallization and melting of atomic systems, to optimal packing of objects and subdivision of space. Here we study an analogous problem-that of determining the optimal shapes of closely packed compact strings. This problem is a mathematical idealization of situations commonly encountered in biology, chemistry and physics, involving the optimal structure of folded polymeric chains. We find that, in cases where boundary effects are not dominant, helices with a particular pitch-radius ratio are selected. Interestingly, the same geometry is observed in helices in naturally-occurring proteins. (author)

  5. Stringing physics along

    Energy Technology Data Exchange (ETDEWEB)

    Riordan, M. [Stanford University and the University of California, Santa Cruz (United States)]. E-mail: mriordan@ucsc.edu

    2007-02-15

    In the last few decades, however, physical theory has drifted away from the professional norms advocated by Newton and other enlightenment philosophers. A vast outpouring of hypotheses has occurred under the umbrella of what is widely called string theory. But string theory is not really a 'theory' at all - at least not in the strict sense that scientists generally use the term. It is instead a dense, weedy thicket of hypotheses and conjectures badly in need of pruning. That pruning, however, can come only from observation and experiment, to which string theory (a phrase I will grudgingly continue using) is largely inaccessible. String theory was invented in the 1970s in the wake of the Standard Model of particle physics. Encouraged by the success of gauge theories of the strong, weak and electromagnetic forces, theorists tried to extend similar ideas to energy and distance scales that are orders of magnitude beyond what can be readily observed or measured. The normal, healthy intercourse between theory and experiment - which had led to the Standard Model - has broken down, and fundamental physics now finds itself in a state of crisis. So it is refreshing to hear from a theorist - one who was deeply involved with string theory and championed it in his previous book, Three Roads to Quantum Gravity - that all is not well in this closeted realm. Smolin argues from the outset that viable hypotheses must lead to observable consequences by which they can be tested and judged. String theory by its very nature does not allow for such probing, according to Smolin, and therefore it must be considered as an unprovable conjecture. Towards the end of his book, Smolin suggests other directions fundamental physics can take, particularly in the realm of quantum gravity, to resolve its crisis and reconnect with the observable world. From my perspective, he leans a bit too heavily towards highly speculative ideas such as doubly special relativity, modified Newtonian

  6. On the Dynamical Behavior of the Cysteine Dioxygenase-l-Cysteine Complex in the Presence of Free Dioxygen and l-Cysteine.

    Science.gov (United States)

    Pietra, Francesco

    2017-11-01

    In this work, viable models of cysteine dioxygenase (CDO) and its complex with l-cysteine dianion were built for the first time, under strict adherence to the crystal structure from X-ray diffraction studies, for all atom molecular dynamics (MD). Based on the CHARMM36 FF, the active site, featuring an octahedral dummy Fe(II) model, allowed us observing water exchange, which would have escaped attention with the more popular bonded models. Free dioxygen (O 2 ) and l-cysteine, added at the active site, could be observed being expelled toward the solvating medium under Random Accelerated Molecular Dynamics (RAMD) along major and minor pathways. Correspondingly, free dioxygen (O 2 ), added to the solvating medium, could be observed to follow the same above pathways in getting to the active site under unbiased MD. For the bulky l-cysteine, 600 ns of trajectory were insufficient for protein penetration, and the molecule was stuck at the protein borders. These models pave the way to free energy studies of ligand associations, devised to better clarify how this cardinal enzyme behaves in human metabolism. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  7. Real topological string amplitudes

    Energy Technology Data Exchange (ETDEWEB)

    Narain, K.S. [The Abdus Salam International Centre for Theoretical Physics (ICTP),Strada Costiera 11, Trieste, 34151 (Italy); Piazzalunga, N. [Simons Center for Geometry and Physics, State University of New York,Stony Brook, NY, 11794-3636 (United States); International School for Advanced Studies (SISSA) and INFN, Sez. di Trieste,via Bonomea 265, Trieste, 34136 (Italy); Tanzini, A. [International School for Advanced Studies (SISSA) and INFN, Sez. di Trieste,via Bonomea 265, Trieste, 34136 (Italy)

    2017-03-15

    We discuss the physical superstring correlation functions in type I theory (or equivalently type II with orientifold) that compute real topological string amplitudes. We consider the correlator corresponding to holomorphic derivative of the real topological amplitude G{sub χ}, at fixed worldsheet Euler characteristic χ. This corresponds in the low-energy effective action to N=2 Weyl multiplet, appropriately reduced to the orientifold invariant part, and raised to the power g{sup ′}=−χ+1. We show that the physical string correlator gives precisely the holomorphic derivative of topological amplitude. Finally, we apply this method to the standard closed oriented case as well, and prove a similar statement for the topological amplitude F{sub g}.

  8. Open spinning strings

    International Nuclear Information System (INIS)

    Stefanski, B. Jr.

    2004-01-01

    We find classical open string solutions in the AdS 5 x S 5 /Z 2 orientifold with angular momenta along the five-sphere. The energy of these solutions has an expansion in integral powers of λ with sigma-model corrections suppressed by inverse powers of J - the total angular momentum. This gives a prediction for the exact anomalous dimensions of operators in the large N limit of an N = 2 Sp, Super-Yang-Mills theory with matter. We also find a simple map between open and closed string solutions. This gives a prediction for an all-loop planar relationship between the anomalous dimensions of single-trace and two-quark operators in the dual gauge theory. (author)

  9. New Supersymmetric String Compactifications

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, Shamit

    2002-11-25

    We describe a new class of supersymmetric string compactifications to 4d Minkowski space. These solutions involve type II strings propagating on (orientifolds of) non Calabi-Yau spaces in the presence of background NS and RR fluxes. The simplest examples have descriptions as cosets, generalizing the three-dimensional nilmanifold. They can also be thought of as twisted tori. We derive a formula for the (super)potential governing the light fields, which is generated by the fluxes and certain ''twists'' in the geometry. Detailed consideration of an example also gives strong evidence that in some cases, these exotic geometries are related by smooth transitions to standard Calabi-Yau or G2 compactifications of M-theory.

  10. Unified string theories

    International Nuclear Information System (INIS)

    Gross, D.J.

    1985-01-01

    String theories offer a way of realizing the potential of supersymmetry, Kaluza-Klein and much more. They represent a radical departure from ordinary quantum field theory, but in the direction of increased symmetry and structure. They are based on an enormous increase in the number of degrees of freedom, since in addition to fermionic coordinates and extra dimensions, the basic entities are extended one dimensional objects instead of points. Correspondingly the symmetry group is greatly enlarged, in a way that we are only beginning to comprehend. At the very least this extended symmetry contains the largest group of symmetries that can be contemplated within the framework of point field theories-those of ten-dimensional supergravity and super Yang-Mills theory. Types of string theories and the phenomenology to be expected from them are reviewed

  11. Fractional bosonic strings

    Science.gov (United States)

    Diaz, Victor Alfonzo; Giusti, Andrea

    2018-03-01

    The aim of this paper is to present a simple generalization of bosonic string theory in the framework of the theory of fractional variational problems. Specifically, we present a fractional extension of the Polyakov action, for which we compute the general form of the equations of motion and discuss the connection between the new fractional action and a generalization the Nambu-Goto action. Consequently, we analyze the symmetries of the modified Polyakov action and try to fix the gauge, following the classical procedures. Then we solve the equations of motion in a simplified setting. Finally, we present a Hamiltonian description of the classical fractional bosonic string and introduce the fractional light-cone gauge. It is important to remark that, throughout the whole paper, we thoroughly discuss how to recover the known results as an "integer" limit of the presented model.

  12. The IRC7 gene encodes cysteine desulphydrase activity and confers on yeast the ability to grow on cysteine as a nitrogen source.

    Science.gov (United States)

    Santiago, Margarita; Gardner, Richard C

    2015-07-01

    Although cysteine desulphydrase activity has been purified and characterized from Saccharomyces cerevisiae, the gene encoding this activity in vivo has never been defined. We show that the full-length IRC7 gene, encoded by the YFR055W open reading frame, encodes a protein with cysteine desulphydrase activity. Irc7p purified to homogeneity is able to utilize l-cysteine as a substrate, producing pyruvate and hydrogen sulphide as products of the reaction. Purified Irc7p also utilized l-cystine and some other cysteine conjugates, but not l-cystathionine or l-methionine, as substrates. We further show that, in vivo, the IRC7 gene is both necessary and sufficient for yeast to grow on l-cysteine as a nitrogen source, and that overexpression of the gene results in increased H2 S production. Strains overexpressing IRC7 are also hypersensitive to a toxic analogue, S-ethyl-l-cysteine. While IRC7 has been identified as playing a critical role in converting cysteine conjugates to volatile thiols that are important in wine aroma, its biological role in yeast cells is likely to involve regulation of cysteine and redox homeostasis. Copyright © 2015 John Wiley & Sons, Ltd.

  13. p-adic string

    International Nuclear Information System (INIS)

    Volovich, I.V.

    1987-01-01

    The hypothesis of the possible p-adic structure of spacetime is considered. The p-adic Veneziano amplitude is proposed and the main properties of the p-adic string theory are discussed. The analogous questions on the Galois field are also discussed. In this case the Jacobi sum plays the role of the Veneziano amplitude which can be expressed by means of the I-adic cohomology of the Fermat curves. The corresponding vertex operator is given. (author)

  14. Exactly soluble dynamics of (p,q) string near macroscopic fundamental strings

    International Nuclear Information System (INIS)

    Bak, Dongsu; Rey, Soojong; Yee, Houng

    2004-01-01

    We study dynamics of type-IIB bound-state of a Dirichlet string and n fundamental strings in the background of N fundamental strings. Because of supergravity potential, the bound-state string is pulled to the background fundamental strings, whose motion is described by open string rolling radion field. The string coupling can be made controllably weak and, in the limit 1 2 st n 2 st N, the bound-state energy involved is small compared to the string scale. We thus propose rolling dynamics of open string radion in this system as an exactly solvable analog for rolling dynamics of open string tachyon in decaying D-brane. The dynamics bears a novel feature that the worldsheet electric field increases monotonically to the critical value as the bound-state string falls into the background string. Close to the background string, D string constituent inside the bound-state string decouples from fundamental string constituents. (author)

  15. The theta-structure in string theories - 1: bosonic strings

    International Nuclear Information System (INIS)

    Li Miao.

    1985-09-01

    We explored the theta-structures in bosonic string theories which are similar to those in gauge field theories. The theta-structure of string is due to the multiply connected spatial compact subspace of space-time. The work of this paper shows that there is an energy band E(theta) in the string theory and one may move the tachyon out in theory by choosing some proper theta parameters. (author)

  16. An invariant string propagator

    International Nuclear Information System (INIS)

    Cohen, A.; Moore, G.; Nelson, P.; Polchinski, J.

    1986-01-01

    The authors show that the Polyakov path integral is used to define off-shell quantities in string theory. The path integral of Polyakov gives an elegant description of strings and their interactions. However, its use has been limited to obtaining the Koba-Nielsen expressions for S-matrix elements. It is not yet clear what quantities make sense in string theory. This study shows that the path integral can be used to define off-shell quantities as well. In particular it defines a natural n-point function in loop space as the sum of all world surfaces bounded by n specific spacetime curves. The reader is referred for more detail. The report first outlines general evaluation then discusses the additional features added by boundaries. Locally, the three gauge freedoms ξ/sup a/ and δphi can be used to take g/sub ab/ (σ) to the unit matrix. Globally, this is not quite possible. In general the researchers choose a family of fiducial metrics g/sub ab/ (σ,tau), depending on a finite number of Teichmuller parameters tau, and every metric is gauge equivalent to one of these

  17. Thermodynamical string fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Nadine [Theoretical Particle Physics, Department of Astronomy and Theoretical Physics, Lund University,Sölvegatan 14A, Lund, SE-223 62 (Sweden); School of Physics and Astronomy, Monash University,Wellington Road, Clayton, VIC-3800 (Australia); Sjöstrand, Torbjörn [Theoretical Particle Physics, Department of Astronomy and Theoretical Physics, Lund University,Sölvegatan 14A, Lund, SE-223 62 (Sweden)

    2017-01-31

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  18. Building GUTs from strings

    International Nuclear Information System (INIS)

    Aldazabal, G.; Ibanez, L.E.; Uranga, A.M.

    1996-01-01

    We study in detail the structure of Grand Unified Theories derived as the low-energy limit of orbifold four-dimensional strings. To this aim, new techniques for building level-two symmetric orbifold theories are presented. New classes of GUTs in the context of symmetric orbifolds are then constructed. The method of permutation modding is further explored and SO(10) GUTs with both 45- or 54-plets are obtained. SU(5) models are also found through this method. It is shown that, in the context of symmetric orbifold SO(10) GUTs, only a single GUT Higgs, either a 54 or a 45, can be present and it always resides in an order-two untwisted sector. Very restrictive results also hold in the case of SU(5). General properties and selection rules for string GUTs are described. Some of these selection rules forbid the presence of some particular GUT-Higgs couplings which are sometimes used in SUSY-GUT model building. Some semi-realistic string GUT examples are presented and their properties briefly discussed. (orig.)

  19. Fingerprints in Compressed Strings

    DEFF Research Database (Denmark)

    Bille, Philip; Cording, Patrick Hagge; Gørtz, Inge Li

    2013-01-01

    The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string S of size N compressed by a context-free grammar of size n that answers fingerprint queries...... derivative that captures LZ78 compression and its variations) we get O(loglogN) query time. Hence, our data structures has the same time and space complexity as for random access in SLPs. We utilize the fingerprint data structures to solve the longest common extension problem in query time O(logNlogℓ) and O....... That is, given indices i and j, the answer to a query is the fingerprint of the substring S[i,j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(logN) query time, and for Linear SLPs (an SLP...

  20. Cysteine Supplementation May be Beneficial in a Subgroup of Mitochondrial Translation Deficiencies.

    Science.gov (United States)

    Bartsakoulia, Marina; Mϋller, Juliane S; Gomez-Duran, Aurora; Yu-Wai-Man, Patrick; Boczonadi, Veronika; Horvath, Rita

    2016-08-30

    Mitochondrial encephalomyopathies are severe, relentlessly progressive conditions and there are very few effective therapies available to date. We have previously suggested that in two rare forms of reversible mitochondrial disease (reversible infantile respiratory chain deficiency and reversible infantile hepatopathy) supplementation with L-cysteine can improve mitochondrial protein synthesis, since cysteine is required for the 2-thiomodification of mitochondrial tRNAs. We studied whether supplementation with L-cysteine or N-acetyl-cysteine (NAC) results in any improvement of the mitochondrial function in vitro in fibroblasts of patients with different genetic forms of abnormal mitochondrial translation. We studied in vitro in fibroblasts of patients carrying the common m.3243A>G and m.8344A>G mutations or autosomal recessive mutations in genes affecting mitochondrial translation, whether L-cysteine or N-acetyl-cysteine supplementation have an effect on mitochondrial respiratory chain function. Here we show that supplementation with L-cysteine, but not with N-acetyl-cysteine partially rescues the mitochondrial translation defect in vitro in fibroblasts of patients carrying the m.3243A>G and m.8344A>G mutations. In contrast, N-acetyl-cysteine had a beneficial effect on mitochondrial translation in TRMU and MTO1 deficient fibroblasts. Our results suggest that L-cysteine or N-acetyl-cysteine supplementation may be a potential treatment for selected subgroups of patients with mitochondrial translation deficiencies. Further studies are needed to explore the full potential of cysteine supplementation as a treatment for patients with mitochondrial disease.

  1. Biotin Switch Assays for Quantitation of Reversible Cysteine Oxidation.

    Science.gov (United States)

    Li, R; Kast, J

    2017-01-01

    Thiol groups in protein cysteine residues can be subjected to different oxidative modifications by reactive oxygen/nitrogen species. Reversible cysteine oxidation, including S-nitrosylation, S-sulfenylation, S-glutathionylation, and disulfide formation, modulate multiple biological functions, such as enzyme catalysis, antioxidant, and other signaling pathways. However, the biological relevance of reversible cysteine oxidation is typically underestimated, in part due to the low abundance and high reactivity of some of these modifications, and the lack of methods to enrich and quantify them. To facilitate future research efforts, this chapter describes detailed procedures to target the different modifications using mass spectrometry-based biotin switch assays. By switching the modification of interest to a biotin moiety, these assays leverage the high affinity between biotin and avidin to enrich the modification. The use of stable isotope labeling and a range of selective reducing agents facilitate the quantitation of individual as well as total reversible cysteine oxidation. The biotin switch assay has been widely applied to the quantitative analysis of S-nitrosylation in different disease models and is now also emerging as a valuable research tool for other oxidative cysteine modifications, highlighting its relevance as a versatile, robust strategy for carrying out in-depth studies in redox proteomics. © 2017 Elsevier Inc. All rights reserved.

  2. How to simulate global cosmic strings with large string tension

    Energy Technology Data Exchange (ETDEWEB)

    Klaer, Vincent B.; Moore, Guy D., E-mail: vklaer@theorie.ikp.physik.tu-darmstadt.de, E-mail: guy.moore@physik.tu-darmstadt.de [Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 2, Darmstadt, D-64289 Germany (Germany)

    2017-10-01

    Global string networks may be relevant in axion production in the early Universe, as well as other cosmological scenarios. Such networks contain a large hierarchy of scales between the string core scale and the Hubble scale, ln( f {sub a} / H ) ∼ 70, which influences the network dynamics by giving the strings large tensions T ≅ π f {sub a} {sup 2} ln( f {sub a} / H ). We present a new numerical approach to simulate such global string networks, capturing the tension without an exponentially large lattice.

  3. Maximal unbordered factors of random strings

    DEFF Research Database (Denmark)

    Cording, Patrick Hagge; Knudsen, Mathias Bæk Tejs

    2016-01-01

    A border of a string is a non-empty prefix of the string that is also a suffix of the string, and a string is unbordered if it has no border. Loptev, Kucherov, and Starikovskaya [CPM 2015] conjectured the following: If we pick a string of length n from a fixed alphabet uniformly at random...

  4. 35S cystein chlorhydrate preparation

    International Nuclear Information System (INIS)

    Emiliozzi, R.; Pichat, P.; Herbert, M.

    1960-01-01

    35 S cystein chlorhydrate has been prepared with a quantitative yield by electrolytic reduction of 35 S cystin in hydrochloric medium on a vibrating mercury cathode. Reprint of a paper published in Bulletin de la Societe chimique de France, no. 2653, 4. quarter 1959, p. 1544-1545 [fr

  5. Dynamics of chaotic strings

    International Nuclear Information System (INIS)

    Schaefer, Mirko

    2011-01-01

    The main topic of this thesis is the investigation of dynamical properties of coupled Tchebycheff map networks. The results give insights into the chaotic string model and its network generalization from a dynamical point of view. As a first approach, discrete symmetry transformations of the model are studied. These transformations are formulated in a general way in order to be also applicable to similar dynamics on bipartite network structures. The dynamics is studied numerically via Lyapunov measures, spatial correlations, and ergodic properties. It is shown that the zeros of the interaction energy are distinguished only with respect to this specific observable, but not by a more general dynamical principle. The original chaotic string model is defined on a one-dimensional lattice (ring-network) as the underlying network topology. This thesis studies a modification of the model based on the introduction of tunable disorder. The effects of inhomogeneous coupling weights as well as small-world perturbations of the ring-network structure on the interaction energy are discussed. Synchronization properties of the chaotic string model and its network generalization are studied in later chapters of this thesis. The analysis is based on the master stability formalism, which relates the stability of the synchronized state to the spectral properties of the network. Apart from complete synchronization, where the dynamics at all nodes of the network coincide, also two-cluster synchronization on bipartite networks is studied. For both types of synchronization it is shown that depending on the type of coupling the synchronized dynamics can display chaotic as well as periodic or quasi-periodic behaviour. The semi-analytical calculations reveal that the respective synchronized states are often stable for a wide range of coupling values even for the ring-network, although the respective basins of attraction may inhabit only a small fraction of the phase space. To provide

  6. Quantum backreaction in string theory

    International Nuclear Information System (INIS)

    Evnin, O.

    2012-01-01

    There are situations in string theory when a finite number of string quanta induce a significant backreaction upon the background and render the perturbation theory infrared-divergent. The simplest example is D0-brane recoil under an impact by closed strings. A more physically interesting case is backreaction on the evolution of a totally compact universe due to closed string gas. Such situations necessitate qualitative amendments to the traditional formulation of string theory in a fixed classical background. In this contribution to the proceedings of the XVII European Workshop on String Theory in Padua, I review solved problems and current investigations in relation to this kind of quantum backreaction effects. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Fast Searching in Packed Strings

    DEFF Research Database (Denmark)

    Bille, Philip

    2009-01-01

    Given strings P and Q the (exact) string matching problem is to find all positions of substrings in Q matching P. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time....... However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let m...... word-RAM with logarithmic word size we present an algorithm using time O(n/log(sigma) n + m + occ) Here occ is the number of occurrences of P in Q. For m = o(n) this improves the O(n) bound...

  8. Comparing double string theory actions

    International Nuclear Information System (INIS)

    De Angelis, L.; Gionti, S.J.G.; Marotta, R.; Pezzella, F.

    2014-01-01

    Aimed to a deeper comprehension of a manifestly T-dual invariant formulation of string theory, in this paper a detailed comparison between the non-covariant action proposed by Tseytlin and the covariant one proposed by Hull is done. These are obtained by making both the string coordinates and their duals explicitly appear, on the same footing, in the world-sheet action, so “doubling” the string coordinates along the compact dimensions. After a discussion on the nature of the constraints in both the models and the relative quantization, it results that the string coordinates and their duals behave like “non-commuting” phase space coordinates but their expressions in terms of Fourier modes generate the oscillator algebra of the standard bosonic string. A proof of the equivalence of the two formulations is given. Furthermore, open-string solutions are also discussed

  9. Comparing double string theory actions

    Energy Technology Data Exchange (ETDEWEB)

    De Angelis, L. [Dipartimento di Fisica, Università degli Studi “Federico II” di Napoli,Complesso Universitario Monte S. Angelo ed. 6, via Cintia, 80126 Napoli (Italy); Gionti, S.J.G. [Specola Vaticana, Vatican City, V-00120, Vatican City State and Vatican Observatory Research Group, Steward Observatory, The University Of Arizona, 933 North Cherry Avenue, Tucson, Arizona 85721 (United States); Marotta, R.; Pezzella, F. [Istituto Nazionale di Fisica Nucleare, Sezione di Napoli,Complesso Universitario di Monte S. Angelo ed. 6, via Cintia, 80126 Napoli (Italy)

    2014-04-28

    Aimed to a deeper comprehension of a manifestly T-dual invariant formulation of string theory, in this paper a detailed comparison between the non-covariant action proposed by Tseytlin and the covariant one proposed by Hull is done. These are obtained by making both the string coordinates and their duals explicitly appear, on the same footing, in the world-sheet action, so “doubling” the string coordinates along the compact dimensions. After a discussion on the nature of the constraints in both the models and the relative quantization, it results that the string coordinates and their duals behave like “non-commuting” phase space coordinates but their expressions in terms of Fourier modes generate the oscillator algebra of the standard bosonic string. A proof of the equivalence of the two formulations is given. Furthermore, open-string solutions are also discussed.

  10. Downregulation of reversion-inducing cysteine-rich protein with Kazal motifs in malignant melanoma: inverse correlation with membrane-type 1-matrix metalloproteinase and tissue inhibitor of metalloproteinase 2.

    Science.gov (United States)

    Jacomasso, Thiago; Trombetta-Lima, Marina; Sogayar, Mari C; Winnischofer, Sheila M B

    2014-02-01

    The invasive phenotype of many tumors is associated with an imbalance between the matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of metalloproteinases (TIMPs), and the membrane-anchored reversion-inducing cysteine-rich protein with Kazal motifs (RECK). RECK inhibits MMP-2, MMP-9, and MT1-MMP, and has been linked to patient survival and better prognosis in several types of tumors. However, despite the wide implication of these MMPs in melanoma establishment and progression, the role of RECK in this type of tumor is still unknown. Here, we analyzed the expression of RECK, TIMP1, TIMP2, TIMP3, MT1MMP, MMP2, and MMP9 in two publicly available melanoma microarray datasets and in a panel of human melanoma cell lines. We found that RECK is downregulated in malignant melanoma, accompanied by upregulation of MT1MMP and TIMP2. In both datasets, we observed that the group of samples displaying higher RECK levels show lower median expression levels of MT1MMP and TIMP2 and higher levels of TIMP3. When tested in a sample-wise manner, these correlations were statistically significant. Inverse correlations between RECK, MT1MMP, and TIMP2 were verified in a panel of human melanoma cell lines and in a further reduced model that includes a pair of matched primary tumor-derived and metastasis-derived cell lines. Taken together, our data indicate a consistent correlation between RECK, MT1MMP, and TIMP2 across different models of clinical samples and cell lines and suggest evidence of the potential use of this subset of genes as a gene signature for diagnosing melanoma.

  11. Regularized strings with extrinsic curvature

    International Nuclear Information System (INIS)

    Ambjoern, J.; Durhuus, B.

    1987-07-01

    We analyze models of discretized string theories, where the path integral over world sheet variables is regularized by summing over triangulated surfaces. The inclusion of curvature in the action is a necessity for the scaling of the string tension. We discuss the physical properties of models with extrinsic curvature terms in the action and show that the string tension vanishes at the critical point where the bare extrinsic curvature coupling tends to infinity. Similar results are derived for models with intrinsic curvature. (orig.)

  12. Classical theory of radiating strings

    Science.gov (United States)

    Copeland, Edmund J.; Haws, D.; Hindmarsh, M.

    1990-01-01

    The divergent part of the self force of a radiating string coupled to gravity, an antisymmetric tensor and a dilaton in four dimensions are calculated to first order in classical perturbation theory. While this divergence can be absorbed into a renormalization of the string tension, demanding that both it and the divergence in the energy momentum tensor vanish forces the string to have the couplings of compactified N = 1 D = 10 supergravity. In effect, supersymmetry cures the classical infinities.

  13. Cosmic string induced CMB maps

    International Nuclear Information System (INIS)

    Landriau, M.; Shellard, E. P. S.

    2011-01-01

    We compute maps of CMB temperature fluctuations seeded by cosmic strings using high resolution simulations of cosmic strings in a Friedmann-Robertson-Walker universe. We create full-sky, 18 deg. and 3 deg. CMB maps, including the relevant string contribution at each resolution from before recombination to today. We extract the angular power spectrum from these maps, demonstrating the importance of recombination effects. We briefly discuss the probability density function of the pixel temperatures, their skewness, and kurtosis.

  14. Introduction to strings and superstrings

    International Nuclear Information System (INIS)

    Traubenberg, M.R. de.

    1988-01-01

    We discuss the main features on the formulation of string theory that, in a primitive level, describe the hadronic phenomenon of duality. We also study an extension of the models of closed and strings with spin. Then, by using supersymmetry, it is formulated the theory of superstrings and heterotic strings with the aim of unify the fundamental interactions and matter. (M.W.O.) [pt

  15. Experimenting with string musical instruments

    Science.gov (United States)

    LoPresto, Michael C.

    2012-03-01

    What follows are several investigations involving string musical instruments developed for and used in a Science of Sound & Light course. The experiments make use of a guitar, orchestral string instruments and data collection and graphing software. They are designed to provide students with concrete examples of how mathematical formulae, when used in physics, represent reality that can actually be observed, in this case, the operation of string musical instruments.

  16. String breaking with Wilson loops?

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    A convincing, uncontroversial observation of string breaking, when the static potential is extracted from Wilson loops only, is still missing. This failure can be understood if the overlap of the Wilson loop with the broken string is exponentially small. In that case, the broken string ground state will only be seen if the Wilson loop is long enough. Our preliminary results show string breaking in the context of the 3d SU(2) adjoint static potential, using the L\\"uscher-Weisz exponential variance reduction approach. As a by-product, we measure the fundamental SU(2) static potential with improved accuracy and see clear deviations from Casimir scaling.

  17. A primer on string theory

    CERN Document Server

    Schomerus, Volker

    2017-01-01

    Since its conception in the 1960s, string theory has been hailed as one of the most promising routes we have to unify quantum mechanics and general relativity. This book provides a concise introduction to string theory explaining central concepts, mathematical tools and covering recent developments in physics including compactifications and gauge/string dualities. With string theory being a multidisciplinary field interfacing with high energy physics, mathematics and quantum field theory, this book is ideal for both students with no previous knowledge of the field and scholars from other disciplines who are looking for an introduction to basic concepts.

  18. Open problems in string cosmology

    International Nuclear Information System (INIS)

    Toumbas, N.

    2010-01-01

    Some of the open problems in string cosmology are highlighted within the context of the recently constructed thermal and quantum superstring cosmological solutions. Emphasis is given on the high temperature cosmological regime, where it is argued that thermal string vacua in the presence of gravito-magnetic fluxes can be used to bypass the Hagedorn instabilities of string gas cosmology. This article is based on a talk given at the workshop on ''Cosmology and Strings'', Corfu, September 6-13, 2009. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  19. Multiflavor string-net models

    Science.gov (United States)

    Lin, Chien-Hung

    2017-05-01

    We generalize the string-net construction to multiple flavors of strings, each of which is labeled by the elements of an Abelian group Gi. The same flavor of strings can branch, while different flavors of strings can cross one another and thus they form intersecting string nets. We systematically construct the exactly soluble lattice Hamiltonians and the ground-state wave functions for the intersecting string-net condensed phases. We analyze the braiding statistics of the low-energy quasiparticle excitations and find that our model can realize all the topological phases as the string-net model with group G =∏iGi . In this respect, our construction provides various ways of building lattice models which realize topological order G , corresponding to different partitions of G and thus different flavors of string nets. In fact, our construction concretely demonstrates the Künneth formula by constructing various lattice models with the same topological order. As an example, we construct the G =Z2×Z2×Z2 string-net model which realizes a non-Abelian topological phase by properly intersecting three copies of toric codes.

  20. The ABCDEFG of Little Strings

    OpenAIRE

    Haouzi, Nathan; Kozçaz, Can

    2017-01-01

    Starting from type IIB string theory on an $ADE$ singularity, the (2,0) little string arises when one takes the string coupling $g_s$ to 0. In this setup, we give a unified description of the codimension-two defects of the little string, for any simple Lie algebra ${\\mathfrak{g}}$. Geometrically, these are D5 branes wrapping 2-cycles of the singularity. Equivalently, the defects are specified by a certain set of weights of $^L {\\mathfrak{g}}$, the Langlands dual of ${\\mathfrak{g}}$. As a firs...

  1. String Theory in a Nutshell

    CERN Document Server

    Kiritsis, Elias

    2007-01-01

    This book is the essential new introduction to modern string theory, by one of the world's authorities on the subject. Concise, clearly presented, and up-to-date, String Theory in a Nutshell brings together the best understood and most important aspects of a theory that has been evolving since the early 1980s. A core model of physics that substitutes one-dimensional extended ""strings"" for zero-dimensional point-like particles (as in quantum field theory), string theory has been the leading candidate for a theory that would successfully unify all fundamental forces of nature, includin

  2. Splitting strings on integrable backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Vicedo, Benoit

    2011-05-15

    We use integrability to construct the general classical splitting string solution on R x S{sup 3}. Namely, given any incoming string solution satisfying a necessary self-intersection property at some given instant in time, we use the integrability of the worldsheet {sigma}-model to construct the pair of outgoing strings resulting from a split. The solution for each outgoing string is expressed recursively through a sequence of dressing transformations, the parameters of which are determined by the solutions to Birkhoff factorization problems in an appropriate real form of the loop group of SL{sub 2}(C). (orig.)

  3. Strings and superstrings. Electron linear colliders

    International Nuclear Information System (INIS)

    Alessandrini, V.; Bambade, P.; Binetruy, P.; Kounnas, C.; Le Duff, J.; Schwimmer, A.

    1989-01-01

    Basic string theory; strings in interaction; construction of strings and superstrings in arbitrary space-time dimensions; compactification and phenomenology; linear e+e- colliders; and the Stanford linear collider were discussed [fr

  4. Strings, Branes and Symmetries

    International Nuclear Information System (INIS)

    Westerberg, A.

    1997-01-01

    Recent dramatic progress in the understanding of the non-perturbative structure of superstring theory shows that extended objects of various kinds, collectively referred to as p-branes, are an integral part of the theory. In this thesis, comprising an introductory text and seven appended research papers, we study various aspects of p-branes with relevance for superstring theory. The first part of the introductory text is a brief review of string theory focussing on the role of p-branes. In particular, we consider the so-called D-branes which currently are attracting a considerable amount of attention. The purpose of this part is mainly to put into context the results of paper 4, 5 and 6 concerning action functionals describing the low-energy dynamics of D-branes. The discussion of perturbative string theory given in this part of the introduction is also intended to provide some background to paper 2 which contains an application of the Reggeon-sewing approach to the construction of string vertices. The second part covers a rather different subject, namely higher-dimensional loop algebras and their cohomology, with the aim of facilitating the reading of papers 1, 3 and 7. The relation to p-branes is to be found in paper 1 where we introduce a certain higher-dimensional generalization of the loop algebra and discuss its potential applicability as a symmetry algebra for p-branes. Papers 3 and 7 are mathematically oriented out-growths of this paper addressing the issue of realizing algebras of this kind, known in physics as current algebras, in terms of pseudo differential operators (PSDOs). The main result of paper 3 is a proof of the equivalence between certain Lie-algebra cocycles on the space of second-quantizable PSDOs

  5. Topics in string theory

    Science.gov (United States)

    Gorbatov, Elie

    In the first part of the dissertation we study noncommutative field theories at finite temperature. We find evidence for winding states and observe the existence of a transition to a new phase where there is a reduction of the degrees of freedom in the non-planar sector of the theory. We emphasize that such a transition is generic and insensitive to the particulars of the UV definition of the theory. In the second part we investigate some aspects of M-theory compactifications on orbifolds. The heterotic E8 x E 8 string compactified on T4/ ZN has gauge group G x G˜ with massless states in the twisted sector charged under both factors. In the dual M-theory description on T4/ ZN x S1/Z 2 the two groups do not communicate with each other since they reside on the boundary of the eleven dimensional spacetime. This leads to a conundrum for the twisted states of the perturbative heterotic string for there does not seem to be local degrees of freedom which carry charges under both G and G˜. We propose a resolution of this apparent paradox by nonperturbative states in M-theory. In support of our argument we review the consideration of six-dimensional gauge couplings and verify the local anomaly cancellation. In order to understand the dynamical properties of these states we deform the orbifold geometry, find an equivalent string theory background, and brane engineer the low energy six-dimensional field theories. In the process we encounter many exotic and surprising phenomena which are intrinsically M-theoretic and completely invisible to the perturbative observer.

  6. Drill string gas data

    Energy Technology Data Exchange (ETDEWEB)

    Siciliano, E.R.

    1998-05-12

    Data and supporting documentation were compiled and analyzed for 26 cases of gas grab samples taken during waste-tank core sampling activities between September 1, 1995 and December 31, 1997. These cases were tested against specific criteria to reduce uncertainties associated with in-tank sampling location and conditions. Of the 26 possible cases, 16 qualified as drill-string grab samples most likely to represent recently released waste gases. The data from these 16 ``confirmed`` cases were adjusted to remove non-waste gas contributions from core-sampling activities (argon or nitrogen purge), the atmospheric background, and laboratory sampler preparation (helium). The procedure for subtracting atmospheric, laboratory, and argon purge gases was unambiguous. No reliable method for determining the exact amount of nitrogen purge gas was established. Thus, the final set of ``Adjusted`` drill string gas data for the 6 nitrogen-purged cases had a greater degree of uncertainty than the final results for the 10 argon-purged cases. Including the appropriate amounts of uncertainty, this final set of data was added to the set of high-quality results from the Retained Gas Sampler (RGS), and good agreement was found for the N{sub 2}, H{sub 2}, and N{sub 2}O mole fractions sampled from common tanks. These results indicate that under favorable sampling conditions, Drill-String (DS) grab samples can provide reasonably accurate information about the dominant species of released gas. One conclusion from this set of total gas data is that the distribution of the H{sub 2} mole fractions is bimodal in shape, with an upper bound of 78%.

  7. Transmutations for Strings

    Directory of Open Access Journals (Sweden)

    Amin Boumenir

    2008-07-01

    Full Text Available We investigate the existence and representation of transmutations, also known as transformation operators, for strings. Using measure theory and functional analytic methods we prove their existence and study their representation. We show that in general they are not close to unity since their representation does not involve a Volterra operator but rather the eigenvalue parameter. We also obtain conditions under which the transmutation is either a bounded or a compact operator. Explicit examples show that they cannot be reduced to Volterra type operators.  

  8. Sequestering in string theory

    International Nuclear Information System (INIS)

    Kachru, Shamit; McAllister, Liam; Sundrum, Raman

    2007-01-01

    We study sequestering, a prerequisite for flavor-blind supersymmetry breaking in several high-scale mediation mechanisms, in compactifications of type IIB string theory. We find that although sequestering is typically absent in unwarped backgrounds, strongly warped compactifications do readily sequester. The AdS/CFT dual description in terms of conformal sequestering plays an important role in our analysis, and we establish how sequestering works both on the gravity side and on the gauge theory side. We pay special attention to subtle compactification effects that can disrupt sequestering. Our result is a step toward realizing an appealing pattern of soft terms in a KKLT compactification

  9. Drilling string lifter

    Energy Technology Data Exchange (ETDEWEB)

    Shakhobalov, A B; Galiopa, A A; Ponomarev, G V; Ushakov, A M

    1981-04-28

    A drilling string lifter is suggested which includes a rotating tower installed on a fixed base, hydraulic cylinder and pipe-clamping assembly connected through a chain gear to the drive motor. In order to simplify the design of the hydraulic lifter, the drive motor is installed on a fixed base so that the axis of the outlet shaft of the drive motor coincides with the axis of rotation of the tower. In addition, the axis of rotation of the tower is made in the form of a tubular element, and the outlet shaft of the drive motor is ranged between the tubular element.

  10. Nuclear fuel string assembly

    International Nuclear Information System (INIS)

    Ip, A.K.; Koyanagi, K.; Tarasuk, W.R.

    1976-01-01

    A method of fabricating rodded fuels suitable for use in pressure tube type reactors and in pressure vessel type reactors is described. Fuel rods are secured as an inner and an outer sub-assembly, each rod attached between mounting rings secured to the rod ends. The two sub-assemblies are telescoped together and positioned by spaced thimbles located between them to provide precise positioning while permittng differential axial movement between the sub-assemblies. Such sub-assemblies are particularly suited for mounting as bundle strings. The method provides particular advantages in the assembly of annular-section fuel pins, which includes booster fuel containing enriched fuel material. (LL)

  11. The mechanism of cysteine detection in biological media by means of vanadium oxide nanoparticles

    International Nuclear Information System (INIS)

    Bezerra, A. G.; Barison, A.; Oliveira, V. S.; Foti, L.; Krieger, M. A.; Dhalia, R.; Viana, I. F. T.; Schreiner, W. H.

    2012-01-01

    We report on the interaction of vanadate nanoparticles, produced using the laser ablation in liquids synthesis, with cysteine in biological molecules. Cysteine is a very important amino acid present in most proteins, but also because cysteine and the tripeptide glutathione are the main antioxidant molecules in our body system. Detailed UV–Vis absorption spectra and dynamic light scattering measurements were done to investigate the detection of cysteine in large biological molecules. The intervalence band of the optical absorption spectra shows capability for quantitative cysteine sensing in the μM range in biological macromolecules. Tests included cytoplasmic repetitive antigen and flagellar repetitive antigen proteins of the Trypanosoma cruzi protozoa, as well as the capsid p24 proteins from Human Immunodeficiency Virus type 1 and type 2. Detailed NMR measurements for hydrogen, carbon, and vanadium nuclei show that cysteine in contact with the vanadate looses hydrogen of the sulphydryl side chain, while the vanadate is reduced. The subsequent detachment of two deprotonated molecules to form cystine and the slow return to the vanadate complete the oxidation–reduction cycle. Therefore, the vanadate acts as a charge exchanging catalyst on cysteine to form cystine. The NMR results also indicate that the nanoparticles are not formed by the common orthorhombic V 2 O 5 form.

  12. The mechanism of cysteine detection in biological media by means of vanadium oxide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Bezerra, A. G. [Universidade Tecnologica Federal do Parana, Departamento Academico de Fisica (Brazil); Barison, A. [Universidade Federal do Parana, Departamento de Quimica (Brazil); Oliveira, V. S. [Universidade Federal do Parana, Departamento de Fisica (Brazil); Foti, L.; Krieger, M. A. [Fundacao Oswaldo Cruz, Instituto de Biologia Molecular do Parana (Brazil); Dhalia, R.; Viana, I. F. T. [Fundacao Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhaes (Brazil); Schreiner, W. H., E-mail: wido@fisica.ufpr.br [Universidade Federal do Parana, Departamento de Fisica (Brazil)

    2012-09-15

    We report on the interaction of vanadate nanoparticles, produced using the laser ablation in liquids synthesis, with cysteine in biological molecules. Cysteine is a very important amino acid present in most proteins, but also because cysteine and the tripeptide glutathione are the main antioxidant molecules in our body system. Detailed UV-Vis absorption spectra and dynamic light scattering measurements were done to investigate the detection of cysteine in large biological molecules. The intervalence band of the optical absorption spectra shows capability for quantitative cysteine sensing in the {mu}M range in biological macromolecules. Tests included cytoplasmic repetitive antigen and flagellar repetitive antigen proteins of the Trypanosoma cruzi protozoa, as well as the capsid p24 proteins from Human Immunodeficiency Virus type 1 and type 2. Detailed NMR measurements for hydrogen, carbon, and vanadium nuclei show that cysteine in contact with the vanadate looses hydrogen of the sulphydryl side chain, while the vanadate is reduced. The subsequent detachment of two deprotonated molecules to form cystine and the slow return to the vanadate complete the oxidation-reduction cycle. Therefore, the vanadate acts as a charge exchanging catalyst on cysteine to form cystine. The NMR results also indicate that the nanoparticles are not formed by the common orthorhombic V{sub 2}O{sub 5} form.

  13. Vacuum strings in FRW models

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, C C; Oattes, L M; Starkman, G D

    1988-01-01

    The authors find that vacuum string solutions cannot be embedded in an FRW model in the spirit of the swiss cheese model for inhomogeneities. Since all standard lensing calculations rely implicitly on the Swiss Cheese model, this result indicates that the previous lensing results for the vacuum string may be in error.

  14. Tadpole resummations in string theory

    International Nuclear Information System (INIS)

    Kitazawa, Noriaki

    2008-01-01

    While R-R tadpoles should be canceled for consistency, string models with broken supersymmetry generally have uncanceled NS-NS tadpoles. Their presence signals that the background does not solve the field equations, so that these models are in 'wrong' vacua. In this Letter we investigate, with reference to some prototype examples, whether the true values of physical quantities can be recovered resumming the NS-NS tadpoles, hence by an approach that is related to the analysis based on String Field Theory by open-closed duality. We show that, indeed, the positive classical vacuum energy of a Dp-brane of the bosonic string is exactly canceled by the negative contribution arising from tree-level tadpole resummation, in complete agreement with Sen's conjecture on open-string tachyon condensation and with the consequent analysis based on String Field Theory. We also show that the vanishing classical vacuum energy of the SO(8192) unoriented bosonic open-string theory does not receive any tree-level corrections from the tadpole resummation. This result is consistent with the fact that this (unstable) configuration is free from tadpoles of massless closed-string modes, although there is a tadpole of the closed string tachyon. The application of this method to superstring models with broken supersymmetry is also discussed

  15. String theory and water waves

    International Nuclear Information System (INIS)

    Iyer, Ramakrishnan; Johnson, Clifford V; Pennington, Jeffrey S

    2011-01-01

    We uncover a remarkable role that an infinite hierarchy of nonlinear differential equations plays in organizing and connecting certain c-hat <1 string theories non-perturbatively. We are able to embed the type 0A and 0B (A, A) minimal string theories into this single framework. The string theories arise as special limits of a rich system of equations underpinned by an integrable system known as the dispersive water wave hierarchy. We observe that there are several other string-like limits of the system, and conjecture that some of them are type IIA and IIB (A, D) minimal string backgrounds. We explain how these and several string-like special points arise and are connected. In some cases, the framework endows the theories with a non-perturbative definition for the first time. Notably, we discover that the Painleve IV equation plays a key role in organizing the string theory physics, joining its siblings, Painleve I and II, whose roles have previously been identified in this minimal string context.

  16. Cool Runnings For String 2

    CERN Multimedia

    2001-01-01

    String 2 is a series of superconducting magnets that are prototypes of those which will be installed in the LHC. It was cooled down to 1.9 Kelvin on September 14th. On Thursday last week, the dipoles of String 2 were successfully taken to nominal current, 11850 A.

  17. N-loop string amplitude

    International Nuclear Information System (INIS)

    Mandelstam, S.

    1986-06-01

    Work on the derivation of an explicit perturbation series for string and superstring amplitudes is reviewed. The light-cone approach is emphasized, but some work on the Polyakov approach is also mentioned, and the two methods are compared. The calculation of the measure factor is outlined in the interacting-string picture

  18. String-localized quantum fields

    International Nuclear Information System (INIS)

    Mund, Jens; Santos, Jose Amancio dos; Silva, Cristhiano Duarte; Oliveira, Erichardson de

    2009-01-01

    Full text. The principles of physics admit (unobservable) quantum fields which are localized not on points, but on strings in the sense of Mandelstam: a string emanates from a point in Minkowski space and extends to infinity in some space-like direction. This type of localization might permit the construction of new models, for various reasons: (a) in general, weaker localization implies better UV behaviour. Therefore, the class of renormalizable interactions in the string-localized has a chance to be larger than in the point-localized case; (b) for certain particle types, there are no point-localized (free) quantum fields - for example Anyons in d = 2 + 1, and Wigner's massless 'infinite spin' particles. For the latter, free string-localized quantum fields have been constructed; (c) in contrast to the point-localized case, string-localization admits covariant vector/tensor potentials for fotons and gravitons in a Hilbert space representation with positive energy. We shall present free string-localized quantum fields for various particle types, and some ideas about the perturbative construction of interacting string-localized fields. A central point will be an analogue of gauge theories, completely within a Hilbert space and without ghosts, trading gauge dependence with dependence on the direction of the localization string. In order to discuss renormalizability (item (a)), methods from microlocal analysis (wave front set and scaling degree) are needed. (author)

  19. A Platonic Sextet for Strings

    Science.gov (United States)

    Schaffer, Karl

    2012-01-01

    The use of traditional string figures by the Dr. Schaffer and Mr. Stern Dance Ensemble led to experimentation with polyhedral string constructions. This article presents a series of polyhedra made with six loops of three colors which sequence through all the Platonic Solids.

  20. Symmetry breaking in string theory

    International Nuclear Information System (INIS)

    Potting, R.

    1998-01-01

    A mechanism for a spontaneous breakdown of CPT symmetry appears in string theory, with possible implications for particle models. A realistic string theory might exhibit CPT violation at levels detectable in current or future experiments. A possible new mechanism for baryogenesis in the early Universe is also discussed

  1. Energy in a String Wave

    Science.gov (United States)

    Ng, Chiu-king

    2010-01-01

    When one end of a taut horizontal elastic string is shaken repeatedly up and down, a transverse wave (assume sine waveform) will be produced and travel along it. College students know this type of wave motion well. They know when the wave passes by, each element of the string will perform an oscillating up-down motion, which in mechanics is termed…

  2. String theory : physics or metaphysics?

    CERN Document Server

    Veneziano, Gabriele

    2010-01-01

    I will give arguments for why the enormous progress made during the last century on understanding elementary particles and their fundamental interactions suggests strings as the truly elementary constituents of Nature. I will then address the issue of whether the string paradigm can in principle be falsified or whether it should be considered as mere metaphysics.

  3. Differential formulation in string theories

    International Nuclear Information System (INIS)

    Guzzo, M.M.

    1987-01-01

    The equations of gauge invariance motion for theories of boson open strings and Neveu-Schwarz and Ramond superstring are derived. A construction for string theories using differential formalism, is introduced. The importance of BRST charge for constructing such theories and the necessity of introduction of auxiliary fields are verified. (M.C.K.) [pt

  4. Deformations of topological open strings

    NARCIS (Netherlands)

    Hofman, C.; Ma, Whee Ky

    Deformations of topological open string theories are described, with an emphasis on their algebraic structure. They are encoded in the mixed bulk-boundary correlators. They constitute the Hochschild complex of the open string algebra - the complex of multilinear maps on the boundary Hilbert space.

  5. Towards optimal packed string matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2014-01-01

    -size string-matching instruction wssm is available in contemporary commodity processors. The other word-size maximum-suffix instruction wslm is only required during the pattern pre-processing. Benchmarks show that our solution can be efficiently implemented, unlike some prior theoretical packed string...

  6. Experimenting with String Musical Instruments

    Science.gov (United States)

    LoPresto, Michael C.

    2012-01-01

    What follows are several investigations involving string musical instruments developed for and used in a "Science of Sound & Light" course. The experiments make use of a guitar, orchestral string instruments and data collection and graphing software. They are designed to provide students with concrete examples of how mathematical formulae, when…

  7. Progress in string theory research

    CERN Document Server

    2016-01-01

    At the first look, the String Theory seems just an interesting and non-trivial application of the quantum mechanics and the special relativity to vibrating strings. By itself, the quantization of relativistic strings does not call the attention of the particle physicist as a significant paradigm shift. However, when the string quantization is performed by applying the standard rules of the perturbative Quantum Field Theory, one discovers that the strings in certain states have the same physical properties as the gravity in the flat space-time. Chapter one of this book reviews the construction of the thermal bosonic string and D-brane in the framework of the Thermo Field Dynamics (TFD). It briefly recalls the wellknown light-cone quantization of the bosonic string in the conformal gauge in flat space-time, and gives a bird’s eye view of the fundamental concepts of the TFD. Chapter two examines a visual model inspired by string theory, on the system of interacting anyons. Chapter three investigate the late-ti...

  8. Gauge invariance of string fields

    International Nuclear Information System (INIS)

    Banks, T.; Peskin, M.E.

    1985-10-01

    Some work done to understand the appearance of gauge bosons and gravitons in string theories is reported. An action has been constructed for free (bosonic) string field theory which is invariant under an infinite set of gauge transformations which include Yang-Mills transformations and general coordinate transformations as special cases. 15 refs., 1 tab

  9. String dualities and superpotential

    International Nuclear Information System (INIS)

    Ha, Tae-Won

    2010-09-01

    The main objective of this thesis is the computation of the superpotential induced by D5- branes in the type IIB string theory and by five-branes in the heterotic string theory. Both superpotentials have the same functional form which is the chain integral of the holomorphic three-form. Using relative (co)homology we can unify the flux and brane superpotential. The chain integral can be seen as an example of the Abel-Jacobi map. We discuss many structures such as mixed Hodge structure which allows for the computation of Picard-Fuchs differential equations crucial for explicit computations. We blow up the Calabi-Yau threefold along the submanifold wrapped by the brane to obtain geometrically more appropriate configuration. The resulting geometry is non-Calabi-Yau and we have a canonically given divisor. This blown-up geometry makes it possible to restrict our attention to complex structure deformations. However, the direct computation is yet very difficult, thus the main tool for computation will be the lift of the brane configuration to a F-theory compactification. In F-theory, since complex structure, brane and, if present, bundlemoduli are all contained in the complex structure moduli space of the elliptic Calabi-Yau fourfold, the computation can be dramatically simplified. The heterotic/F-theory duality is extended to include the blow-up geometry and thereby used to give the blow-up geometry amore physical meaning. (orig.)

  10. String dualities and superpotential

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Tae-Won

    2010-09-15

    The main objective of this thesis is the computation of the superpotential induced by D5- branes in the type IIB string theory and by five-branes in the heterotic string theory. Both superpotentials have the same functional form which is the chain integral of the holomorphic three-form. Using relative (co)homology we can unify the flux and brane superpotential. The chain integral can be seen as an example of the Abel-Jacobi map. We discuss many structures such as mixed Hodge structure which allows for the computation of Picard-Fuchs differential equations crucial for explicit computations. We blow up the Calabi-Yau threefold along the submanifold wrapped by the brane to obtain geometrically more appropriate configuration. The resulting geometry is non-Calabi-Yau and we have a canonically given divisor. This blown-up geometry makes it possible to restrict our attention to complex structure deformations. However, the direct computation is yet very difficult, thus the main tool for computation will be the lift of the brane configuration to a F-theory compactification. In F-theory, since complex structure, brane and, if present, bundlemoduli are all contained in the complex structure moduli space of the elliptic Calabi-Yau fourfold, the computation can be dramatically simplified. The heterotic/F-theory duality is extended to include the blow-up geometry and thereby used to give the blow-up geometry amore physical meaning. (orig.)

  11. Cosmology from string theory

    International Nuclear Information System (INIS)

    Anchordoqui, Luis; Nawata, Satoshi; Goldberg, Haim; Nunez, Carlos

    2007-01-01

    We explore the cosmological content of Salam-Sezgin six-dimensional supergravity, and find a solution to the field equations in qualitative agreement with observation of distant supernovae, primordial nucleosynthesis abundances, and recent measurements of the cosmic microwave background. The carrier of the acceleration in the present de Sitter epoch is a quintessence field slowly rolling down its exponential potential. Intrinsic to this model is a second modulus which is automatically stabilized and acts as a source of cold dark matter, with a mass proportional to an exponential function of the quintessence field (hence realizing varying mass particle models within a string context). However, any attempt to saturate the present cold dark matter component in this manner leads to unacceptable deviations from cosmological data--a numerical study reveals that this source can account for up to about 7% of the total cold dark matter budget. We also show that (1) the model will support a de Sitter energy in agreement with observation at the expense of a miniscule breaking of supersymmetry in the compact space; (2) variations in the fine structure constant are controlled by the stabilized modulus and are negligible; (3) ''fifth'' forces are carried by the stabilized modulus and are short range; (4) the long time behavior of the model in four dimensions is that of a Robertson-Walker universe with a constant expansion rate (w=-1/3). Finally, we present a string theory background by lifting our six-dimensional cosmological solution to ten dimensions

  12. Poisson hierarchy of discrete strings

    International Nuclear Information System (INIS)

    Ioannidou, Theodora; Niemi, Antti J.

    2016-01-01

    The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.

  13. Basic Concepts of String Theory

    CERN Document Server

    Blumenhagen, Ralph; Theisen, Stefan

    2013-01-01

    The purpose of this book is to thoroughly prepare the reader for research in string theory. It is intended as a textbook in the sense that, starting from the basics, the material is presented in a pedagogical and self-contained fashion. The emphasis is on the world-sheet perspective of closed strings and of open strings ending on D-branes, where two-dimensional conformal field theory is the main tool. Compactifications of string theory, with and without fluxes, and string dualities are also discussed from the space-time point of view, i.e. in geometric language. End-of-chapter references have been added to guide the reader intending to pursue further studies or to start research in the topics covered by this book.

  14. Strings, conformal fields and topology

    International Nuclear Information System (INIS)

    Kaku, Michio

    1991-01-01

    String Theory has advanced at an astonishing pace in the last few years, and this book aims to acquaint the reader with the most active topics of research in the field. Building on the foundations laid in his Introduction to Superstrings, Professor Kaku discusses such topics as the classification of conformal string theories, knot theory, the Yang-Baxter relation, quantum groups, the non-polynominal closed string field theory, matrix models, and topological field theory. Several chapters review the fundamentals of string theory, making the presentation of the material self-contained while keeping overlap with the earlier book to a minimum. The book conveys the vitality of current research in string theory and places readers at its forefront. (orig.) With 40 figs. in 50 parts

  15. Poisson hierarchy of discrete strings

    Energy Technology Data Exchange (ETDEWEB)

    Ioannidou, Theodora, E-mail: ti3@auth.gr [Faculty of Civil Engineering, School of Engineering, Aristotle University of Thessaloniki, 54249, Thessaloniki (Greece); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2016-01-28

    The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.

  16. Basic concepts of string theory

    International Nuclear Information System (INIS)

    Blumenhagen, Ralph

    2013-01-01

    The purpose of this book is to thoroughly prepare the reader for research in string theory. It is intended as a textbook in the sense that, starting from the basics, the material is presented in a pedagogical and self-contained fashion. The emphasis is on the world-sheet perspective of closed strings and of open strings ending on D-branes, where two-dimensional conformal field theory is the main tool. Compactifications of string theory, with and without fluxes, and string dualities are also discussed from the space-time point of view, i.e. in geometric language. End-of-chapter references have been added to guide the reader intending to pursue further studies or to start research in the topics covered by this book.

  17. Testing string theory at LHC?

    CERN Multimedia

    CERN. Geneva

    2002-01-01

    A theory with such mathematical beauty cannot be wrong: this is one of the main arguments in favour of string theory, which unifies all known physical theories of fundamental interactions in a single coherent description of the universe. But no one has ever observed strings, not even indirectly, nor the space of extra dimensions where they live. However there are good reasons to believe that the 'hidden' dimensions of string theory may be much larger than what we thought in the past and that they may be within experimental reach in the near future - together with the strings themselves. In my talk, I will give an elementary introduction of string theory and describe the main experimental predictions.Organiser(s): Jasper Kirkby / EP DivisionNote: Tea & coffee will be served at 16.00 hrs.

  18. Salivary agglutinin and lung scavenger receptor cysteine-rich glycoprotein 340 have broad anti-influenza activities and interactions with surfactant protein D that vary according to donor source and sialylation

    DEFF Research Database (Denmark)

    Hartshorn, Kevan L.; Ligtenberg, Antoon; White, Mitchell R.

    2006-01-01

    We previously found that scavenger receptor cysteine-rich gp-340 (glycoprotein-340), isolated from lung or saliva, directly inhibits human IAVs (influenza A viruses). We now show that salivary gp-340 has broad antiviral activity against human, equine and porcine IAV strains. Although lung...

  19. Oriented open-closed string theory revisited

    International Nuclear Information System (INIS)

    Zwiebach, B.

    1998-01-01

    String theory on D-brane backgrounds is open-closed string theory. Given the relevance of this fact, we give details and elaborate upon our earlier construction of oriented open-closed string field theory. In order to incorporate explicitly closed strings, the classical sector of this theory is open strings with a homotopy associative A ∞ algebraic structure. We build a suitable Batalin-Vilkovisky algebra on moduli spaces of bordered Ricmann surfaces, the construction of which involves a few subtleties arising from the open string punctures and cyclicity conditions. All vertices coupling open and closed strings through disks are described explicitly. Subalgebras of the algebra of surfaces with boundaries are used to discuss symmetries of classical open string theory induced by the closed string sector, and to write classical open string field theory on general closed string backgrounds. We give a preliminary analysis of the ghost-dilaton theorem. copyright 1998 Academic Press, Inc

  20. A string theory which isn't about strings

    Science.gov (United States)

    Lee, Kanghoon; Rey, Soo-Jong; Rosabal, J. A.

    2017-11-01

    Quantization of closed string proceeds with a suitable choice of worldsheet vacuum. A priori, the vacuum may be chosen independently for left-moving and right-moving sectors. We construct ab initio quantized bosonic string theory with left-right asymmetric worldsheet vacuum and explore its consequences and implications. We critically examine the validity of new vacuum and carry out first-quantization using standard operator formalism. Remarkably, the string spectrum consists only of a finite number of degrees of freedom: string gravity (massless spin-two, Kalb-Ramond and dilaton fields) and two massive spin-two Fierz-Pauli fields. The massive spin-two fields have negative norm, opposite mass-squared, and provides a Lee-Wick type extension of string gravity. We compute two physical observables: tree-level scattering amplitudes and one-loop cosmological constant. Scattering amplitude of four dilatons is shown to be a rational function of kinematic invariants, and in D = 26 factorizes into contributions of massless spin-two and a pair of massive spin-two fields. The string one loop partition function is shown to perfectly agree with one loop Feynman diagram of string gravity and two massive spin-two fields. In particular, it does not exhibit modular invariance. We critically compare our construction with recent studies and contrast differences.

  1. Conformal techniques in string theory and string field theory

    International Nuclear Information System (INIS)

    Giddings, S.B.

    1987-01-01

    The application of some conformal and Riemann surface techniques to string theory and string field theory is described. First a brief review of Riemann surface techniques and of the Polyakov approach to string theory is presented. This is followed by a discussion of some features of string field theory and of its Feynman rules. Specifically, it is shown that the Feynman diagrams for Witten's string field theory respect modular invariance, and in particular give a triangulation of moduli space. The Polyakov formalism is then used to derive the Feynman rules that should follow from this theory upon gauge-fixing. It should also be possible to apply this derivation to deduce the Feynman rules for other gauge-fixed string field theories. Following this, Riemann surface techniques are turned to the problem of proving the equivalence of the Polyakov and light-cone formalisms. It is first shown that the light-cone diagrams triangulate moduli space. Then the Polyakov measure is worked out for these diagrams, and shown to equal that deduced from the light-cone gauge fixed formalism. Also presented is a short description of the comparison of physical states in the two formalisms. The equivalence of the two formalisms in particular constitutes a proof of the unitarity of the Polyakov framework for the closed bosonic string

  2. Enhancement of thioredoxin/glutaredoxin-mediated L-cysteine synthesis from S-sulfocysteine increases L-cysteine production in Escherichia coli

    Science.gov (United States)

    2012-01-01

    Background Escherichia coli has two L-cysteine biosynthetic pathways; one is synthesized from O-acetyl L-serine (OAS) and sulfate by L-cysteine synthase (CysK), and another is produced via S-sulfocysteine (SSC) from OAS and thiosulfate by SSC synthase (CysM). SSC is converted into L-cysteine and sulfite by an uncharacterized reaction. As thioredoxins (Trx1 and Trx2) and glutaredoxins (Grx1, Grx2, Grx3, Grx4, and NrdH) are known as reductases of peptidyl disulfides, overexpression of such reductases might be a good way for improving L-cysteine production to accelerate the reduction of SSC in E. coli. Results Because the redox enzymes can reduce the disulfide that forms on proteins, we first tested whether these enzymes catalyze the reduction of SSC to L-cysteine. All His-tagged recombinant enzymes, except for Grx4, efficiently convert SSC into L-cysteine in vitro. Overexpression of Grx1 and NrdH enhanced a 15-40% increase in the E. coliL-cysteine production. On the other hand, disruption of the cysM gene cancelled the effect caused by the overexpression of Grx1 and NrdH, suggesting that its improvement was due to the efficient reduction of SSC under the fermentative conditions. Moreover, L-cysteine production in knockout mutants of the sulfite reductase genes (ΔcysI and ΔcysJ) and the L-cysteine synthase gene (ΔcysK) each decreased to about 50% of that in the wild-type strain. Interestingly, there was no significant difference in L-cysteine production between wild-type strain and gene deletion mutant of the upstream pathway of sulfite (ΔcysC or ΔcysH). These results indicate that sulfite generated from the SSC reduction is available as the sulfur source to produce additional L-cysteine molecule. It was finally found that in the E. coliL-cysteine producer that co-overexpress glutaredoxin (NrdH), sulfite reductase (CysI), and L-cysteine synthase (CysK), there was the highest amount of L-cysteine produced per cell. Conclusions In this work, we showed that Grx1 and

  3. Bacteria binding by DMBT1/SAG/gp-340 is confined to the VEVLXXXXW motif in its scavenger receptor cysteine-rich domains

    DEFF Research Database (Denmark)

    Bikker, Floris J; Ligtenberg, Antoon J M; End, Caroline

    2004-01-01

    The scavenger receptor cysteine-rich (SRCR) proteins form an archaic group of metazoan proteins characterized by the presence of SRCR domains. These proteins are classified in group A and B based on the number of conserved cysteine residues in their SRCR domains, i.e. six for group A and eight fo...

  4. String model of elementary particles

    International Nuclear Information System (INIS)

    Kikkawa, Keiji

    1975-01-01

    Recent development of the models of elementary particles is described. The principal features of elementary particle physics can be expressed by quark model, mass spectrum, the Regge behavior of scattering amplitude, and duality. Venezians showed in 1968 that the B function can express these features. From the analysis of mass spectrum, the string model was introduced. The quantization of the string is performed with the same procedure as the ordinary quantum mechanics. The motion of the string is determined by the Nambu-Goto action integral, and the Schroedinger equation is obtained. Mass spectrum from the string model was same as that from the duality model such as Veneziano model. The interaction between strings can be introduced, and the Lagrangian can be formulated. The relation between the string model and the duality model has been studied. The string model is the first theory of non-local field, and the further development is attractive. The relation between this model and the quark model is still not clear. (Kato, T.)

  5. String bit models for superstring

    International Nuclear Information System (INIS)

    Bergman, O.; Thorn, C.B.

    1995-01-01

    The authors extend the model of string as a polymer of string bits to the case of superstring. They mainly concentrate on type II-B superstring, with some discussion of the obstacles presented by not II-B superstring, together with possible strategies for surmounting them. As with previous work on bosonic string work within the light-cone gauge. The bit model possesses a good deal less symmetry than the continuous string theory. For one thing, the bit model is formulated as a Galilei invariant theory in (D - 2) + 1 dimensional space-time. This means that Poincare invariance is reduced to the Galilei subgroup in D - 2 space dimensions. Naturally the supersymmetry present in the bit model is likewise dramatically reduced. Continuous string can arise in the bit models with the formation of infinitely long polymers of string bits. Under the right circumstances (at the critical dimension) these polymers can behave as string moving in D dimensional space-time enjoying the full N = 2 Poincare supersymmetric dynamics of type II-B superstring

  6. String bit models for superstring

    Energy Technology Data Exchange (ETDEWEB)

    Bergman, O.; Thorn, C.B.

    1995-12-31

    The authors extend the model of string as a polymer of string bits to the case of superstring. They mainly concentrate on type II-B superstring, with some discussion of the obstacles presented by not II-B superstring, together with possible strategies for surmounting them. As with previous work on bosonic string work within the light-cone gauge. The bit model possesses a good deal less symmetry than the continuous string theory. For one thing, the bit model is formulated as a Galilei invariant theory in (D {minus} 2) + 1 dimensional space-time. This means that Poincare invariance is reduced to the Galilei subgroup in D {minus} 2 space dimensions. Naturally the supersymmetry present in the bit model is likewise dramatically reduced. Continuous string can arise in the bit models with the formation of infinitely long polymers of string bits. Under the right circumstances (at the critical dimension) these polymers can behave as string moving in D dimensional space-time enjoying the full N = 2 Poincare supersymmetric dynamics of type II-B superstring.

  7. Fermions on the electroweak string

    CERN Document Server

    Moreno, J M; Quirós, Mariano; Moreno, J M; Oaknin, D H; Quiros, M

    1995-01-01

    We construct a simple class of exact solutions of the electroweak theory including the naked Z--string and fermion fields. It consists in the Z--string configuration (\\phi,Z_\\theta), the {\\it time} and z components of the neutral gauge bosons (Z_{0,3},A_{0,3}) and a fermion condensate (lepton or quark) zero mode. The Z--string is not altered (no feed back from the rest of fields on the Z--string) while fermion condensates are zero modes of the Dirac equation in the presence of the Z--string background (no feed back from the {\\it time} and z components of the neutral gauge bosons on the fermion fields). For the case of the n--vortex Z--string the number of zero modes found for charged leptons and quarks is (according to previous results by Jackiw and Rossi) equal to |n|, while for (massless) neutrinos is |n|-1. The presence of fermion fields in its core make the obtained configuration a superconducting string, but their presence (as well as that of Z_{0,3},A_{0,3}) does not enhance the stability of the Z--stri...

  8. Gravity and strings

    CERN Document Server

    Ortín, Tomás

    2015-01-01

    Self-contained and comprehensive, this definitive new edition of Gravity and Strings is a unique resource for graduate students and researchers in theoretical physics. From basic differential geometry through to the construction and study of black-hole and black-brane solutions in quantum gravity - via all the intermediate stages - this book provides a complete overview of the intersection of gravity, supergravity, and superstrings. Now fully revised, this second edition covers an extensive array of topics, including new material on non-linear electric-magnetic duality, the electric-tensor formalism, matter-coupled supergravity, supersymmetric solutions, the geometries of scalar manifolds appearing in 4- and 5-dimensional supergravities, and much more. Covering reviews of important solutions and numerous solution-generating techniques, and accompanied by an exhaustive index and bibliography, this is an exceptional reference work.

  9. Fingerprints in compressed strings

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Cording, Patrick Hagge

    2017-01-01

    In this paper we show how to construct a data structure for a string S of size N compressed into a context-free grammar of size n that supports efficient Karp–Rabin fingerprint queries to any substring of S. That is, given indices i and j, the answer to a query is the fingerprint of the substring S......[i,j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(log⁡N) query time, and for Linear SLPs (an SLP derivative that captures LZ78 compression and its variations) we get O(log⁡log⁡N) query time...

  10. Field theory and strings

    International Nuclear Information System (INIS)

    Bonara, L.; Cotta-Ramusino, P.; Rinaldi, M.

    1987-01-01

    It is well-known that type I and heterotic superstring theories have a zero mass spectrum which correspond to the field content of N=1 supergravity theory coupled to supersymmetric Yang-Mills theory in 10-D. The authors study the field theory ''per se'', in the hope that simple consistency requirements will determine the theory completely once one knows the field content inherited from string theory. The simplest consistency requirements are: N=1 supersymmetry; and absence of chiral anomalies. This is what the authors discuss in this paper here leaving undetermined the question of the range of validity of the resulting field theory. As is known, a model of N=1 supergravity (SUGRA) coupled to supersymmetric Yang-Mills (SYM) theory was known in the form given by Chapline and Manton. The coupling of SUGRA to SYM was determined by the definition of the ''field strength'' 3-form H in this paper

  11. Cysteine Protease Inhibitors as Chemotherapy: Lessons from a Parasite Target

    Science.gov (United States)

    Selzer, Paul M.; Pingel, Sabine; Hsieh, Ivy; Ugele, Bernhard; Chan, Victor J.; Engel, Juan C.; Bogyo, Matthew; Russell, David G.; Sakanari, Judy A.; McKerrow, James H.

    1999-09-01

    Papain family cysteine proteases are key factors in the pathogenesis of cancer invasion, arthritis, osteoporosis, and microbial infections. Targeting this enzyme family is therefore one strategy in the development of new chemotherapy for a number of diseases. Little is known, however, about the efficacy, selectivity, and safety of cysteine protease inhibitors in cell culture or in vivo. We now report that specific cysteine protease inhibitors kill Leishmania parasites in vitro, at concentrations that do not overtly affect mammalian host cells. Inhibition of Leishmania cysteine protease activity was accompanied by defects in the parasite's lysosome/endosome compartment resembling those seen in lysosomal storage diseases. Colocalization of anti-protease antibodies with biotinylated surface proteins and accumulation of undigested debris and protease in the flagellar pocket of treated parasites were consistent with a pathway of protease trafficking from flagellar pocket to the lysosome/endosome compartment. The inhibitors were sufficiently absorbed and stable in vivo to ameliorate the pathology associated with a mouse model of Leishmania infection.

  12. Dynamical evolution of cosmic strings

    International Nuclear Information System (INIS)

    Bouchet, F.R.

    1988-01-01

    The author have studied by means of numerical simulations the dynamical evolution of a network of cosmic strings, both in the radiation and matter era. Our basic conclusion is that a scaling solution exists, i.e., the string energy density evolves as t -2 . This means that the process by which long strings dump their energy into closed loops (which can gravitationally radiate away) is efficient enough to prevent the string domination over other forms of energy. This conclusion does not depend on the initial string energy density, nor on the various numerical parameters. On the other hand, the generated spectrum of loop sizes does depend on the value of our numerical lower cutoff (i.e., the minimum length of loop we allow to be chopped off the network). Furthermore, the network evolution is very different from what was assumed before), namely the creation of a few horizon sized loops per horizon volume and per hubble time, which subsequently fragment into about 10 smaller daughter loops. Rather, many tiny loops are directly cut from the network of infinite strings, and it appears that the only fundamental scale (the horizon) has been lost. This is probably because a fundamental ingredient had been overlooked, namely the kinks. These kinks are created in pairs at each intercommutation, and very rapidly, the long strings appear to be very kinky. Thus the number of long strings per horizon is still of the order of a few, but their total length is fairly large. Furthermore, a large number of kinks favors the formation of small loops, and their sizes might well be governed by the kink density along the long strings. Finally, we computed the two-point correlation function of the loops and found significant differences from the work of Turok

  13. Casimir energy of a nonuniform string

    Science.gov (United States)

    Hadasz, L.; Lambiase, G.; Nesterenko, V. V.

    2000-07-01

    The Casimir energy of a nonuniform string built up from two pieces with different speeds of sound is calculated. A standard procedure of subtracting the energy of an infinite uniform string is applied, the subtraction being interpreted as the renormalization of the string tension. It is shown that in the case of a homogeneous string this method is completely equivalent to zeta renormalization.

  14. Test particle trajectories near cosmic strings

    Indian Academy of Sciences (India)

    We present a detailed analysis of the motion of test particle in the gravitational field of cosmic strings in different situations using the Hamilton–Jacobi (H–J) formalism. We have discussed the trajectories near static cosmic string, cosmic string in Brans–Dicke theory and cosmic string in dilaton gravity.

  15. String Formatting Considered Harmful for Novice Programmers

    Science.gov (United States)

    Hughes, Michael C.; Jadud, Matthew C.; Rodrigo, Ma. Mercedes T.

    2010-01-01

    In Java, "System.out.printf" and "String.format" consume a specialised kind of string commonly known as a format string. In our study of first-year students at the Ateneo de Manila University, we discovered that format strings present a substantial challenge for novice programmers. Focusing on their first laboratory we found…

  16. M-strings, Elliptic Genera and N=4 String Amplitudes

    CERN Document Server

    Hohenegger, Stefan

    2014-01-01

    We study mass-deformed N=2 gauge theories from various points of view. Their partition functions can be computed via three dual approaches: firstly, (p,q)-brane webs in type II string theory using Nekrasov's instanton calculus, secondly, the (refined) topological string using the topological vertex formalism and thirdly, M theory via the elliptic genus of certain M-strings configurations. We argue for a large class of theories that these approaches yield the same gauge theory partition function which we study in detail. To make their modular properties more tangible, we consider a fourth approach by connecting the partition function to the equivariant elliptic genus of R^4 through a (singular) theta-transform. This form appears naturally as a specific class of one-loop scattering amplitudes in type II string theory on T^2, which we calculate explicitly.

  17. Covariant N-string amplitude

    International Nuclear Information System (INIS)

    Di Vecchia, P.; Sciuto, S.; Nakayama, R.; Petersen, J.L.; Sidenius, J.R.

    1986-11-01

    The BRST-invariant N-Reggeon vertex (for the bosonic string) previously given by us in the operator formulation is considered in more detail. In particular we present a direct derivation from the string path integral. Several crucial symmetry properties found a posteriori before, become a priori clearer in this formulation. A number of delicate points related to zero modes, cut off procedures and normal ordering prescriptions are treated in some detail. The old technique of letting the string field acquire a small dimension ε/2 → 0 + is found especially elegant. (orig.)

  18. Plucked Strings and the Harpsichord

    Science.gov (United States)

    GIORDANO, N.; WINANS, J. P.

    1999-07-01

    The excitation of a harpsichord string when it is set into motion, i.e., plucked, by a plectrum is studied. We find that the amplitude of the resulting string vibration is approximately independent of the velocity with which the key is depressed. This result is in accord with conventional wisdom, but at odds with a recent theoretical model. A more realistic theoretical treatment of the plucking process is then described, and shown to be consistent with our measurements. The experiments reveal several other interesting aspects of the plectrum-string interaction.

  19. Worldsheet geometries of ambitwistor string

    Energy Technology Data Exchange (ETDEWEB)

    Ohmori, Kantaro [Department of Physics, the University of Tokyo,Hongo, Bunkyo-ku, Tokyo 133-0022 (Japan)

    2015-06-12

    Mason and Skinner proposed the ambitwistor string theory which directly reproduces the formulas for the amplitudes of massless particles proposed by Cachazo, He and Yuan. In this paper we discuss geometries of the moduli space of worldsheets associated to the bosonic or the RNS ambitwistor string. Further, we investigate the factorization properties of the amplitudes when an internal momentum is near on-shell in the abstract CFT language. Along the way, we propose the existence of the ambitwistor strings with three or four fermionic worldsheet currents.

  20. Spin chain for quantum strings

    International Nuclear Information System (INIS)

    Beisert, N.

    2005-01-01

    We review and compare the integrable structures in N=4 gauge theory and string theory on AdS 5 x S 5 . Recently, Bethe ansaetze for gauge theory/weak coupling and string theory/strong coupling were proposed to describe scaling dimensions in the su(2) subsector. Here we investigate the Bethe equations for quantum string theory, naively extrapolated to weak coupling. Excitingly, we find a spin chain Hamiltonian similar, but not equal, to the gauge theory dilatation operator. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

  1. Geometry, topology, and string theory

    Energy Technology Data Exchange (ETDEWEB)

    Varadarajan, Uday [Univ. of California, Berkeley, CA (United States)

    2003-01-01

    A variety of scenarios are considered which shed light upon the uses and limitations of classical geometric and topological notions in string theory. The primary focus is on situations in which D-brane or string probes of a given classical space-time see the geometry quite differently than one might naively expect. In particular, situations in which extra dimensions, non-commutative geometries as well as other non-local structures emerge are explored in detail. Further, a preliminary exploration of such issues in Lorentzian space-times with non-trivial causal structures within string theory is initiated.

  2. Geometry, topology, and string theory

    International Nuclear Information System (INIS)

    Varadarajan, Uday

    2003-01-01

    A variety of scenarios are considered which shed light upon the uses and limitations of classical geometric and topological notions in string theory. The primary focus is on situations in which D-brane or string probes of a given classical space-time see the geometry quite differently than one might naively expect. In particular, situations in which extra dimensions, non-commutative geometries as well as other non-local structures emerge are explored in detail. Further, a preliminary exploration of such issues in Lorentzian space-times with non-trivial causal structures within string theory is initiated

  3. String cosmology modern string theory concepts from the cosmic structure

    CERN Document Server

    2009-01-01

    The field of string cosmology has matured considerably over the past few years, attracting many new adherents to this multidisciplinary Field. This book fills a critical gap by bringing together strains of current research into one single volume. The resulting collection of selected articles presents the latest, ongoing results from renowned experts currently working in the field. This offers the possibility for practitioners to become conversant with many different aspects of string cosmology

  4. String cosmology. Large-field inflation in string theory

    International Nuclear Information System (INIS)

    Westphal, Alexander

    2014-09-01

    This is a short review of string cosmology. We wish to connect string-scale physics as closely as possible to observables accessible to current or near-future experiments. Our possible best hope to do so is a description of inflation in string theory. The energy scale of inflation can be as high as that of Grand Unification (GUT). If this is the case, this is the closest we can possibly get in energy scales to string-scale physics. Hence, GUT-scale inflation may be our best candidate phenomenon to preserve traces of string-scale dynamics. Our chance to look for such traces is the primordial gravitational wave, or tensor mode signal produced during inflation. For GUT-scale inflation this is strong enough to be potentially visible as a B-mode polarization of the cosmic microwave background (CMB). Moreover, a GUT-scale inflation model has a trans-Planckian excursion of the inflaton scalar field during the observable amount of inflation. Such large-field models of inflation have a clear need for symmetry protection against quantum corrections. This makes them ideal candidates for a description in a candidate fundamental theory like string theory. At the same time the need of large-field inflation models for UV completion makes them particularly susceptible to preserve imprints of their string-scale dynamics in the inflationary observables, the spectral index n s and the fractional tensor mode power r. Hence, we focus this review on axion monodromy inflation as a mechanism of large-field inflation in string theory.

  5. Preparation, crystallization and X-ray diffraction analysis to 1.5 Å resolution of rat cysteine dioxygenase, a mononuclear iron enzyme responsible for cysteine thiol oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R. [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States); Hao, Quan [MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853-8001 (United States); Stipanuk, Martha H., E-mail: mhs6@cornell.edu [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States)

    2005-11-01

    Recombinant rat cysteine dioxygenase (CDO) has been expressed, purified and crystallized and X-ray diffraction data have been collected to 1.5 Å resolution. Cysteine dioxygenase (CDO; EC 1.13.11.20) is an ∼23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O{sub 2}, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Å resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Å, α = β = γ = 90°. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  6. Charting the Landscape of Supercritical String Theory

    International Nuclear Information System (INIS)

    Hellerman, Simeon; Swanson, Ian

    2007-01-01

    Special solutions of string theory in supercritical dimensions can interpolate in time between theories with different numbers of spacetime dimensions and different amounts of world sheet supersymmetry. These solutions connect supercritical string theories to the more familiar string duality web in ten dimensions and provide a precise link between supersymmetric and purely bosonic string theories. Dimension quenching and c duality appear to be natural concepts in string theory, giving rise to large networks of interconnected theories

  7. String and Sticky Tape Experiments.

    Science.gov (United States)

    Edge, R. D., Ed.

    1979-01-01

    Explains how to demonstrate the fundamentals of one dimensional kinematics such as Newton's third law of motion, and collision between bodies, using simple materials of marbles, strings, sticky tape, drinking straws, and rubber bands. (GA)

  8. String theory or field theory?

    International Nuclear Information System (INIS)

    Marshakov, A.V.

    2002-01-01

    The status of string theory is reviewed, and major recent developments - especially those in going beyond perturbation theory in the string theory and quantum field theory frameworks - are analyzed. This analysis helps better understand the role and place of experimental phenomena, it is emphasized that there are some insurmountable problems inherent in it - notably the impossibility to formulate the quantum theory of gravity on its basis - which prevent it from being a fundamental physical theory of the world of microscopic distances. It is this task, the creation of such a theory, which string theory, currently far from completion, is expected to solve. In spite of its somewhat vague current form, string theory has already led to a number of serious results and greatly contributed to progress in the understanding of quantum field theory. It is these developments, which are our concern in this review [ru

  9. String moduli inflation. An overview

    Energy Technology Data Exchange (ETDEWEB)

    Cicoli, Michele [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Quevedo, Fernando [Cambridge Univ. (United Kingdom). DAMTP/CMS; Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)

    2011-06-15

    We present an overview of inflationary models derived from string theory focusing mostly on closed string moduli as inflatons. After a detailed discussion of the {eta}-problem and different approaches to address it, we describe possible ways to obtain a de Sitter vacuum with all closed string moduli stabilised. We then look for inflationary directions and present some of the most promising scenarios where the inflatons are either the real or the imaginary part of Kaehler moduli. We pay particular attention on extracting potential observable implications, showing how most of the scenarios predict negligible gravitational waves and could therefore be ruled out by the Planck satellite. We conclude by briefly mentioning some open challenges in string cosmology beyond deriving just inflation. (orig.)

  10. Spin chains and string theory.

    Science.gov (United States)

    Kruczenski, Martin

    2004-10-15

    Recently, an important test of the anti de Sitter/conformal field theory correspondence has been done using rotating strings with two angular momenta. We show that such a test can be described more generally as the agreement between two actions: one a low energy description of a spin chain appearing in the field theory side, and the other a limit of the string action in AdS5xS5. This gives a map between the mean value of the spin in the boundary theory and the position of the string in the bulk, and shows how a string action can emerge from a gauge theory in the large-N limit.

  11. Pattern recognition and string matching

    CERN Document Server

    Cheng, Xiuzhen

    2002-01-01

    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  12. String moduli inflation. An overview

    International Nuclear Information System (INIS)

    Cicoli, Michele; Quevedo, Fernando

    2011-06-01

    We present an overview of inflationary models derived from string theory focusing mostly on closed string moduli as inflatons. After a detailed discussion of the η-problem and different approaches to address it, we describe possible ways to obtain a de Sitter vacuum with all closed string moduli stabilised. We then look for inflationary directions and present some of the most promising scenarios where the inflatons are either the real or the imaginary part of Kaehler moduli. We pay particular attention on extracting potential observable implications, showing how most of the scenarios predict negligible gravitational waves and could therefore be ruled out by the Planck satellite. We conclude by briefly mentioning some open challenges in string cosmology beyond deriving just inflation. (orig.)

  13. String Formation Beyond Leading Colour

    CERN Document Server

    Christiansen, Jesper R.

    2015-08-03

    We present a new model for the hadronisation of multi-parton systems, in which colour correlations beyond leading $N_C$ are allowed to influence the formation of confining potentials (strings). The multiplet structure of $SU(3)$ is combined with a minimisation of the string potential energy, to decide between which partons strings should form, allowing also for "baryonic" configurations (e.g., two colours can combine coherently to form an anticolour). In $e^+e^-$collisions, modifications to the leading-colour picture are small, suppressed by both colour and kinematics factors. But in $pp$ collisions, multi-parton interactions increase the number of possible subleading connections, counteracting their naive $1/N_C^2$ suppression. Moreover, those that reduce the overall string lengths are kinematically favoured. The model, which we have implemented in the PYTHIA 8 generator, is capable of reaching agreement not only with the important $\\left(n_\\mathrm{charged})$ distribution but also with measured rates (and ra...

  14. IgG antibodies to endothelial protein C receptor-binding Cysteine-rich interdomain region domains of Plasmodium falciparum erythrocyte membrane protein 1 are acquired early in life in individuals exposed to malaria

    DEFF Research Database (Denmark)

    Turner, Louise; Lavstsen, Thomas; Mmbando, Bruno P

    2015-01-01

    Severe malaria syndromes are precipitated by Plasmodium falciparum parasites binding to endothelial receptors on the vascular lining. This binding is mediated by members of the highly variant P. falciparum erythrocyte membrane protein 1 (PfEMP1) family. We have previously identified a subset of Pf...

  15. Strings in the abelized picture

    International Nuclear Information System (INIS)

    Embacher, F.

    1990-01-01

    The transformation properties of the bosonic string variables under the recently discovered abelizing operator are exhibited. The intimate relation of this operator to the light-cone gauge condition is illustrated for the classical string. As an application of the formalism, the derivation of the BRST cohomology by the method of Freemann and Olive is carried over to the abelized picture, where it takes a particularly simple from. (orig.)

  16. The W3 string spectrum

    International Nuclear Information System (INIS)

    Pope, C.N.; Stelle, K.S.

    1991-08-01

    We study the spectrum of W 3 strings. In particular, we show that for appropriately chosen space-time signature, one of the scalar fields is singled out be the spin-3 constraint and is ''frozen'': no creation operators from it can appear in physical states and the corresponding momentum must assume a specific fixed value. The remaining theory is unitary and resembles an ordinary string theory in d contains 26 with anomalies cancelled by appropriate background charges. (author). 8 refs

  17. Cooldown of superconducting magnet strings

    International Nuclear Information System (INIS)

    Yuecel, A.; Carcagno, R.H.

    1995-01-01

    A numerical model for the cooldown of the superconducting magnet strings in the Accelerator System String Test (ASST) Facility at the Superconducting Super Collider (SSC) Laboratory is presented. Numerical results are compared with experimental data from the ASST test runs. Agreement between the numerical predictions and experiments is very good over the entire range from room temperature to liquid helium temperatures. The model can be readily adapted to predict the cooldown and warmup behavior of other superconducting magnets or cold masses

  18. Strings in the abelized picture

    International Nuclear Information System (INIS)

    Embacher, F.

    1990-01-01

    The transformation properties of the bosonic string variables under the recently discovered abelizing operator are exhibited. The intimate relation of this operator to the light-cone gauge condition is illustrated for the classical string. As an application of the formalism, the derivation of the BRST cohomology by the method of Freeman and Olive is carried over to the abelized picture, where it takes a particulary simple form. 14 refs. (Author)

  19. An introduction to string theory

    OpenAIRE

    West, Peter C

    1989-01-01

    These notes are based on lectures given by Michael Green during Part III of the Mathematics Tripos (the Certificate for Advanced Study in Mathematics) in the Spring of 2003. The course provided an introduction to string theory, focussing on the Bosonic string, but treating the superstring as well. A background in quantum field theory and general relativity is assumed. Some background in particle physics, group theory and conformal field theory is useful, though not essential. A number of appe...

  20. Black strings and classical hair

    International Nuclear Information System (INIS)

    Horowitz, G.T.; Yang, H.

    1997-01-01

    We examine the geometry near the event horizon of a family of black string solutions with traveling waves. It has previously been shown that the metric is continuous there. Contrary to expectations, we find that the geometry is not smooth, and the horizon becomes singular whenever a wave is present. Both five-dimensional and six-dimensional black strings are considered with similar results. copyright 1997 The American Physical Society

  1. On Field Theory of Open Strings, Tachyon Condensation and Closed Strings

    OpenAIRE

    Shatashvili, Samson L.

    2001-01-01

    I review the physical properties of different vacua in the background independent open string field theory. Talk presented at Strings 2001, Mumbai, India, http://theory.theory.tifr.res.in/strings/Proceedings/#sha-s.

  2. Fast searching in packed strings

    DEFF Research Database (Denmark)

    Bille, Philip

    2011-01-01

    Given strings P and Q the (exact) string matching problem is to find all positions of substrings in Q matching P. The classical Knuth–Morris–Pratt algorithm [SIAM J. Comput. 6 (2) (1977) 323–350] solves the string matching problem in linear time which is optimal if we can only read one character...... at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation....... Let m⩽n be the lengths P and Q, respectively, and let σ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using timeO(nlogσn+m+occ). Here occ is the number of occurrences of P in Q. For m=o(n) this improves the O(n) bound of the Knuth...

  3. Experimental observation of Bethe strings

    Science.gov (United States)

    Wang, Zhe; Wu, Jianda; Yang, Wang; Bera, Anup Kumar; Kamenskyi, Dmytro; Islam, A. T. M. Nazmul; Xu, Shenglong; Law, Joseph Matthew; Lake, Bella; Wu, Congjun; Loidl, Alois

    2018-02-01

    Almost a century ago, string states—complex bound states of magnetic excitations—were predicted to exist in one-dimensional quantum magnets. However, despite many theoretical studies, the experimental realization and identification of string states in a condensed-matter system have yet to be achieved. Here we use high-resolution terahertz spectroscopy to resolve string states in the antiferromagnetic Heisenberg-Ising chain SrCo2V2O8 in strong longitudinal magnetic fields. In the field-induced quantum-critical regime, we identify strings and fractional magnetic excitations that are accurately described by the Bethe ansatz. Close to quantum criticality, the string excitations govern the quantum spin dynamics, whereas the fractional excitations, which are dominant at low energies, reflect the antiferromagnetic quantum fluctuations. Today, Bethe’s result is important not only in the field of quantum magnetism but also more broadly, including in the study of cold atoms and in string theory; hence, we anticipate that our work will shed light on the study of complex many-body systems in general.

  4. Dynamics of strings between walls

    International Nuclear Information System (INIS)

    Eto, Minoru; Fujimori, Toshiaki; Nagashima, Takayuki; Nitta, Muneto; Ohashi, Keisuke; Sakai, Norisuke

    2009-01-01

    Configurations of vortex strings stretched between or ending on domain walls were previously found to be 1/4 Bogomol'nyi-Prasad-Sommerfield (BPS) states in N=2 supersymmetric gauge theories in 3+1 dimensions. Among zero modes of string positions, the center of mass of strings in each region between two adjacent domain walls is shown to be non-normalizable whereas the rests are normalizable. We study dynamics of vortex strings stretched between separated domain walls by using two methods, the moduli space (geodesic) approximation of full 1/4 BPS states and the charged particle approximation for string end points in the wall effective action. In the first method we explicitly obtain the effective Lagrangian in the strong coupling limit, which is written in terms of hypergeometric functions, and find the 90 deg. scattering for head-on collision. In the second method the domain wall effective action is assumed to be U(1) N gauge theory, and we find a good agreement between two methods for well-separated strings.

  5. Is the string theory doomed?

    International Nuclear Information System (INIS)

    Le Meur, H.; Daninos, F.; Bachas, C.

    2007-01-01

    Since its beginning, in the sixties, the string theory has succeeded in overcoming a lot of theoretical difficulties but now the complete absence of experimental validation entertains doubts about its ability to represent the real world and questions its hegemony in today's theoretical physics. Other space-time theories like the twistors, or the non-commutative geometry, or the loop quantum gravity, or the causal dynamics triangulation might begin receiving more attention. Despite all that, the string theory can be given credit for 4 achievements. First, the string theory has provided a consistent quantum description of gravity. Secondly, the string theory has built a theoretical frame that has allowed the unification of the 4 basic interactions. Thirdly, the string theory applied to astrophysics issues has demonstrated that the evaporation of a black hole does not necessarily lead to a loss of information which comforts the universality of the conservation of the quantity of information in any system and as a consequence put a fatal blow to the so-called paradox observed in black holes. Fourthly, the string theory has given a new and original meaning on the true nature of space-time. (A.C.)

  6. String theory on the edge

    International Nuclear Information System (INIS)

    Thorlacius, L.

    1989-01-01

    Open string vacuum configurations are described in terms of a one-dimensional field theory on the worldsheet boundary. The one-dimensional path integral has direct physical interpretation as a source term for closed string fields. This means that the vacuum divergences (Mobius infinities) of the path integral must be renormalized correctly. The author shows that reparametrization invariance Ward identities, apart from specifying the equations of motion of spacetime background gauge fields, also serve to fix the renormalization scheme of the vacuum divergences. He argues that vacuum configurations of open strings correspond to Caldeira-Leggett models of dissipative quantum mechanics (DQM) evaluated at a delocalization critical point. This connection reveals that critical DQM will manifest reparametrization invariance (inherited from the conformal invariance of string theory) rather than just scale invariance. This connection should open up new ways of constructing analytic and approximate solutions of open string theory (in particular, topological solitons such as monopoles and instantons). Type I superstring theory gives rise to a supersymmetric boundary field theory. Bose-Fermi cancellation eliminates vacuum divergences but the one-loop beta function remains the same as in the bosonic theory. Reparametrization invariance Ward identities dictate a boundary state normalization which yields consistent string-loop corrections to spacetime equations of motion, in both the periodic and anti-periodic fermion sectors

  7. Chern-Simons couplings for dielectric F-strings in matrix string theory

    International Nuclear Information System (INIS)

    Brecher, Dominic; Janssen, Bert; Lozano, Yolanda

    2002-01-01

    We compute the non-abelian couplings in the Chern-Simons action for a set of coinciding fundamental strings in both the type IIA and type IIB Matrix string theories. Starting from Matrix theory in a weakly curved background, we construct the linear couplings of closed string fields to type IIA Matrix strings. Further dualities give a type IIB Matrix string theory and a type IIA theory of Matrix strings with winding. (Abstract Copyright[2002], Wiley Periodicals, Inc.)

  8. New expressions for string loop amplitudes leading to an ultra-simple conception of string dynamics

    International Nuclear Information System (INIS)

    Chan Hongmo; Tsou Sheungtsun; Bordes, J.; Nellen, L.

    1990-11-01

    New expressions are derived for string loop amplitudes as overlap integrals of string wave functionals. They are shown to take the form of exchange terms coming from the Bose-Einstein symmetrisation between string segments. One is thus led to the ultra-simple conception that string theory is basically free, and that 'string interactions' are due merely to the fact that strings are composite objects with Bose-Einstein segments as constituents. (author)

  9. Gravity from strings

    International Nuclear Information System (INIS)

    Deser, S.

    1987-01-01

    We obtain the Einstein action plus quadratic curvature corrections generated by closed bosonic, heterotic and supersymmetric strings by matching the four-graviton amplitude (to first order in the slope parameter and fourth power of momenta) with an effective local gravitational action. The resulting corrections are first shown to be of the Gauss-Bonnet form. It is then noted that, by the very nature of the slope expansion, the field-redefinition theorem applies. Consequently, only the curvature-squared term is determined, while squares of its contractions are explicitly seen not to contribute. This latter property has a generalization to all orders which implies that the effective gravitational action is unavoidably ghost-free. The properties of solutions to these corrected theories are then examined. First neglecting dilatons, we find the explicit 'Schwarzschild' metrics. Both asymptotically flat and de Sitter solutions are present. The latter are however shown to be unstable. The former have horizons and singularities which are respectively smaller and less violent than in Einstein gravity; the correct sign of the slope parameter also ensures absence of naked singularities. When dilatons are included, the cosmological vacua are gratifyingly excluded. (orig.)

  10. Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation.

    Science.gov (United States)

    Huang, Chien-Wei; Walker, Michelle E; Fedrizzi, Bruno; Gardner, Richard C; Jiranek, Vladimir

    2017-08-01

    An early burst of hydrogen sulfide (H2S) produced by Saccharomyces cerevisiae during fermentation could increase varietal thiols and therefore enhance desirable tropical aromas in varieties such as Sauvignon Blanc. Here we attempted to identify genes affecting H2S formation from cysteine by screening yeast deletion libraries via a colony colour assay on media resembling grape juice. Both Δlst4 and Δlst7 formed lighter coloured colonies and produced significantly less H2S than the wild type on high concentrations of cysteine, likely because they are unable to take up cysteine efficiently. We then examined the nine known cysteine permeases and found that deletion of AGP1, GNP1 and MUP1 led to reduced production of H2S from cysteine. We further showed that deleting genes involved in the SPS-sensing pathway such as STP1 and DAL81 also reduced H2S from cysteine. Together, this study indirectly confirms that Agp1p, Gnp1p and Mup1p are the major cysteine permeases and that they are regulated by the SPS-sensing and target of rapamycin pathways under the grape juice-like, cysteine-supplemented, fermentation conditions. The findings highlight that cysteine transportation could be a limiting factor for yeast to generate H2S from cysteine, and therefore selecting wine yeasts without defects in cysteine uptake could maximise thiol production potential. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. The effect of L-cysteine on the portion-selective uptake of cadmium in the renal proximal tubule

    International Nuclear Information System (INIS)

    Murakami, Masataka; Sano, Kenichi; Webb, M.

    1987-01-01

    Cadmium (Cd), co-administered with an excess of L-cysteine, accumulates rapidly in the kidneys of the rat. After subcutaneous (s.c.) injection of 3 μmol CdCl 2 /kg body wt the concentrations of Cd in the blood and kidneys increase with the dose of cysteine over the range 0.06-5.0 mmol/kg body wt. At cysteine doses of less than 1.5 mmol/kg body wt the ratio of the concentrations of Cd in the outer medulla and cortex of the kidney remains the same as that after the injection of Cd alone. This ratio, however, is more than doubled at dose levels of 5-10 mmol cysteine/kg body wt. Hepatic uptake of Cd is unaffected by doses of cysteine below 1.5 mmol/kg body wt but decreases markedly at higher doses. In animals that are dosed simultaneously with 5 mmol cysteine/kg body wt, renal uptake of 109 Cd is known to occur in the straight segments of the proximal tubules. At a dose level of less than 1.5 mmol cysteine/kg body wt the present autoradiographical studies show that 109 Cd is taken up predominantly by the proximal convoluted tubules of the kidney cortex. At the critical dose level (1.5 mmol/kg body wt), cysteine decreases the retention of Cd at the s.c. injection site, but probably has little effect on the distribution of Cd between protein and other carrier molecules in the blood. This distribution, however, is altered at higher cysteine dose levels. It is suggested that, under the latter conditions, stable Cd-cysteine complexes are formed in the blood and are filtered readily through the glomeruli. These complexes are taken up in the kidney at the sites of cysteine reabsorption which, by studies with L-[ 35 S]-cysteine, are identified as the straight segments of the proximal tubules. (orig.)

  12. Effects of randomized supplementation of methionine or alanine on cysteine and glutathione production during the early phase of treatment of children with edematous malnutrition

    Science.gov (United States)

    We have shown that a low glutathione concentration and synthesis rate in erythrocytes are associated with a shortage of protein-derived cysteine in children with edematous severe acute malnutrition (SAM). We tested the hypothesis that methionine supplementation may increase protein-derived cysteine ...

  13. Functional integral approach to string theories

    International Nuclear Information System (INIS)

    Sakita, B.

    1987-01-01

    Fermionic string theory can be made supersymmetric: the superstring. It contains among others mass zero gauge fields of spin 1 and 2. The recent revival of interests in string field theories is due to the recognition of the compactified superstring theory as a viable theory of grandunification of all interactions, especially after Green and Schwarz's discovery of the gauge and gravitational anomaly cancellation in 0(32) superstring theory. New developments include string phenomenology, general discussions of compactification, new models, especially the heterotic string. These are either applications or extensions of string field theories. Although these are very exciting developments, the author limits his attention to the basics of the bosonic string theory

  14. String Theory for Pedestrians (1/3)

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    This is a non-technical rapid course on string theory. Lecture 1 is an introduction to the basics of the subject: classical and quantum strings, D(irichlet) branes and string-string dualities. In lecture 2 I will discuss string unification of the fundamental forces, covering both its successes and failures. Finally in lecture 3 I will review string models of black hole microstates, the holographic gauge/gravity duality and, if time permits, potential applications to the physics of the strong interactions.

  15. String Theory for Pedestrians (2/3)

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    This is a non-technical rapid course on string theory. Lecture 1 is an introduction to the basics of the subject: classical and quantum strings, D(irichlet) branes and string-string dualities. In lecture 2 I will discuss string unification of the fundamental forces, covering both its successes and failures. Finally in lecture 3 I will review string models of black hole microstates, the holographic gauge/gravity duality and, if time permits, potential applications to the physics of the strong interactions.

  16. String Theory for Pedestrians (3/3)

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    This is a non-technical rapid course on string theory. Lecture 1 is an introduction to the basics of the subject: classical and quantum strings, D(irichlet) branes and string-string dualities. In lecture 2 I will discuss string unification of the fundamental forces, covering both its successes and failures. Finally in lecture 3 I will review string models of black hole microstates, the holographic gauge/gravity duality and, if time permits, potential applications to the physics of the strong interactions.

  17. The Cysteine S-Alkylation Reaction as a Synthetic Method to Covalently Modify Peptide Sequences.

    Science.gov (United States)

    Calce, Enrica; De Luca, Stefania

    2017-01-05

    Synthetic methodologies to chemically modify peptide molecules have long been investigated for their impact in the field of chemical biology. They allow the introduction of biochemical probes useful for studying protein functions, for manipulating peptides with therapeutic potential, and for structure-activity relationship investigations. The commonly used approach was the derivatization of an amino acid side chain. In this regard, the cysteine, for its unique reactivity, has been widely employed as the substrate for such modifications. Herein, we report on methodologies developed to modify the cysteine thiol group through the S-alkylation reaction. Some procedures perform the alkylation of cysteine derivatives, in order to prepare building blocks to be used during the peptide synthesis, whilst some others selectively modify peptide sequences containing a cysteine residue with a free thiol group, both in solution and in the solid phase. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Development of a cysteine-deprived and C-terminally truncated GLP-1 receptor

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Knudsen, Lotte Bjerre; Garibay, Patrick W.

    2013-01-01

    The glucagon-like peptide-1 receptor (GLP-1R) belongs to family B of the G-protein coupled receptors (GPCRs), and has become a promising target for the treatment of type 2 diabetes. Here we describe the development and characterization of a fully functional cysteine-deprived and C......-terminally truncated GLP-1R. Single cysteines were initially substituted with alanine, and functionally redundant cysteines were subsequently changed simultaneously. Our results indicate that Cys174, Cys226, Cys296 and Cys403 are important for the GLP-1-mediated response, whereas Cys236, Cys329, Cys341, Cys347, Cys438...... that the membrane proximal part of the C-terminal is involved in receptor expression at the cell surface. The results show that seven cysteines and more than half of the C-terminal tail can be removed from GLP-1R without compromising GLP-1 binding or function....

  19. Differential labelling of cysteines for simultaneous identification of thioredoxin h-reducible disulphides in native protein extracts: insight into recognition and regulation of proteins in barley seeds by thioredoxin h

    DEFF Research Database (Denmark)

    Maeda, Kenji; Finnie, Christine; Svensson, Birte

    2005-01-01

    . Mass shifts of 15 peptides, induced by treatment with thioredoxin h and differential alkylation, identified specific reduction of nine disulphides in BASI, four a-amylase/trypsin inhibitors and a protein of unknown function. Two specific disulphides, located structurally close to the alpha-amylase...... binding surfaces of BASI and alpha-amylase inhibitor BMAI-1 were demonstrated to be reduced to a particularly high extent. For the first time, specificity of thioredoxin h for particular disulphide bonds is demonstrated, providing a basis to study structural aspects of the recognition mechanism......) to be distinguished from those inaccessible or disulphide bound form (pyridylethylated) according to the mass difference in the peptide mass maps obtained by matrixassistend laser desorption/ionisation-time of flight mass spectrometry. Using this approach, in vitro reduction of disulphides in recombinant barley a-amylase...

  20. L-Cysteine inhibits root elongation through auxin/PLETHORA and SCR/SHR pathway in Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Zhen; Mao, Jie-Li; Zhao, Ying-Jun; Li, Chuan-You; Xiang, Cheng-Bin

    2015-02-01

    L-Cysteine plays a prominent role in sulfur metabolism of plants. However, its role in root development is largely unknown. Here, we report that L-cysteine reduces primary root growth in a dosage-dependent manner. Elevating cellular L-cysteine level by exposing Arabidopsis thaliana seedlings to high L-cysteine, buthionine sulphoximine, or O-acetylserine leads to altered auxin maximum in root tips, the expression of quiescent center cell marker as well as the decrease of the auxin carriers PIN1, PIN2, PIN3, and PIN7 of primary roots. We also show that high L-cysteine significantly reduces the protein level of two sets of stem cell specific transcription factors PLETHORA1/2 and SCR/SHR. However, L-cysteine does not downregulate the transcript level of PINs, PLTs, or SCR/SHR, suggesting that an uncharacterized post-transcriptional mechanism may regulate the accumulation of PIN, PLT, and SCR/SHR proteins and auxin transport in the root tips. These results suggest that endogenous L-cysteine level acts to maintain root stem cell niche by regulating basal- and auxin-induced expression of PLT1/2 and SCR/SHR. L-Cysteine may serve as a link between sulfate assimilation and auxin in regulating root growth. © 2014 Institute of Botany, Chinese Academy of Sciences.

  1. Mass spectrometric analysis of L-cysteine metabolism: physiological role and fate of L-cysteine in the enteric protozoan parasite Entamoeba histolytica.

    Science.gov (United States)

    Jeelani, Ghulam; Sato, Dan; Soga, Tomoyoshi; Watanabe, Haruo; Nozaki, Tomoyoshi

    2014-11-04

    L-cysteine is essential for virtually all living organisms, from bacteria to higher eukaryotes. Besides having a role in the synthesis of virtually all proteins and of taurine, cysteamine, glutathione, and other redox-regulating proteins, L-cysteine has important functions under anaerobic/microaerophilic conditions. In anaerobic or microaerophilic protozoan parasites, such as Entamoeba histolytica, L-cysteine has been implicated in growth, attachment, survival, and protection from oxidative stress. However, a specific role of this amino acid or related metabolic intermediates is not well understood. In this study, using stable-isotope-labeled L-cysteine and capillary electrophoresis-time of flight mass spectrometry, we investigated the metabolism of L-cysteine in E. histolytica. [U-(13)C3, (15)N]L-cysteine was rapidly metabolized into three unknown metabolites, besides L-cystine and L-alanine. These metabolites were identified as thiazolidine-4-carboxylic acid (T4C), 2-methyl thiazolidine-4-carboxylic acid (MT4C), and 2-ethyl-thiazolidine-4-carboxylic acid (ET4C), the condensation products of L-cysteine with aldehydes. We demonstrated that these 2-(R)-thiazolidine-4-carboxylic acids serve for storage of L-cysteine. Liberation of L-cysteine occurred when T4C was incubated with amebic lysates, suggesting enzymatic degradation of these L-cysteine derivatives. Furthermore, T4C and MT4C significantly enhanced trophozoite growth and reduced intracellular reactive oxygen species (ROS) levels when it was added to cultures, suggesting that 2-(R)-thiazolidine-4-carboxylic acids are involved in the defense against oxidative stress. Amebiasis is a human parasitic disease caused by the protozoan parasite Entamoeba histolytica. In this parasite, L-cysteine is the principal low-molecular-weight thiol and is assumed to play a significant role in supplying the amino acid during trophozoite invasion, particularly when the parasites move from the anaerobic intestinal lumen to highly

  2. String Theory in a Nutshell

    International Nuclear Information System (INIS)

    Skenderis, Kostas

    2007-01-01

    The book 'String Theory in a Nutshell' by Elias Kiritsis provides a comprehensive introduction to modern string theory. String theory is the leading candidate for a theory that successfully unifies all fundamental forces of nature, including gravity. The subject has been continuously developing since the early 1970s, with classic textbooks on the subject being those of Green, Schwarz and Witten (1987) and Polchinski (1998). Since the latter was published there have been substantial developments, in particular in understanding black holes and gravity/gauge theory dualities. A textbook treatment of this important material is clearly needed, both by students and researchers in string theory and by mathematicians and physicists working in related fields. This book has a good selection of material, starting from basics and moving into classic and modern topics. In particular, Kiritsis' presentation of the basic material is complementary to that of the earlier textbooks and he includes a number of topics which are not easily found or covered adequately elsewhere, for example, loop corrections to string effective couplings. Overall the book nicely covers the major advances of the last ten years, including (non-perturbative) string dualities, black hole physics, AdS/CFT and matrix models. It provides a concise but fairly complete introduction to these subjects which can be used both by students and by researchers. Moreover the emphasis is on results that are reasonably established, as is appropriate for a textbook; concise summaries are given for subjects which are still in flux, with references to relevant reviews and papers. A positive feature of the book is that the bibliography sections at the end of each chapter provide a comprehensive guide to the literature. The bibliographies point to reviews and pedagogical papers on subjects covered in this book as well as those that were omitted. It is rare for a textbook to contain such a self-contained and detailed guide to

  3. Functional analysis of C1 family cysteine peptidases in the larval gut of Tenebrio molitor and Tribolium castaneum

    Science.gov (United States)

    We studied protein digestion the tenebrionids Tenebrio molitor and Tribolium castaneum, pests of stored grains and grain products, to identify potential targets for biopesticide development. Tenebrionid larvae have highly compartmentalized guts, with primarily cysteine peptidases in the acidic anter...

  4. The papain inhibitor (SPI) of Streptomyces mobaraensis inhibits bacterial cysteine proteases and is an antagonist of bacterial growth

    NARCIS (Netherlands)

    S. Zindel (Stephan); W.E. Kaman (Wendy); S. Fröls (Sabrina); F. Pfeifer (Felicitas); A. Peters (Annette); J.P. Hays (John); H.-L. Fuchsbauer (Hans-Lothar)

    2013-01-01

    textabstractA novel papain inhibitory protein (SPI) from Streptomyces mobaraensis was studied to measure its inhibitory effect on bacterial cysteine protease activity (Staphylococcus aureus SspB) and culture supernatants (Porphyromonas gingivalis, Bacillus anthracis). Further, growth of Bacillus

  5. String Resonances at Hadron Colliders

    CERN Document Server

    Anchordoqui, Luis A; Dai, De-Chang; Feng, Wan-Zhe; Goldberg, Haim; Huang, Xing; Lust, Dieter; Stojkovic, Dejan; Taylor, Tomasz R

    2014-01-01

    [Abridged] We consider extensions of the standard model based on open strings ending on D-branes. Assuming that the fundamental string mass scale M_s is in the TeV range and that the theory is weakly coupled, we discuss possible signals of string physics at the upcoming HL-LHC run (3000 fb^{-1}) with \\sqrt{s} = 14 TeV, and at potential future pp colliders, HE-LHC and VLHC, operating at \\sqrt{s} = 33 and 100 TeV, respectively. In such D-brane constructions, the dominant contributions to full-fledged string amplitudes for all the common QCD parton subprocesses leading to dijets and \\gamma + jet are completely independent of the details of compactification, and can be evaluated in a parameter-free manner. We make use of these amplitudes evaluated near the first (n=1) and second (n=2) resonant poles to determine the discovery potential for Regge excitations of the quark, the gluon, and the color singlet living on the QCD stack. We show that for string scales as large as 7.1 TeV (6.1 TeV), lowest massive Regge exc...

  6. Differential geometry in string models

    International Nuclear Information System (INIS)

    Alvarez, O.

    1986-01-01

    In this article the author reviews the differential geometric approach to the quantization of strings. A seminal paper demonstrates the connection between the trace anomaly and the critical dimension. The role played by the Faddeev-Popov ghosts has been instrumental in much of the subsequent work on the quantization of strings. This paper discusses the differential geometry of two dimensional surfaces and its importance in the quantization of strings. The path integral quantization approach to strings will be carefully analyzed to determine the correct effective measure for string theories. The choice of measure for the path integral is determined by differential geometric considerations. Once the measure is determined, the manifest diffeomorphism invariance of the theory will have to be broken by using the Faddeev-Popov ansatz. The gauge fixed theory is studied in detail with emphasis on the role of conformal and gravitational anomalies. In the analysis, the path integral formulation of the gauge fixed theory requires summing over all the distinct complex structures on the manifold

  7. String theory or field theory?

    International Nuclear Information System (INIS)

    Marshakov, Andrei V

    2002-01-01

    The status of string theory is reviewed, and major recent developments - especially those in going beyond perturbation theory in the string theory and quantum field theory frameworks - are analyzed. This analysis helps better understand the role and place of string theory in the modern picture of the physical world. Even though quantum field theory describes a wide range of experimental phenomena, it is emphasized that there are some insurmountable problems inherent in it - notably the impossibility to formulate the quantum theory of gravity on its basis - which prevent it from being a fundamental physical theory of the world of microscopic distances. It is this task, the creation of such a theory, which string theory, currently far from completion, is expected to solve. In spite of its somewhat vague current form, string theory has already led to a number of serious results and greatly contributed to progress in the understanding of quantum field theory. It is these developments which are our concern in this review. (reviews of topical problems)

  8. Topological strings from quantum mechanics

    International Nuclear Information System (INIS)

    Grassi, Alba; Marino, Marcos; Hatsuda, Yasuyuki

    2014-12-01

    We propose a general correspondence which associates a non-perturbative quantum-mechanical operator to a toric Calabi-Yau manifold, and we conjecture an explicit formula for its spectral determinant in terms of an M-theoretic version of the topological string free energy. As a consequence, we derive an exact quantization condition for the operator spectrum, in terms of the vanishing of a generalized θ function. The perturbative part of this quantization condition is given by the Nekrasov-Shatashvili limit of the refined topological string, but there are non-perturbative corrections determined by the conventional topological string. We analyze in detail the cases of local P 2 , local P 1 x P 1 and local F 1 . In all these cases, the predictions for the spectrum agree with the existing numerical results. We also show explicitly that our conjectured spectral determinant leads to the correct spectral traces of the corresponding operators, which are closely related to topological string theory at orbifold points. Physically, our results provide a Fermi gas picture of topological strings on toric Calabi-Yau manifolds, which is fully non-perturbative and background independent. They also suggest the existence of an underlying theory of M2 branes behind this formulation. Mathematically, our results lead to precise, surprising conjectures relating the spectral theory of functional difference operators to enumerative geometry.

  9. An exact bosonization rule for c = 1 noncritical string theory

    International Nuclear Information System (INIS)

    Ishibashi, Nobuyuki; Yamaguchi, Atsushi

    2007-01-01

    We construct a string field theory for c = 1 noncritical strings using the loop variables as the string field. We show how one can express the nonrelativistic free fermions which describes the theory, in terms of these string fields

  10. Modulation of Escherichia coli serine acetyltransferase catalytic activity in the cysteine synthase complex

    Czech Academy of Sciences Publication Activity Database

    Benoni, Roberto; De Bei, O.; Paredi, G.; Hayes, C. S.; Franko, N.; Mozzarelli, A.; Bettati, S.; Campanini, B.

    2017-01-01

    Roč. 591, č. 9 (2017), s. 1212-1224 ISSN 0014-5793 Institutional support: RVO:61388963 Keywords : cysteine synthase * protein - protein interaction * serine acetyltransferase Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 3.623, year: 2016

  11. Cysteine proteases: Modes of activation and future prospects as pharmacological targets

    Directory of Open Access Journals (Sweden)

    Sonia eVerma

    2016-04-01

    Full Text Available Proteolytic enzymes are crucial for a variety of biological processes in organisms ranging from lower (virus, bacteria and parasite to the higher organisms (mammals. Proteases cleave proteins into smaller fragments by catalyzing peptide bonds hydrolysis. Proteases are classified according to their catalytic site, and distributed into four major classes: cysteine proteases, serine proteases, aspartic proteases and metallo-proteases. This review will cover only cysteine proteases, papain family enzymes which are involved in multiple functions such as extracellular matrix turnover, antigen presentation, processing events, digestion, immune invasion, hemoglobin hydrolysis, parasite invasion, parasite egress and processing surface proteins. Therefore, they are promising drug targets for various diseases. For preventing unwanted digestion, cysteine proteases are synthesized as zymogens, and contain a pro-domain (regulatory and a mature domain (catalytic. The prodomain acts as an endogenous inhibitor of the mature enzyme. For activation of the mature enzyme, removal of the prodomain is necessary and achieved by different modes. The pro-mature domain interaction can be categorized as protein-protein interactions (PPIs and may be targeted in a range of diseases. Cysteine protease inhibitors are available that can block the active site but no such inhibitor available yet that can be targeted to block the pro-mature domain interactions and prevent it activation. This review specifically highlights the modes of activation (processing of papain family enzymes, which involve auto-activation, trans-activation and also clarifies the future aspects of targeting PPIs to prevent the activation of cysteine proteases.

  12. Ga2O3 photocatalyzed on-line tagging of cysteine to facilitate peptide mass fingerprinting.

    Science.gov (United States)

    Qiao, Liang; Su, Fangzheng; Bi, Hongyan; Girault, Hubert H; Liu, Baohong

    2011-09-01

    β-Ga(2)O(3) is a wide-band-gap semiconductor having strong oxidation ability under light irradiation. Herein, the steel target plates modified with β-Ga(2)O(3) nanoparticles have been developed to carry out in-source photo-catalytic oxidative reactions for online peptide tagging during laser desorption/ionization mass spectrometry (LDI-MS) analysis. Under UV laser irradiation, β-Ga(2)O(3) can catalyze the photo-oxidation of 2-methoxyhydroquinone added to a sample mixture to 2-methoxy benzoquinone that can further react with the thiol groups of cysteine residues by Michael addition reaction. The tagging process leads to appearance of pairs of peaks with an m/z shift of 138.1Th. This online labelling strategy is demonstrated to be sensitive and efficient with a detection-limit at femtomole level. Using the strategy, the information on cysteine content in peptides can be obtained together with peptide mass, therefore constraining the database searching for an advanced identification of cysteine-containing proteins from protein mixtures. The current peptide online tagging method can be important for specific analysis of cysteine-containing proteins especially the low-abundant ones that cannot be completely isolated from other high-abundant non-cysteine-proteins. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Cosmic strings and black holes

    International Nuclear Information System (INIS)

    Aryal, M.; Ford, L.H.; Vilenkin, A.

    1986-01-01

    The metric for a Schwarzschild black hole with a cosmic string passing through it is discussed. The thermodynamics of such an object is considered, and it is shown that S = (1/4)A, where S is the entropy and A is the horizon area. It is noted that the Schwarzschild mass parameter M, which is the gravitational mass of the system, is no longer identical to its energy. A solution representing a pair of black holes held apart by strings is discussed. It is nearly identical to a static, axially symmetric solution given long ago by Bach and Weyl. It is shown how these solutions, which were formerly a mathematical curiosity, may be given a more physical interpretation in terms of cosmic strings

  14. Cooperative strings and glassy interfaces.

    Science.gov (United States)

    Salez, Thomas; Salez, Justin; Dalnoki-Veress, Kari; Raphaël, Elie; Forrest, James A

    2015-07-07

    We introduce a minimal theory of glass formation based on the ideas of molecular crowding and resultant string-like cooperative rearrangement, and address the effects of free interfaces. In the bulk case, we obtain a scaling expression for the number of particles taking part in cooperative strings, and we recover the Adam-Gibbs description of glassy dynamics. Then, by including thermal dilatation, the Vogel-Fulcher-Tammann relation is derived. Moreover, the random and string-like characters of the cooperative rearrangement allow us to predict a temperature-dependent expression for the cooperative length ξ of bulk relaxation. Finally, we explore the influence of sample boundaries when the system size becomes comparable to ξ. The theory is in agreement with measurements of the glass-transition temperature of thin polymer films, and allows quantification of the temperature-dependent thickness hm of the interfacial mobile layer.

  15. Vector superconductivity in cosmic strings

    International Nuclear Information System (INIS)

    Dvali, G.R.; Mahajan, S.M.

    1992-03-01

    We argue that in most realistic cases, the usual Witten-type bosonic superconductivity of the cosmic string is automatically (independent of the existence of superconducting currents) accompanied by the condensation of charged gauge vector bosons in the core giving rise to a new vector type superconductivity. The value of the charged vector condensate is related with the charged scalar expectation value, and vanishes only if the latter goes to zero. The mechanism for the proposed vector superconductivity, differing fundamentally from those in the literature, is delineated using the simplest realistic example of the two Higgs doublet standard model interacting with the extra cosmic string. It is shown that for a wide range of parameters, for which the string becomes scalarly superconducting, W boson condensates (the sources of vector superconductivity) are necessarily excited. (author). 14 refs

  16. QCD string in the baryon

    International Nuclear Information System (INIS)

    Kalashnikova, Yu.S.; Nefediev, A.V.

    1997-01-01

    The QCD-motivated constituent string model is extended to consider the baryon. The system of three quarks propagating in the confining background field is studied in the Wilson loop approach, and the effective action is obtained. The resulting Lagrangian at large interquark distances corresponds to the Mercedes Benz string configuration. Assuming the quarks to be heavy enough to allow the adiabatic separation of quark and string junction motion and using the hyperspherical expansion for the quark subsystem we write out and solve the classical equation of motion for the junction. We quantize the motion of the junction and demonstrate that the account of these modes leads to the effective swelling of baryon in comparison with standard potential picture. The effects of finite gluonic correlation length which do not affect the excited states but appear to be substantial for the baryonic ground state, reducing the swelling considerably is discussed

  17. Noncompact symmetries in string theory

    International Nuclear Information System (INIS)

    Maharana, J.; Schwarz, J.H.

    1993-01-01

    Noncompact groups, similar to those that appeared in various supergravity theories in the 1970's have been turning up in recent studies of string theory. First it was discovered that moduli spaces of toroidal compactification are given by noncompact groups modded out by their maximal compact subgroups and discrete duality groups. Then it was found that many other moduli spaces have analogous descriptions. More recently, noncompact group symmetries have turned up in effective actions used to study string cosmology and other classical configurations. This paper explores these noncompact groups in the case of toroidal compactification both from the viewpoint of low-energy effective field theory, using the method of dimensional reduction, and from the viewpoint of the string theory world-sheet. The conclusion is that all these symmetries are intimately related. In particular, we find that Chern-Simons terms in the three-form field strength H μνρ play a crucial role. (orig.)

  18. Introduction to strings and superstrings

    International Nuclear Information System (INIS)

    Rausch de Traubenberg, M.

    1988-01-01

    The string theory is applied in the construction of a theory which allows the coupling of the four fundamental interactions and matter. The original model of the string theory describes the hadronic phenomenon of duality. The model extension, which describes the closed strings and those with a spin, is studied. The supersymmetry and the supersymmetric partner concepts are considered, in order to obtain a superstrings theory. The supersymmetry allows the formulation of a ''supertheory'', including matter, fields and gravitation. In order to explain the mass of the observable particles, the mechanism of symmetry breaking must be taken into account. The scalar state concept, originated from the supersymmetry breaking, is analyzed. This ''supertheory'' is not entirely accepted by the scientific world [fr

  19. The NMSSM and string theory

    International Nuclear Information System (INIS)

    Lebedev, Oleg; Ramos-Sanchez, Saul

    2009-12-01

    We study the possibility of constructing the NMSSM from the heterotic string. String derived NMSSMs are much more rare than MSSMs due to the extra requirement that there exist a light singlet which couples to the Higgs pairs. They share the common feature that the singlet self-interactions are typically suppressed, leading to either the ''decoupling'' or to the Peccei-Quinn limit of the NMSSM. In the latter case, the spectrum contains a light pseudoscalar which may be relevant to the MSSM fine-tuning problem.We provide a Z 6 heterotic orbifold example of the NMSSM with approximate Peccei-Quinn symmetry, whose origin lies in the string selection rules combined with our choice of the vacuum configuration. (orig.)

  20. On the string equation at c=1

    International Nuclear Information System (INIS)

    Nakatsu, Toshio.

    1994-07-01

    The analogue of the string equation which specifies the partition function of c=1 string with a compactification radius β is an element of Z ≥1 is described in the framework of Toda lattice hierarchy. (author)

  1. Metastable cosmic strings in realistic models

    International Nuclear Information System (INIS)

    Holman, R.

    1992-01-01

    The stability of the electroweak Z-string is investigated at high temperatures. The results show that, while finite temperature corrections can improve the stability of the Z-string, their effect is not strong enough to stabilize the Z-string in the standard electroweak model. Consequently, the Z-string will be unstable even under the conditions present during the electroweak phase transition. Phenomenologically viable models based on the gauge group SU(2) L x SU(2) R x U(1) B-L are then considered, and it is shown that metastable strings exist and are stable to small perturbations for a large region of the parameter space for these models. It is also shown that these strings are superconducting with bosonic charge carriers. The string superconductivity may be able to stabilize segments and loops against dynamical contraction. Possible implications of these strings for cosmology are discussed

  2. Covariant amplitudes in Polyakov string theory

    International Nuclear Information System (INIS)

    Aoyama, H.; Dhar, A.; Namazie, M.A.

    1986-01-01

    A manifestly Lorentz-covariant and reparametrization-invariant procedure for computing string amplitudes using Polyakov's formulation is described. Both bosonic and superstring theories are dealt with. The computation of string amplitudes is greatly facilitated by this formalism. (orig.)

  3. Cosmic string induced peculiar velocities

    International Nuclear Information System (INIS)

    van Dalen, A.; Schramm, D.N.

    1987-02-01

    We calculate analytically the probability distribution for peculiar velocities on scales from 10h -1 to 60h -1 Mpc with cosmic string loops as the dominant source of primordial gravitational perturbations. We consider a range of parameters βGμ appropriate for both hot (HDM) and cold (CDM) dark matter scenarios. An Ω = 1 CDM Universe is assumed with the loops randomly placed on a smooth background. It is shown how the effects can be estimated of loops breaking up and being born with a spectrum of sizes. It is found that to obtain large scale streaming velocities of at least 400 km/s it is necessary that either a large value for βGμ or the effect of loop fissioning and production details be considerable. Specifically, for optimal CDM string parameters Gμ = 10 -6 , β = 9, h = .5, and scales of 60h -1 Mpc, the parent size spectrum must be 36 times larger than the evolved daughter spectrum to achieve peculiar velocities of at least 400 km/s with a probability of 63%. With this scenario the microwave background dipole will be less than 800 km/s with only a 10% probability. The string induced velocity spectrum is relatively flat out to scales of about 2t/sub eq//a/sub eq/ and then drops off rather quickly. The flatness is a signature of string models of galaxy formation. With HDM a larger value of βGμ is necessary for galaxy formation since accretion on small scales starts later. Hence, with HDM, the peculiar velocity spectrum will be larger on large scales and the flat region will extend to larger scales. If large scale peculiar velocities greater than 400 km/s are real then it is concluded that strings plus CDM have difficulties. The advantages of strings plus HDM in this regard will be explored in greater detail in a later paper. 27 refs., 4 figs., 1 tab

  4. Topics in string theory

    Science.gov (United States)

    Jejjala, Vishnumohan

    2002-01-01

    This Thesis explores aspects of superstring theory on orbifold spaces and applies some of the intuition gleaned from the study of the non-commutative geometry of space-time to understanding the fractional quantum Hall effect. The moduli space of vacua of marginal and relevant deformations of N = 4 super-Yang-Mills gauge theory in four dimensions is interpreted in terms of non-commutative geometry. A formalism for thinking about the algebraic geometry of the moduli space is developed. Within this framework, the representation theory of the algebras studied provides a natural exposition of D-brane fractionation. The non-commutative moduli space of deformations preserving N = 1 supersymmetry is examined in detail through various examples. In string theory, by the AdS/CFT correspondence, deformations of the N = 4 field theory are dual to the near-horizon geometries of D-branes on orbifolds of AdS5 x S 5. The physics of D-branes on the dual AdS backgrounds is explored. Quivers encapsulate the matter content of supersymmetric field theories on the worldvolumes of D-branes at orbifold singularities. New techniques for constructing quivers are presented here. When N is a normal subgroup of a finite group G, the quiver corresponding to fixed points of the orbifold M/G is computed from a G/N action on the quiver corresponding to M/G . These techniques prove useful for constructing non-Abelian quivers and for examining discrete torsion orbifolds. Quivers obtained through our constructions contain interesting low-energy phenomenology. The matter content on a brane at an isolated singularity of the Delta27 orbifold embeds the Standard Model. The symmetries of the quiver require exactly three generations of fields in the particle spectrum. Lepton masses are suppressed relative to quark masses because lepton Yukawa couplings do not appear in the superpotential. Lepton masses are generated through the Kahler potential and are related to the supersymmetry breaking scale. The model

  5. Warped models in string theory

    International Nuclear Information System (INIS)

    Acharya, B.S.; Benini, F.; Valandro, R.

    2006-12-01

    Warped models, originating with the ideas of Randall and Sundrum, provide a fascinating extension of the standard model with interesting consequences for the LHC. We investigate in detail how string theory realises such models, with emphasis on fermion localisation and the computation of Yukawa couplings. We find, in contrast to the 5d models, that fermions can be localised anywhere in the extra dimension, and that there are new mechanisms to generate exponential hierarchies amongst the Yukawa couplings. We also suggest a way to distinguish these string theory models with data from the LHC. (author)

  6. Heterotic strings on homogeneous spaces

    International Nuclear Information System (INIS)

    Israel, D.; Kounnas, C.; Orlando, D.; Petropoulos, P.M.

    2005-01-01

    We construct heterotic string backgrounds corresponding to families of homogeneous spaces as exact conformal field theories. They contain left cosets of compact groups by their maximal tori supported by NS-NS 2-forms and gauge field fluxes. We give the general formalism and modular-invariant partition functions, then we consider some examples such as SU(2)/U(1)∝S 2 (already described in a previous paper) and the SU(3)/U(1) 2 flag space. As an application we construct new supersymmetric string vacua with magnetic fluxes and a linear dilaton. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

  7. Precise Analysis of String Expressions

    DEFF Research Database (Denmark)

    Christensen, Aske Simon; Møller, Anders; Schwartzbach, Michael Ignatieff

    2003-01-01

    We perform static analysis of Java programs to answer a simple question: which values may occur as results of string expressions? The answers are summarized for each expression by a regular language that is guaranteed to contain all possible values. We present several applications of this analysis...... are automatically produced. We present extensive benchmarks demonstrating that the analysis is efficient and produces results of useful precision......., including statically checking the syntax of dynamically generated expressions, such as SQL queries. Our analysis constructs flow graphs from class files and generates a context-free grammar with a nonterminal for each string expression. The language of this grammar is then widened into a regular language...

  8. New twistor string theories revisited

    International Nuclear Information System (INIS)

    Broedel, Johannes; Wurm, Bernhard

    2009-01-01

    A gauged version of Berkovits twistor string theory featuring the particle content of N=8 supergravity was suggested by Abou-Zeid, Hull and Mason. The equations of motion for a particular multiplet in the modified theory are examined on the level of basic twistor fields and thereby shown to imply the vanishing of the negative helicity graviton on-shell. Additionally, the restrictions emerging from the equation of motion for the new gauge field B-bar reveal the chiral nature of interactions in theories constructed in this manner. Moreover, a particular amplitude in Berkovits open string theory is shown to be in agreement with the corresponding result in Einstein gravity.

  9. Introduction to field theory of strings

    International Nuclear Information System (INIS)

    Kikkawa, K.

    1987-01-01

    The field theory of bosonic string is reviewed. First, theory is treated in a light-cone gauge. After a brief survey of the first quantized theory of free string, the second quantization is discussed. All possible interactions of strings are introduced based on a smoothness condition of work sheets swept out by strings. Perturbation theory is developed. Finally a possible way to the manifest covariant formalism is discussed

  10. Twenty-five questions for string theorists

    Energy Technology Data Exchange (ETDEWEB)

    Binetruy, Pierre; /Orsay, LPT; Kane, G.L.; /Michigan U., MCTP; Lykken, Joseph D.; /Fermilab; Nelson, Brent D.; /Pennsylvania U.

    2005-09-01

    In an effort to promote communication between the formal and phenomenological branches of the high-energy theory community, we provide a description of some important issues in supersymmetric and string phenomenology. We describe each within the context of string constructions, illustrating them with specific examples where applicable. Each topic culminates in a set of questions that we believe are amenable to direct consideration by string theorists, and whose answers we think could help connect string theory and phenomenology.

  11. Hosotani model in closed string theory

    International Nuclear Information System (INIS)

    Shiraishi, Kiyoshi.

    1988-11-01

    Hosotani mechanism in the closed string theory with current algebra symmetry is described by the (old covariant) operator method. We compare the gauge symmetry breaking mechanism in a string theory which has SU(2) symmetry with the one in an equivalent compactified closed string theory. We also investigate the difference between Hosotani mechanism and Higgs mechanism in closed string theories by calculation of a fourpoint amplitude of 'Higgs' bosons at tree level. (author)

  12. Key Role of Cysteine Residues in Catalysis and Subcellular Localization of Sulfur Oxygenase-Reductase of Acidianus tengchongensis

    DEFF Research Database (Denmark)

    Chen, Z. W.; Jiang, C. Y.; She, Qunxin

    2005-01-01

    ). The thio-modifying reagent N-ethylmaleimide and Zn2+ strongly inhibited the activities of the SORs of A. tengchongensis, suggesting that cysteine residues are important. Site-directed mutagenesis was used to construct four mutant SORs with cysteines replaced by serine or alanine. The purified mutant......Analysis of known sulfur oxygenase-reductases (SORs) and the SOR-like sequences identified from public databases indicated that they all possess three cysteine residues within two conserved motifs (V-G-P-K-V-C31 and C101-X-X-C104; numbering according to the Acidianus tengchongensis numbering system...... proteins were investigated in parallel with the wild-type SOR. Replacement of any cysteine reduced SOR activity by 98.4 to 100%, indicating that all the cysteine residues are crucial to SOR activities. Circular-dichroism and fluorescence spectrum analyses revealed that the wild-type and mutant SORs have...

  13. Identification, classification and expression pattern analysis of sugarcane cysteine proteinases

    Directory of Open Access Journals (Sweden)

    Gustavo Coelho Correa

    2001-12-01

    Full Text Available Cysteine proteases are peptidyl hydrolyses dependent on a cysteine residue at the active center. The physical and chemical properties of cysteine proteases have been extensively characterized, but their precise biological functions have not yet been completely understood, although it is known that they are involved in a number of events such as protein turnover, cancer, germination, programmed cell death and senescence. Protein sequences from different cysteine proteinases, classified as members of the E.C.3.4.22 sub-sub-class, were used to perform a T-BLAST-n search on the Brazilian Sugarcane Expressed Sequence Tags project (SUCEST data bank. Sequence homology was found with 76 cluster sequences that corresponded to possible cysteine proteinases. The alignments of these SUCEST clusters with the sequence of cysteine proteinases of known origins provided important information about the classification and possible function of these sugarcane enzymes. Inferences about the expression pattern of each gene were made by direct correlation with the SUCEST cDNA libraries from which each cluster was derived. Since no previous reports of sugarcane cysteine proteinases genes exists, this study represents a first step in the study of new biochemical, physiological and biotechnological aspects of sugarcane cysteine proteases.Proteinases cisteínicas são peptidil-hidrolases dependentes de um resíduo de cisteína em seu sítio ativo. As propriedades físico-químicas destas proteinases têm sido amplamente caracterizadas, entretanto suas funções biológicas ainda não foram completamente elucidadas. Elas estão envolvidas em um grande número de eventos, tais como: processamento e degradação protéica, câncer, germinação, morte celular programada e processos de senescência. Diferentes proteinases cisteínicas, classificadas pelo Comitê de Nomenclatura da União Internacional de Bioquímica e Biologia Molecular (IUBMB como pertencentes à sub

  14. Acid-Mediated Tumor Proteolysis: Contribution of Cysteine Cathepsins

    Directory of Open Access Journals (Sweden)

    Jennifer M Rothberg

    2013-10-01

    Full Text Available One of the noncellular microenvironmental factors that contribute to malignancy of solid tumors is acidic peritumoral pH. We have previously demonstrated that extracellular acidosis leads to localization of the cysteine pro-tease cathepsin B on the tumor cell membrane and its secretion. The objective of the present study was to determine if an acidic extracellular pH such as that observed in vivo (i.e., pHe 6.8 affects the activity of proteases, e.g., cathepsin B, that contribute to degradation of collagen IV by tumor cells when grown in biologically relevant three-dimensional (3D cultures. For these studies, we used 1 3D reconstituted basement membrane overlay cultures of human carcinomas, 2 live cell imaging assays to assess proteolysis, and 3 in vivo imaging of active tumor proteases. At pHe 6.8, there were increases in pericellular active cysteine cathepsins and in degradation of dye-quenched collagen IV, which was partially blocked by a cathepsin B inhibitor. Imaging probes for active cysteine cathepsins localized to tumors in vivo. The amount of bound probe decreased in tumors in bicarbonate-treated mice, a treatment previously shown to increase peritumoral pHe and reduce local invasion of the tumors. Our results are consistent with the acid-mediated invasion hypothesis and with a role for cathepsin B in promoting degradation of a basement membrane protein substrate, i.e., type IV collagen, in an acidic peritumoral environment.

  15. Hollow micro string based calorimeter device

    DEFF Research Database (Denmark)

    2014-01-01

    positions so as to form a free released double clamped string in-between said two longitudinally distanced positions said micro-channel string comprising a microfluidic channel having a closed cross section and extending in the longitudinal direction of the hollow string, acoustical means adapted...

  16. String field representation of the Virasoro algebra

    Energy Technology Data Exchange (ETDEWEB)

    Mertes, Nicholas [Institute of Physics AS CR,Na Slovance 2, Prague 8 (Czech Republic); Department of Physics, University of Miami,Coral Gables, FL (United States); Schnabl, Martin [Institute of Physics AS CR,Na Slovance 2, Prague 8 (Czech Republic)

    2016-12-29

    We construct a representation of the zero central charge Virasoro algebra using string fields in Witten’s open bosonic string field theory. This construction is used to explore extensions of the KBc algebra and find novel algebraic solutions of open string field theory.

  17. Transverse structure of the QCD string

    International Nuclear Information System (INIS)

    Meyer, Harvey B.

    2010-01-01

    The characterization of the transverse structure of the QCD string is discussed. We formulate a conjecture as to how the stress-energy tensor of the underlying gauge theory couples to the string degrees of freedom. A consequence of the conjecture is that the energy density and the longitudinal-stress operators measure the distribution of the transverse position of the string, to leading order in the string fluctuations, whereas the transverse-stress operator does not. We interpret recent numerical measurements of the transverse size of the confining string and show that the difference of the energy and longitudinal-stress operators is a particularly natural probe at next-to-leading order. Second, we derive the constraints imposed by open-closed string duality on the transverse structure of the string. We show that a total of three independent ''gravitational'' form factors characterize the transverse profile of the closed string, and obtain the interpretation of recent effective string theory calculations: the square radius of a closed string of length β defined from the slope of its gravitational form factor, is given by (d-1/2πσ)log(β/4r 0 ) in d space dimensions. This is to be compared with the well-known result that the width of the open string at midpoint grows as (d-1/2πσ)log(r/r 0 ). We also obtain predictions for transition form factors among closed-string states.

  18. Regularization of finite temperature string theories

    International Nuclear Information System (INIS)

    Leblanc, Y.; Knecht, M.; Wallet, J.C.

    1990-01-01

    The tachyonic divergences occurring in the free energy of various string theories at finite temperature are eliminated through the use of regularization schemes and analytic continuations. For closed strings, we obtain finite expressions which, however, develop an imaginary part above the Hagedorn temperature, whereas open string theories are still plagued with dilatonic divergences. (orig.)

  19. String loop divergences and effective lagrangians

    International Nuclear Information System (INIS)

    Fischler, W.; Klebanov, I.; Susskind, L.

    1988-01-01

    We isolate logarithmic divergences from bosonic string amplitudes on a disc. These divergences are compared with 'tadpole' divergences in the effective field theory, with a covariant cosmological term implied by the counting of string coupling constants. We find an inconsistency between the two. This might be a problem in eliminating divergences from the bosonic string. (orig.)

  20. The issue of supersymmetry breaking in strings

    International Nuclear Information System (INIS)

    Binetruy, P.

    1989-12-01

    We discuss the central role that supersymmetry plays in string models, both in spacetime and at the level of the string world-sheet. The problems associated with supersymmetry-breaking are reviewed together with some of the attempts to solve them, in the string as well as the field theory approach

  1. String duality and novel theories without gravity

    International Nuclear Information System (INIS)

    Kachru, Shamit

    1998-01-01

    We describe some of the novel 6d quantum field theories which have been discovered in studies of string duality. The role these theories (and their 4d descendants) may play in alleviating the vacuum degeneracy problem in string theory is reviewed. The DLCQ of these field theories is presented as one concrete way of formulating them, independent of string theory

  2. Architectures and representations for string transduction

    NARCIS (Netherlands)

    Chrupala, Grzegorz

    2015-01-01

    String transduction problems are ubiquitous in natural language processing: they include transliteration, grapheme-to-phoneme conversion, text normalization and translation. String transduction can be reduced to the simpler problems of sequence labeling by expressing the target string as a sequence

  3. Symmetries and Interactions in Matrix String Theory

    NARCIS (Netherlands)

    Hacquebord, F.H.

    1999-01-01

    This PhD-thesis reviews matrix string theory and recent developments therein. The emphasis is put on symmetries, interactions and scattering processes in the matrix model. We start with an introduction to matrix string theory and a review of the orbifold model that flows out of matrix string theory

  4. Exotic configurations for gauge theory strings

    International Nuclear Information System (INIS)

    Yajnik, U.A.

    1987-01-01

    This paper discusses a class of string configurations occuring in nonabelian gauge theories, which are such that a component of the charged scalar field responsible for the string has a nonvanishing expectation value in the core of the string. A systematic procedure is given for setting up the ansatz for such configurations. (orig.)

  5. General relativity invariance and string field theory

    International Nuclear Information System (INIS)

    Aref'eva, I.Ya.; Volovich, I.V.

    1987-04-01

    The general covariance principle in the string field theory is considered. The algebraic properties of the string Lie derivative are discussed. The string vielbein and spin connection are introduced and an action invariant under general co-ordinate transformation is proposed. (author). 18 refs

  6. Test particle trajectories near cosmic strings

    Indian Academy of Sciences (India)

    Gauge strings have their energy concentrated in a very thin tube, the radius of which is of the order of the symmetry- breaking scale whereas the global strings are such that their energy extends to regions far beyond the central core. Strings have an important astrophysical consequence, namely, the double quasar problem ...

  7. Are Stopped Strings Preferred in Sad Music?

    Directory of Open Access Journals (Sweden)

    David Huron

    2017-01-01

    Full Text Available String instruments may be played either with open strings (where the string vibrates between the bridge and a hard wooden nut or with stopped strings (where the string vibrates between the bridge and a performer's finger pressed against the fingerboard. Compared with open strings, stopped strings permit the use of vibrato and exhibit a darker timbre. Inspired by research on the timbre of sad speech, we test whether there is a tendency to use stopped strings in nominally sad music. Specifically, we compare the proportion of potentially open-to-stopped strings in a sample of slow, minor-mode movements with matched major-mode movements. By way of illustration, a preliminary analysis of Samuel Barber's famous Adagio from his Opus 11 string quartet shows that the selected key (B-flat minor provides the optimum key for minimizing open string tones. However, examination of a broader controlled sample of quartet movements by Haydn, Mozart and Beethoven failed to exhibit the conjectured relationship. Instead, major-mode movements were found to avoid possible open strings more than slow minor-mode movements.

  8. Introduction to the theory of strings

    International Nuclear Information System (INIS)

    Peskin, M.E.

    1985-10-01

    These lectures present, from an introductory perspective, some basic aspects of the quantum theory of strings. They treat (1) the kinematics, spectrum, and scattering amplitude of the bosonic string, (2) the spectrum and supersymmetry of Green-Schwarz superstring, and (3) the identification of the underlying gauge invariances of the string theory. 43 refs

  9. Open bosonic string in background electromagnetic field

    International Nuclear Information System (INIS)

    Nesterenko, V.V.

    1987-01-01

    The classical and quantum dynamics of an open string propagating in the D-dimensional space-time in the presence of a background electromagnetic field is investigated. An important point in this consideration is the use of the generalized light-like gauge. There are considered the strings of two types; the neutral strings with charges at their ends obeying the condition q 1 +q 2 =0 and the charged strings having a net charge q 1 +q 2 ≠ 0. The consistency of theory demands that the background electric field does not exceed its critical value. The distance between the mass levels of the neutral open string decreases (1-e 2 ) times in comparison with the free string, where e is the dimensionless strength of the electric field. The magnetic field does not affect this distance. It is shown that at a classical level the squared mass of the neutral open string has a tachyonic contribution due to the motion of the string as a whole in transverse directions. The tachyonic term disappears if one considers, instead of M 2 , the string energy in a special reference frame where the projection of the total canonical momentum of the string onto the electric field vanishes. The contributions due to zero point fluctuations to the energy spectrum of the neutral string and to the Virasoro operators in the theory of charged string are found

  10. 2-Dim. gravity and string theory

    International Nuclear Information System (INIS)

    Narain, K.S.

    1991-01-01

    The role of 2-dim. gravity in string theory is discussed. In particular d=25 string theory coupled to 2-d. gravity is described and shown to give rise to the physics of the usual 26-dim. string theory (where one does not quantise 2-d. gravity. (orig.)

  11. L-cysteine supplementation upregulates glutathione (GSH) and vitamin D binding protein (VDBP) in hepatocytes cultured in high glucose and in vivo in liver, and increases blood levels of GSH, VDBP, and 25-hydroxy-vitamin D in Zucker diabetic fatty rats.

    Science.gov (United States)

    Jain, Sushil K; Kanikarla-Marie, Preeti; Warden, Cassandra; Micinski, David

    2016-05-01

    Vitamin D binding protein (VDBP) status has an effect on and can potentially improve the status of 25(OH) vitamin D and increase the metabolic actions of 25(OH) vitamin D under physiological and pathological conditions. Diabetes is associated with lower levels of glutathione (GSH) and 25(OH) vitamin D. This study examined the hypothesis that upregulation of GSH will also upregulate blood levels of VDBP and 25(OH) vitamin D in type 2 diabetic rats. L-cysteine (LC) supplementation was used to upregulate GSH status in a FL83B hepatocyte cell culture model and in vivo using Zucker diabetic fatty (ZDF) rats. Results show that LC supplementation upregulates both protein and mRNA expression of VDBP and vitamin D receptor (VDR) and GSH status in hepatocytes exposed to high glucose, and that GSH deficiency, induced by glutamate cysteine ligase knockdown, resulted in the downregulation of GSH, VDBP, and VDR and an increase in oxidative stress levels in hepatocytes. In vivo, LC supplementation increased GSH and protein and mRNA expression of VDBP and vitamin D 25-hydroxylase (CYP2R1) in the liver, and simultaneously resulted in elevated blood levels of LC and GSH, as well as increases in VDBP and 25(OH) vitamin D levels, and decreased inflammatory biomarkers in ZDF rats compared with those in placebo-supplemented ZDF rats consuming a similar diet. LC supplementation may provide a novel approach by which to raise blood levels of VDBP and 25(OH) vitamin D in type 2 diabetes. © 2016 The Authors. Molecular Nutrition & Food Research Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Preparation, Crystallization and X-ray Diffraction Analysis to 1.5 A Resolution of Rat Cysteine Dioxygenase, a Mononuclear Iron Enzyme Responsible for Cysteine Thiol Oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons,C.; Hao, Q.; Stipanuk, M.

    2005-01-01

    Cysteine dioxygenase (CDO; EC 1.13.11.20) is an {approx}23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O2, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Angstroms resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Angstrom, {alpha} = {beta} = {gamma} = 90. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  13. Global analysis of gene expression in response to L-Cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica

    Science.gov (United States)

    2011-01-01

    Background Entamoeba histolytica, an enteric protozoan parasite, causes amebic colitis and extra intestinal abscesses in millions of inhabitants of endemic areas. E. histolytica completely lacks glutathione metabolism but possesses L-cysteine as the principle low molecular weight thiol. L-Cysteine is essential for the structure, stability, and various protein functions, including catalysis, electron transfer, redox regulation, nitrogen fixation, and sensing for regulatory processes. Recently, we demonstrated that in E. histolytica, L-cysteine regulates various metabolic pathways including energy, amino acid, and phospholipid metabolism. Results In this study, employing custom-made Affymetrix microarrays, we performed time course (3, 6, 12, 24, and 48 h) gene expression analysis upon L-cysteine deprivation. We identified that out of 9,327 genes represented on the array, 290 genes encoding proteins with functions in metabolism, signalling, DNA/RNA regulation, electron transport, stress response, membrane transport, vesicular trafficking/secretion, and cytoskeleton were differentially expressed (≥3 fold) at one or more time points upon L-cysteine deprivation. Approximately 60% of these modulated genes encoded proteins of no known function and annotated as hypothetical proteins. We also attempted further functional analysis of some of the most highly modulated genes by L-cysteine depletion. Conclusions To our surprise, L-cysteine depletion caused only limited changes in the expression of genes involved in sulfur-containing amino acid metabolism and oxidative stress defense. In contrast, we observed significant changes in the expression of several genes encoding iron sulfur flavoproteins, a major facilitator super-family transporter, regulator of nonsense transcripts, NADPH-dependent oxido-reductase, short chain dehydrogenase, acetyltransferases, and various other genes involved in diverse cellular functions. This study represents the first genome-wide analysis of

  14. Global analysis of gene expression in response to L-Cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Jeelani Ghulam

    2011-05-01

    Full Text Available Abstract Background Entamoeba histolytica, an enteric protozoan parasite, causes amebic colitis and extra intestinal abscesses in millions of inhabitants of endemic areas. E. histolytica completely lacks glutathione metabolism but possesses L-cysteine as the principle low molecular weight thiol. L-Cysteine is essential for the structure, stability, and various protein functions, including catalysis, electron transfer, redox regulation, nitrogen fixation, and sensing for regulatory processes. Recently, we demonstrated that in E. histolytica, L-cysteine regulates various metabolic pathways including energy, amino acid, and phospholipid metabolism. Results In this study, employing custom-made Affymetrix microarrays, we performed time course (3, 6, 12, 24, and 48 h gene expression analysis upon L-cysteine deprivation. We identified that out of 9,327 genes represented on the array, 290 genes encoding proteins with functions in metabolism, signalling, DNA/RNA regulation, electron transport, stress response, membrane transport, vesicular trafficking/secretion, and cytoskeleton were differentially expressed (≥3 fold at one or more time points upon L-cysteine deprivation. Approximately 60% of these modulated genes encoded proteins of no known function and annotated as hypothetical proteins. We also attempted further functional analysis of some of the most highly modulated genes by L-cysteine depletion. Conclusions To our surprise, L-cysteine depletion caused only limited changes in the expression of genes involved in sulfur-containing amino acid metabolism and oxidative stress defense. In contrast, we observed significant changes in the expression of several genes encoding iron sulfur flavoproteins, a major facilitator super-family transporter, regulator of nonsense transcripts, NADPH-dependent oxido-reductase, short chain dehydrogenase, acetyltransferases, and various other genes involved in diverse cellular functions. This study represents the first

  15. String formation beyond leading colour

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, Jesper R. [Department of Astronomy and Theoretical Physics, Lund University,Sölvegatan 14, Lund (Sweden); Theoretical Physics, CERN,CH-1211, Geneva 23 (Switzerland); Skands, Peter Z. [Theoretical Physics, CERN,CH-1211, Geneva 23 (Switzerland); School of Physics and Astronomy, Monash University,VIC-3800 (Australia)

    2015-08-03

    We present a new model for the hadronisation of multi-parton systems, in which colour correlations beyond leading N{sub C} are allowed to influence the formation of confining potentials (strings). The multiplet structure of SU(3) is combined with a minimisation of the string potential energy, to decide between which partons strings should form, allowing also for “baryonic” configurations (e.g., two colours can combine coherently to form an anticolour). In e{sup +}e{sup −}collisions, modifications to the leading-colour picture are small, suppressed by both colour and kinematics factors. But in pp collisions, multi-parton interactions increase the number of possible subleading connections, counteracting their naive 1/N{sub C}{sup 2} suppression. Moreover, those that reduce the overall string lengths are kinematically favoured. The model, which we have implemented in the PYTHIA 8 generator, is capable of reaching agreement not only with the important 〈p{sub ⊥}〉(n{sub charged}) distribution but also with measured rates (and ratios) of kaons and hyperons, in both ee and pp collisions. Nonetheless, the shape of their p{sub ⊥} spectra remains challenging to explain.

  16. Confinement and strings in MQCD

    International Nuclear Information System (INIS)

    Hanany, A.; Strassler, M.J.; Zaffaroni, A.

    1998-01-01

    We study aspects of confinement in the M-theory fivebrane version of QCD (MQCD). We show heavy quarks are confined in hadrons (which take the form of membrane-fivebrane bound states) for N=1 and softly broken N=2 SU(N) MQCD. We explore and clarify the transition from the exotic physics of the latter to the standard physics of the former. In particular, the many strings and quark-antiquark mesons found in N=2 field theory by Douglas and Shenker are reproduced. It is seen that in the N=1 limit all but one such meson disappears while all of the strings survive. The strings of softly broken N=2, N=1, and even non-supersymmetric SU(N) MQCD have a common ratio for their tensions as a function of the amount of flux they carry. We also comment on the almost BPS properties of the Douglas-Shenker strings and discuss the brane picture for monopole confinement on N=2 QCD Higgs branches. (orig.)

  17. Monads, strings, and M theory

    NARCIS (Netherlands)

    Hofman, C.; Park, J.-S.

    1997-01-01

    The recent developmen ts in string theory suggest that the space-time coordinates should be generalized to non-comm uting matrices. P ostulating this suggestion as the fun- damen tal geometrical principle, w e form ulate a candidate for covariant second quantized RNS superstrings as a topological

  18. Topological strings and quantum curves

    NARCIS (Netherlands)

    Hollands, L.

    2009-01-01

    This thesis presents several new insights on the interface between mathematics and theoretical physics, with a central role for Riemann surfaces. First of all, the duality between Vafa-Witten theory and WZW models is embedded in string theory. Secondly, this model is generalized to a web of

  19. Probing the string winding sector

    Energy Technology Data Exchange (ETDEWEB)

    Aldazabal, Gerardo; Mayo, Martín [G. Física CAB-CNEA and CONICET, Centro Atómico Bariloche,Av. Bustillo 9500, Bariloche (Argentina); Instituto Balseiro, Centro Atómico Bariloche,Av. Bustillo 9500, Bariloche (Argentina); Nuñez, Carmen [Instituto de Astronomía y Física del Espacio (CONICET-UBA),C.C. 67 - Suc. 28, 1428 Buenos Aires (Argentina); Departamento de Física, FCEN, Universidad de Buenos Aires,C.C. 67 - Suc. 28, 1428 Buenos Aires (Argentina)

    2017-03-17

    We probe a slice of the massive winding sector of bosonic string theory from toroidal compactifications of Double Field Theory (DFT). This string subsector corresponds to states containing one left and one right moving oscillators. We perform a generalized Kaluza Klein compactification of DFT on generic 2n-dimensional toroidal constant backgrounds and show that, up to third order in fluctuations, the theory coincides with the corresponding effective theory of the bosonic string compactified on n-dimensional toroidal constant backgrounds, obtained from three-point amplitudes. The comparison between both theories is facilitated by noticing that generalized diffeomorphisms in DFT allow to fix generalized harmonic gauge conditions that help in identifying the physical degrees of freedom. These conditions manifest as conformal anomaly cancellation requirements on the string theory side. The explicit expression for the gauge invariant effective action containing the physical massless sector (gravity+antisymmetric+gauge+ scalar fields) coupled to towers of generalized Kaluza Klein massive states (corresponding to compact momentum and winding modes) is found. The action acquires a very compact form when written in terms of fields carrying O(n,n) indices, and is explicitly T-duality invariant. The global algebra associated to the generalized Kaluza Klein compactification is discussed.

  20. String theory and cosmological singularities

    Indian Academy of Sciences (India)

    recent times, string theory is providing new perspectives of such singularities which .... holes appear as stacks of a large number of D-branes wrapped in internal .... results into a well-known measure factor which makes the wave function into a.

  1. Hawking radiation in string theories

    International Nuclear Information System (INIS)

    Sakai, N.

    1986-01-01

    String theories in a uniform gravitational field are studied to examine the Hawking radiation. An upper limit is found for the strength of the possible gravitational field: the corresponding Hawking temperature cannot be larger than the Hagedorn limiting temperature divided by π

  2. The Science of String Instruments

    CERN Document Server

    Rossing, Thomas D

    2010-01-01

    Many performing musicians, as well as instrument builders, are coming to realize the importance of understanding the science of musical instruments. This book explains how string instruments produce sound. It presents basic ideas in simple language, and it also translates some more sophisticated ideas in non-technical language. It should be of interest to performers, researchers, and instrument makers alike.

  3. String theory and cosmological singularities

    Indian Academy of Sciences (India)

    Well-known examples are singularities inside black holes and initial or final singularities in expanding or contracting universes. In recent times, string theory is providing new perspectives of such singularities which may lead to an understanding of these in the standard framework of time evolution in quantum mechanics.

  4. Defect branes as Alice strings

    International Nuclear Information System (INIS)

    Okada, Takashi; Sakatani, Yuho

    2015-01-01

    There exist various defect-brane backgrounds in supergravity theories which arise as the low energy limit of string theories. These backgrounds typically have non-trivial monodromies, and if we move a charged probe around the center of a defect, its charge will be changed by the action of the monodromy. During the process, the charge conservation law seems to be violated. In this paper, to resolve this puzzle, we examine a dynamics of the charge changing process and show that the missing charge of the probe is transferred to the background. We then explicitly construct the resultant background after the charge transfer process by utilizing dualities. This background has the same monodromy as the original defect brane, but has an additional charge which does not have any localized source. In the literature, such a charge without localized source is known to appear in the presence of Alice strings. We argue that defect branes can in fact be regarded as a realization of Alice strings in string theory and examine the charge transfer process from that perspective.

  5. Parton fragmentation and string dynamics

    International Nuclear Information System (INIS)

    Andersson, B.; Gustafson, G.; Ingelman, G.; Sjoestrand, T.

    1983-01-01

    While much has been learned recently about quark and gluon interactions in the framework of perturbative Quantum Chromodynamics, the relation between calculated parton properties and observed hadron densities involves models where dynamics and jet empirical rules have to be combined. The purpose of this article is to describe a presently successful approach which is based on a cascade jet model using String dynamics. It can readily lead to Monte Carlo jet programmes of great use when analyzing data. Production processes in an iterative cascade approach, with tunneling in a constant force field, are reviewed. Expected differences between quark and gluon jets are discussed. Low transverse momentum phenomena are also reviewed with emphasis on hyperon polarization. In so far as this approach uses a fragmentation scheme based on String dynamics, it was deemed appropriate to also include under the same cover a special report on the Classical theory of relativistic Strings, seen as the classical limit of the Dual Resonance model. The Equations of motion and interaction among strings are presented. (orig.)

  6. Particles, fields, and now strings

    International Nuclear Information System (INIS)

    Weinberg, S.

    1986-01-01

    The author traces the history of the struggle between two views of the world: a world of particles or a world of fields. These positions were crystallised as quantum field theory and S-matrix theory and now by the reintroduction of string theories. (Auth.)

  7. Modified Steiner functional string action

    International Nuclear Information System (INIS)

    Baillie, C.F.; Johnston, D.A.

    1992-01-01

    It has recently been suggested by Ambartzumian et al. that the modified Steiner functional has desirable properties as an action for random surfaces and hence string world sheets. We perform a simulation of this action on a dynamically triangulated random surface to investigate this claim and find that the surfaces are in a flat phase

  8. String theory in the bathtub

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    The presence of the surrounding medium makes their dynamics dramatically different from those of ordinary string-like objects propagating in empty space, leading to quite peculiar phenomena, observed in experiments and simulations. I will argue that the effective theory provides an optimal theoretical framework to understand such phenomena, and to make precise quantitative predictions about them.

  9. Topological Strings and Integrable Hierarchies

    CERN Document Server

    Aganagic, M; Klemm, A D; Marino, M; Vafa, C; Aganagic, Mina; Dijkgraaf, Robbert; Klemm, Albrecht; Marino, Marcos; Vafa, Cumrun

    2006-01-01

    We consider the topological B-model on local Calabi-Yau geometries. We show how one can solve for the amplitudes by using W-algebra symmetries which encodes the symmetries of holomorphic diffeomorphisms of the Calabi-Yau. In the highly effective fermionic/brane formulation this leads to a free fermion description of the amplitudes. Furthermore we argue that topological strings on Calabi-Yau geometries provide a unifying picture connecting non-critical (super)strings, integrable hierarchies, and various matrix models. In particular we show how the ordinary matrix model, the double scaling limit of matrix models, and Kontsevich-like matrix model are all related and arise from studying branes in specific local Calabi-Yau three-folds. We also show how A-model topological string on P^1 and local toric threefolds (and in particular the topological vertex) can be realized and solved as B-model topological string amplitudes on a Calabi-Yau manifold.

  10. LZ-Compressed String Dictionaries

    OpenAIRE

    Arz, Julian; Fischer, Johannes

    2013-01-01

    We show how to compress string dictionaries using the Lempel-Ziv (LZ78) data compression algorithm. Our approach is validated experimentally on dictionaries of up to 1.5 GB of uncompressed text. We achieve compression ratios often outperforming the existing alternatives, especially on dictionaries containing many repeated substrings. Our query times remain competitive.

  11. Defect branes as Alice strings

    Energy Technology Data Exchange (ETDEWEB)

    Okada, Takashi [Theoretical Biology Laboratory, RIKEN,Wako 351-0198 (Japan); Sakatani, Yuho [Department of Physics and Astronomy,Seoul National University, Seoul 151-747 (Korea, Republic of)

    2015-03-25

    There exist various defect-brane backgrounds in supergravity theories which arise as the low energy limit of string theories. These backgrounds typically have non-trivial monodromies, and if we move a charged probe around the center of a defect, its charge will be changed by the action of the monodromy. During the process, the charge conservation law seems to be violated. In this paper, to resolve this puzzle, we examine a dynamics of the charge changing process and show that the missing charge of the probe is transferred to the background. We then explicitly construct the resultant background after the charge transfer process by utilizing dualities. This background has the same monodromy as the original defect brane, but has an additional charge which does not have any localized source. In the literature, such a charge without localized source is known to appear in the presence of Alice strings. We argue that defect branes can in fact be regarded as a realization of Alice strings in string theory and examine the charge transfer process from that perspective.

  12. The super G-string

    International Nuclear Information System (INIS)

    Gates, V.; Kangaroo, E.; Roachcock, M.; Gall, W.C.

    1986-01-01

    The authors describe a string theory which gives all the phenomenology of symmetry breaking. It makes use of higher dimensions, higher derivatives, higher spin, higher twist, and hierarchy. It discusses the problems of renormalizability of gravity, the cosmological constant, grand unification, supersymmetry breaking, and the command cold

  13. Strings, fields and critical phenomena

    International Nuclear Information System (INIS)

    Ambjoern, J.

    1987-07-01

    The connection between field theory and critical phenomena is reviewed. Emphasis is put on the use of Monte Carlo methods in the study of non-perturbative aspects of field theory. String theory is then described as a statistical theory of random surfaces and the critical behaviour is analyzed both by analytical and numerical methods. (orig.)

  14. Structure and mechanism leading to formation of the cysteine sulfinate product complex of a biomimetic cysteine dioxygenase model.

    Science.gov (United States)

    Sallmann, Madleen; Kumar, Suresh; Chernev, Petko; Nehrkorn, Joscha; Schnegg, Alexander; Kumar, Devesh; Dau, Holger; Limberg, Christian; de Visser, Sam P

    2015-05-11

    Cysteine dioxygenase is a unique nonheme iron enzyme that is involved in the metabolism of cysteine in the body. It contains an iron active site with an unusual 3-His ligation to the protein, which contrasts with the structural features of common nonheme iron dioxygenases. Recently, some of us reported a truly biomimetic model for this enzyme, namely a trispyrazolylborato iron(II) cysteinato complex, which not only has a structure very similar to the enzyme-substrate complex but also represents a functional model: Treatment of the model with dioxygen leads to cysteine dioxygenation, as shown by isolating the cysteine part of the product in the course of the work-up. However, little is known on the conversion mechanism and, so far, not even the structure of the actual product complex had been characterised, which is also unknown in case of the enzyme. In a multidisciplinary approach including density functional theory calculations and X-ray absorption spectroscopy, we have now determined the structure of the actual sulfinato complex for the first time. The Cys-SO2 (-) functional group was found to be bound in an η(2) -O,O-coordination mode, which, based on the excellent resemblance between model and enzyme, also provides the first support for a corresponding binding mode within the enzymatic product complex. Indeed, this is again confirmed by theory, which had predicted a η(2) -O,O-binding mode for synthetic as well as the natural enzyme. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Interacting bosonic strings in subcritical dimensions

    International Nuclear Information System (INIS)

    Hwang, S.; Marnelius, R.

    1988-01-01

    Interaction theory for relativistic bosonic string in spacetime dimensions below the critical value 26 is formulated using BRST techniques with an extra scalar field. One-loop zero-point amplitudes for closed strings are modular invariant. For a free scalar field, vertex operators are constructed leading to, e.g., the old dual N-tachyon tree amplitudes in D < 26. The N-tachyon one-loop expressions contain closed string poles for open strings, and are modular invariant for closed strings. However, the threshold cuts are wrong in D < 25. Only for D=25 to the considered vertex operators lead to consistency. (orig.)

  16. Micro string resonators as temperature sensors

    DEFF Research Database (Denmark)

    Larsen, T.; Schmid, S.; Boisen, A.

    2013-01-01

    The resonance frequency of strings is highly sensitive to temperature. In this work we have investigated the applicability of micro string resonators as temperature sensors. The resonance frequency of strings is a function of the tensile stress which is coupled to temperature by the thermal...... to the low thermal mass of the strings. A temperature resolution of 2.5×10-4 °C has been achieved with silicon nitride strings. The theoretical limit for the temperature resolution of 8×10-8 °C has not been reached yet and requires further improvement of the sensor....

  17. Synthesis and Application of Aurophilic Poly(Cysteine and Poly(Cysteine-Containing Copolymers

    Directory of Open Access Journals (Sweden)

    David Ulkoski

    2017-10-01

    Full Text Available The redox capacity, as well as the aurophilicity of the terminal thiol side groups, in poly(Cysteine lend a unique characteristic to this poly(amino acid or polypeptide. There are two major application fields for this polymer: (i biomedical applications in drug delivery and surface modification of biomedical devices and (ii as coating for electrodes to enhance their electrochemical sensitivity. The intended application determines the synthetic route for p(Cysteine. Polymers to be used in biomedical applications are typically polymerized from the cysteine N-carboxyanhydride by a ring-opening polymerization, where the thiol group needs to be protected during the polymerization. Advances in this methodology have led to conditions under which the polymerization progresses as living polymerization, which allows for a strict control of the molecular architecture, molecular weight and polydispersity and the formation of block copolymers, which eventually could display polyphilic properties. Poly(Cysteine used as electrode coating is typically polymerized onto the electrode by cyclic voltammetry, which actually produces a continuous, pinhole-free film on the electrode via the formation of covalent bonds between the amino group of Cysteine and the carbon of the electrode. This resulting coating is chemically very different from the well-defined poly(Cysteine obtained by ring-opening polymerizations. Based on the structure of cysteine a significant degree of cross-linking within the coating deposited by cyclic voltammetry can be assumed. This manuscript provides a detailed discussion of the ring-opening polymerization of cysteine, a brief consideration of the role of glutathione, a key cysteine-containing tripeptide, and examples for the utilization of poly(Cysteine and poly(Cysteine-containing copolymers, in both, the biomedical as well as electrochemical realm.

  18. String Theory and M-Theory

    Science.gov (United States)

    Becker, Katrin; Becker, Melanie; Schwarz, John H.

    String theory is one of the most exciting and challenging areas of modern theoretical physics. This book guides the reader from the basics of string theory to recent developments. It introduces the basics of perturbative string theory, world-sheet supersymmetry, space-time supersymmetry, conformal field theory and the heterotic string, before describing modern developments, including D-branes, string dualities and M-theory. It then covers string geometry and flux compactifications, applications to cosmology and particle physics, black holes in string theory and M-theory, and the microscopic origin of black-hole entropy. It concludes with Matrix theory, the AdS/CFT duality and its generalizations. This book is ideal for graduate students and researchers in modern string theory, and will make an excellent textbook for a one-year course on string theory. It contains over 120 exercises with solutions, and over 200 homework problems with solutions available on a password protected website for lecturers at www.cambridge.org/9780521860697. Comprehensive coverage of topics from basics of string theory to recent developments Ideal textbook for a one-year course in string theory Includes over 100 exercises with solutions Contains over 200 homework problems with solutions available to lecturers on-line

  19. String theory as a Lilliputian world

    International Nuclear Information System (INIS)

    Ambjørn, J.; Makeenko, Y.

    2016-01-01

    Lattice regularizations of the bosonic string do not allow us to probe the tachyon. This has often been viewed as the reason why these theories have never managed to make any contact to standard continuum string theories when the dimension of spacetime is larger than two. We study the continuum string theory in large spacetime dimensions where simple mean field theory is reliable. By keeping carefully the cutoff we show that precisely the existence of a tachyon makes it possible to take a scaling limit which reproduces the lattice-string results. We compare this scaling limit with another scaling limit which reproduces standard continuum-string results. If the people working with lattice regularizations of string theories are akin to Gulliver they will view the standard string-world as a Lilliputian world no larger than a few lattice spacings.

  20. String theory as a Lilliputian world

    Energy Technology Data Exchange (ETDEWEB)

    Ambjørn, J., E-mail: ambjorn@nbi.dk [The Niels Bohr Institute, Copenhagen University, Blegdamsvej 17, DK-2100 Copenhagen (Denmark); IMAPP, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen (Netherlands); Makeenko, Y., E-mail: makeenko@nbi.dk [The Niels Bohr Institute, Copenhagen University, Blegdamsvej 17, DK-2100 Copenhagen (Denmark); Institute of Theoretical and Experimental Physics, B. Cheremushkinskaya 25, 117218 Moscow (Russian Federation)

    2016-05-10

    Lattice regularizations of the bosonic string do not allow us to probe the tachyon. This has often been viewed as the reason why these theories have never managed to make any contact to standard continuum string theories when the dimension of spacetime is larger than two. We study the continuum string theory in large spacetime dimensions where simple mean field theory is reliable. By keeping carefully the cutoff we show that precisely the existence of a tachyon makes it possible to take a scaling limit which reproduces the lattice-string results. We compare this scaling limit with another scaling limit which reproduces standard continuum-string results. If the people working with lattice regularizations of string theories are akin to Gulliver they will view the standard string-world as a Lilliputian world no larger than a few lattice spacings.