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

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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.

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

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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.

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

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.

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

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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.

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

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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.

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

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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.

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.

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

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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.

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.

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

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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....

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...

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

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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.

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

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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

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

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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.

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

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...

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

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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.

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

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.

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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.

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.

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...

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

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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.

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.

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...

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...

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.

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...

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.

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.

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...

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.

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...

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 ...

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.

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.

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.)

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

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.

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.

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, ...

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.

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.

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

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.

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.

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.

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.

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...

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....

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.

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.

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

Directory of Open Access Journals (Sweden)

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

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

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.

Cysteine Biosynthesis Controls Serratia marcescens Phospholipase Activity.

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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

Effect of free cysteine on the denaturation and aggregation of holo α-lactalbumin

DEFF Research Database (Denmark)

Nielsen, Line R.; Lund, Marianne N.; Davies, Michael J.

2018-01-01

α-Lactalbumin (α-LA) is a key commercial whey protein for nutritional purposes. The holo protein (calcium saturated) is considered the most heat stable whey protein, capable of refolding from unfolded states under many conditions. This is due to the absence of free thiols (cysteine residues......) that are typically involved in thermal aggregation and thiol–disulphide exchange reactions of other whey proteins. Heating (0–120 min at 90 °C, pH 7.0) holo α-LA generates free thiols through thermal cleavage of disulphide bonds, resulting in aggregates comprising unfolded α-LA species. The addition of free cysteine...... promotes the formation of soluble aggregates, effectively decreasing the holding time required to reach a particular aggregate size in a dose-dependent manner (0.35–1.4 mM cysteine). Excess cysteine (≥14 mM) causes a destabilisation of α-LA, shown by decreased denaturation temperature and gel formation...

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

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.

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

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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

Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity.

Science.gov (United States)

Oliveira, Marco A S; Baura, Valter A; Aquino, Bruno; Huergo, Luciano F; Kadowaki, Marco A S; Chubatsu, Leda S; Souza, Emanuel M; Dixon, Ray; Pedrosa, Fábio O; Wassem, Roseli; Monteiro, Rose A

2009-01-01

Herbaspirillum seropedicae is an endophytic diazotrophic bacterium that associates with economically important crops. NifA protein, the transcriptional activator of nif genes in H. seropedicae, binds to nif promoters and, together with RNA polymerase-sigma(54) holoenzyme, catalyzes the formation of open complexes to allow transcription initiation. The activity of H. seropedicae NifA is controlled by ammonium and oxygen levels, but the mechanisms of such control are unknown. Oxygen sensitivity is attributed to a conserved motif of cysteine residues in NifA that spans the central AAA+ domain and the interdomain linker that connects the AAA+ domain to the C-terminal DNA binding domain. Here we mutagenized this conserved motif of cysteines and assayed the activity of mutant proteins in vivo. We also purified the mutant variants of NifA and tested their capacity to bind to the nifB promoter region. Chimeric proteins between H. seropedicae NifA, an oxygen-sensitive protein, and Azotobacter vinelandii NifA, an oxygen-tolerant protein, were constructed and showed that the oxygen response is conferred by the central AAA+ and C-terminal DNA binding domains of H. seropedicae NifA. We conclude that the conserved cysteine motif is essential for NifA activity, although single cysteine-to-serine mutants are still competent at binding DNA.

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

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.

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

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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.

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.

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.

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.

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

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.

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.

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.

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.

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

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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

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

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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.

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

Measuring site occupancy: a new perspective on cysteine oxidation.

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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

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

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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.

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.

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)

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.)

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

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.)

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

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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.

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.

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

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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.

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.

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

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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.

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...

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.

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.)

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.)

Synthesis and Application of Aurophilic Poly(Cysteine and Poly(Cysteine-Containing Copolymers

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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.

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

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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.

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.)

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

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

Mutations at the cysteine codons of the recA gene of Escherichia coli

International Nuclear Information System (INIS)

Weisemann, J.M.; Weinstock, G.M.

1988-01-01

Each of the three cysteine residues in the Escherichia coli RecA protein was replaced with a number of other amino acids. To do this, each cysteine codon was first converted to a chain-terminating amber codon by oligonucleotide-directed mutagenesis. These amber mutants were then either assayed for function in different suppressor strains or reverted by a second round of mutagenesis with oligonucleotides that had random sequences at the amber codon. Thirty-three different amino acid substitutions were obtained. Mutants were tested for three functions of RecA: survival following UV irradiation, homologous recombination, and induction of the SOS response. It was found that although none of the cysteines is essential for activity, mutations at each of these positions can affect one or more of the activities of RecA, depending on the particular amino acid substitution. In addition, the cysteine at position 116 appears to be involved in the RecA-promoted cleavage of the LexA protein

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

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

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

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...

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.)

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.

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

Vortex-strings in N=2 SQCD and bulk-string decoupling

Science.gov (United States)

Gerchkovitz, Efrat; Karasik, Avner

2018-02-01

We study vortex-strings in four-dimensional N=2 supersymmetric SU( N c ) × U(1) gauge theories with N f hypermultiplets in the fundamental representation of SU( N c ) and general U(1) charges. If N f > N c , the vacuum is not gapped and the low-energy theory contains both the vacuum massless excitations and the string zero-modes. The question we address in this work is whether the vacuum and the string moduli decouple at low energies, allowing a description of the low-energy dynamics in terms of a two-dimensional theory on the string worldsheet. We find a simple condition controlling the bulk-string coupling: if there exist two flavors such that the product of their U(1) charge difference with the magnetic flux carried by the string configuration is not an integer multiple of 2 π, the string has zero-modes that decay slower than 1 /r, where r is the radial distance from the string core. These modes are coupled to the vacuum massless excitations even at low energies. If, however, all such products are integer multiples of 2 π, long-range modes of this type do not exist and the string moduli decouple from the bulk at low energies. This condition turns out to coincide with the condition of trivial Aharonov-Bohm phases for the particles in the spectrum. In addition to a derivation of the bulk-string decoupling criterion using classical analysis of the string zero-modes, we provide a non-perturbative derivation of the criterion, which uses supersymmetric localization techniques.

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....

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.

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.

Boundary string field theory and an open string one-loop

International Nuclear Information System (INIS)

Lee, Tae Jin; Viswanathan, K. S.; Yang, Yi

2003-01-01

We discuss the open string one-loop partition function in the tachyon condensation background of an unstable D-brane system. We evaluate the partition function by using the boundary-state formulation and find that it is in complete agreement with the result obtained in the boundary string field theory. This suggests that the open string higher loop diagrams may be produced consistently by using a closed string field theory, where the D-brane plays the role of a source for the closed string field

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.

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 ...

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

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.)

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

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.

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.

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

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

String-coupling constant and dilaton vacuum expectation value in string field theory

International Nuclear Information System (INIS)

Yoneya, Tamiaki

1987-01-01

In the first quantized approaches to strings, it is well known that the string-coupling constant is determined by the vacuum expectation value of the dilaton field. This property, however, has never been demonstrated within the framework of string field theory. An explicit reparametrization of the string field associated with the shifts of the dilaton vacuum expectation value and the string-coupling constant is constructed exhibiting the above property in the light-cone field theory of the closed bosonic string. (orig.)

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.)

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

Simultaneous enrichment of cysteine-containing peptides and phosphopeptides using a cysteine-specific phosphonate adaptable tag (CysPAT) in combination with titanium dioxide (TiO2) chromatography

DEFF Research Database (Denmark)

Huang, Honggang; Pedersen, Martin Haar; Ibañez-Vea, Maria

2016-01-01

to selectively label cysteine-containing peptides (Cys peptides) followed by their enrichment with titanium dioxide (TiO2) and subsequent mass spectrometric analysis. The CysPAT strategy was developed using a synthetic peptide, a standard protein and subsequently the strategy was applied to protein lysates from...

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.

On the elliptic genus of three E-strings and heterotic strings

International Nuclear Information System (INIS)

Cai, Wenhe; Huang, Min-xin; Sun, Kaiwen

2015-01-01

A precise formula for the elliptic genus of three E-strings is presented. The related refined free energy coincides with the result calculated from topological string on local half K3 Calabi-Yau threefold up to genus twelve. The elliptic genus of three heterotic strings computed from M9 domain walls matches with the result from orbifold formula to high orders. This confirms the n=3 case of the recent conjecture that n pairs of E-strings can recombine into n heterotic strings.

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.

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...

Simultaneous electrochemical determination of L-cysteine and L-cysteine disulfide at carbon ionic liquid electrode.

Science.gov (United States)

Safavi, Afsaneh; Ahmadi, Raheleh; Mahyari, Farzaneh Aghakhani

2014-04-01

A linear sweep voltammetric method is used for direct simultaneous determination of L-cysteine and L-cysteine disulfide (cystine) based on carbon ionic liquid electrode. With carbon ionic liquid electrode as a high performance electrode, two oxidation peaks for L-cysteine (0.62 V) and L-cysteine disulfide (1.3 V) were observed with a significant separation of about 680 mV (vs. Ag/AgCl) in phosphate buffer solution (pH 6.0). The linear ranges were obtained as 1.0-450 and 5.0-700 μM and detection limits were estimated to be 0.298 and 4.258 μM for L-cysteine and L-cysteine disulfide, respectively. This composite electrode was applied for simultaneous determination of L-cysteine and L-cysteine disulfide in two real samples, artificial urine and nutrient broth. Satisfactory results were obtained which clearly indicate the applicability of the proposed electrode for simultaneous determination of these compounds in complex matrices.

Photo-fermentative bacteria aggregation triggered by L-cysteine during hydrogen production.

Science.gov (United States)

Xie, Guo-Jun; Liu, Bing-Feng; Xing, De-Feng; Nan, Jun; Ding, Jie; Ren, Nan-Qi

2013-05-03

Hydrogen recovered from organic wastes and solar energy by photo-fermentative bacteria (PFB) has been suggested as a promising bioenergy strategy. However, the use of PFB for hydrogen production generally suffers from a serious biomass washout from photobioreactor, due to poor flocculation of PFB. In the continuous operation, PFB cells cannot be efficiently separated from supernatant and rush out with effluent from reactor continuously, which increased the effluent turbidity, meanwhile led to increases in pollutants. Moreover, to replenish the biomass washout, substrate was continuously utilized for cell growth rather than hydrogen production. Consequently, the poor flocculability not only deteriorated the effluent quality, but also decreased the potential yield of hydrogen from substrate. Therefore, enhancing the flocculability of PFB is urgent necessary to further develop photo-fermentative process. Here, we demonstrated that L-cysteine could improve hydrogen production of Rhodopseudomonas faecalis RLD-53, and more importantly, simultaneously trigger remarkable aggregation of PFB. Experiments showed that L-cysteine greatly promoted the production of extracellular polymeric substances, especially secretion of protein containing more disulfide bonds, and help for enhancement stability of floc of PFB. Through formation of disulfide bonds, L-cysteine not only promoted production of EPS, in particular the secretion of protein, but also stabilized the final confirmation of protein in EPS. In addition, the cell surface elements and functional groups, especially surface charged groups, have also been changed by L-cysteine. Consequently, absolute zeta potential reached a minimum value at 1.0 g/l of L-cysteine, which obviously decreased electrostatic repulsion interaction energy based on DLVO theory. Total interaction energy barrier decreased from 389.77 KT at 0.0 g/l of L-cysteine to 127.21 kT at 1.0 g/l. Thus, the strain RLD-53 overcame the total energy barrier and

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

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.

Long-time treatment by low-dose N-acetyl-L-cysteine enhances proinflammatory cytokine expressions in LPS-stimulated macrophages.

Directory of Open Access Journals (Sweden)

Tomokazu Ohnishi

Full Text Available N-acetyl-L-cysteine is known to act as a reactive oxygen species scavenger and used in clinical applications. Previous reports have shown that high-dose N-acetyl-L-cysteine treatment inhibits the expression of proinflammatory cytokines in activated macrophages. Here, we have found that long-time N-acetyl-L-cysteine treatment at low-concentration increases phosphorylation of extracellular signal-regulated kinase 1/2 and AKT, which are essential for the induction of proinflammatory cytokines including interleukin 1β and interleukin 6 in lipopolysaccharide-stimulated RAW264.7 cells. Furthermore, long-time N-acetyl-L-cysteine treatment decreases expressions of protein phosphatases, catalytic subunit of protein phosphatase-2A and dual specificity phosphatase 1. On the other hand, we have found that short-time N-acetyl-L-cysteine treatment at low dose increases p53 expression, which inhibits expressions of proinflammatory cytokines. These observations suggest that long-time low-dose N-acetyl-L-cysteine treatment increases expressions of proinflammatory cytokines through enhancement of kinase phosphorylation.

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.

Transgenic soybean plants overexpressing O-acetylserine sulfhydrylase accumulate enhanced levels of cysteine and Bowman-Birk protease inhibitor in seeds.

Science.gov (United States)

Kim, Won-Seok; Chronis, Demosthenis; Juergens, Matthew; Schroeder, Amy C; Hyun, Seung Won; Jez, Joseph M; Krishnan, Hari B

2012-01-01

Soybeans provide an excellent source of protein in animal feed. Soybean protein quality can be enhanced by increasing the concentration of sulfur-containing amino acids. Previous attempts to increase the concentration of sulfur-containing amino acids through the expression of heterologous proteins have met with limited success. Here, we report a successful strategy to increase the cysteine content of soybean seed through the overexpression of a key sulfur assimilatory enzyme. We have generated several transgenic soybean plants that overexpress a cytosolic isoform of O-acetylserine sulfhydrylase (OASS). These transgenic soybean plants exhibit a four- to tenfold increase in OASS activity when compared with non-transformed wild-type. The OASS activity in the transgenic soybeans was significantly higher at all the stages of seed development. Unlike the non-transformed soybean plants, there was no marked decrease in the OASS activity even at later stages of seed development. Overexpression of cytosolic OASS resulted in a 58-74% increase in protein-bound cysteine levels compared with non-transformed wild-type soybean seeds. A 22-32% increase in the free cysteine levels was also observed in transgenic soybeans overexpressing OASS. Furthermore, these transgenic soybean plants showed a marked increase in the accumulation of Bowman-Birk protease inhibitor, a cysteine-rich protein. The overall increase in soybean total cysteine content (both free and protein-bound) satisfies the recommended levels required for the optimal growth of monogastric animals.

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.

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.

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

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.

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

BPS limit of multi- D- and DF-strings in boundary string field theory

International Nuclear Information System (INIS)

Go, Gyungchoon; Ishida, Akira; Kim, Yoonbai

2007-01-01

A BPS limit is systematically derived for straight multi- D- and DF-strings from the D3D-bar3 system in the context of boundary superstring field theory. The BPS limit is obtained in the limit of thin D(F)-strings, where the Bogomolny equation supports singular static multi-D(F)-string solutions. For the BPS multi-string configurations with arbitrary separations, BPS sum rule is fulfilled under a Gaussian type tachyon potential and reproduces exactly the descent relation. For the DF-strings ((p,q)-strings), the distribution of fundamental string charge density coincides with its energy density and the Hamiltonian density takes the BPS formula of square-root form

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

Mechanistic understanding of the cysteine capping modifications of antibodies enables selective chemical engineering in live mammalian cells.

Science.gov (United States)

Zhong, Xiaotian; He, Tao; Prashad, Amar S; Wang, Wenge; Cohen, Justin; Ferguson, Darren; Tam, Amy S; Sousa, Eric; Lin, Laura; Tchistiakova, Lioudmila; Gatto, Scott; D'Antona, Aaron; Luan, Yen-Tung; Ma, Weijun; Zollner, Richard; Zhou, Jing; Arve, Bo; Somers, Will; Kriz, Ronald

2017-04-20

Protein modifications by intricate cellular machineries often redesign the structure and function of existing proteins to impact biological networks. Disulfide bond formation between cysteine (Cys) pairs is one of the most common modifications found in extracellularly-destined proteins, key to maintaining protein structure. Unpaired surface cysteines on secreted mammalian proteins are also frequently found disulfide-bonded with free Cys or glutathione (GSH) in circulation or culture, the mechanism for which remains unknown. Here we report that these so-called Cys-capping modifications take place outside mammalian cells, not in the endoplasmic reticulum (ER) where oxidoreductase-mediated protein disulfide formation occurs. Unpaired surface cysteines of extracellularly-arrived proteins such as antibodies are uncapped upon secretion before undergoing disulfide exchange with cystine or oxidized GSH in culture medium. This observation has led to a feasible way to selectively modify the nucleophilic thiol side-chain of cell-surface or extracellular proteins in live mammalian cells, by applying electrophiles with a chemical handle directly into culture medium. These findings provide potentially an effective approach for improving therapeutic conjugates and probing biological systems. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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)

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

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.

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.

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

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.

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....

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.

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.

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.

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

The interaction between thermodynamic stability and buried free cysteines in regulating the functional half-life of fibroblast growth factor-1.

Science.gov (United States)

Lee, Jihun; Blaber, Michael

2009-10-16

Protein biopharmaceuticals are an important and growing area of human therapeutics; however, the intrinsic property of proteins to adopt alternative conformations (such as during protein unfolding and aggregation) presents numerous challenges, limiting their effective application as biopharmaceuticals. Using fibroblast growth factor-1 as model system, we describe a cooperative interaction between the intrinsic property of thermostability and the reactivity of buried free-cysteine residues that can substantially modulate protein functional half-life. A mutational strategy that combines elimination of buried free cysteines and secondary mutations that enhance thermostability to achieve a substantial gain in functional half-life is described. Furthermore, the implementation of this design strategy utilizing stabilizing mutations within the core region resulted in a mutant protein that is essentially indistinguishable from wild type as regard protein surface and solvent structure, thus minimizing the immunogenic potential of the mutations. This design strategy should be generally applicable to soluble globular proteins containing buried free-cysteine residues.

A novel string field theory solving string theory by liberating left and right movers

International Nuclear Information System (INIS)

Nielsen, Holger B.; Ninomiya, Masao

2014-01-01

We put forward ideas to a novel string field theory based on making some “objects” that essentially describe “liberated” left- and right- mover fields X L μ (τ+σ) and X R μ (τ−σ) on the string. Our novel string field theory is completely definitely different from any other string theory in as far as a “null set” of information in the string field theory Fock space has been removed relatively, to the usual string field theories. So our theory is definitely new. The main progress is that we manage to make our novel string field theory provide the correct mass square spectrum for the string. We finally suggest how to obtain the Veneziano amplitude in our model

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

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.

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.

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.

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.

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.)

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

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

String Theory - The Physics of String-Bending and Other Electric Guitar Techniques

Science.gov (United States)

Grimes, David Robert

2014-01-01

Electric guitar playing is ubiquitous in practically all modern music genres. In the hands of an experienced player, electric guitars can sound as expressive and distinct as a human voice. Unlike other more quantised instruments where pitch is a discrete function, guitarists can incorporate micro-tonality and, as a result, vibrato and sting-bending are idiosyncratic hallmarks of a player. Similarly, a wide variety of techniques unique to the electric guitar have emerged. While the mechano-acoustics of stringed instruments and vibrating strings are well studied, there has been comparatively little work dedicated to the underlying physics of unique electric guitar techniques and strings, nor the mechanical factors influencing vibrato, string-bending, fretting force and whammy-bar dynamics. In this work, models for these processes are derived and the implications for guitar and string design discussed. The string-bending model is experimentally validated using a variety of strings and vibrato dynamics are simulated. The implications of these findings on the configuration and design of guitars is also discussed. PMID:25054880

String theory--the physics of string-bending and other electric guitar techniques.

Directory of Open Access Journals (Sweden)

David Robert Grimes

Full Text Available Electric guitar playing is ubiquitous in practically all modern music genres. In the hands of an experienced player, electric guitars can sound as expressive and distinct as a human voice. Unlike other more quantised instruments where pitch is a discrete function, guitarists can incorporate micro-tonality and, as a result, vibrato and sting-bending are idiosyncratic hallmarks of a player. Similarly, a wide variety of techniques unique to the electric guitar have emerged. While the mechano-acoustics of stringed instruments and vibrating strings are well studied, there has been comparatively little work dedicated to the underlying physics of unique electric guitar techniques and strings, nor the mechanical factors influencing vibrato, string-bending, fretting force and whammy-bar dynamics. In this work, models for these processes are derived and the implications for guitar and string design discussed. The string-bending model is experimentally validated using a variety of strings and vibrato dynamics are simulated. The implications of these findings on the configuration and design of guitars is also discussed.

String theory--the physics of string-bending and other electric guitar techniques.

Science.gov (United States)

Grimes, David Robert

2014-01-01

Electric guitar playing is ubiquitous in practically all modern music genres. In the hands of an experienced player, electric guitars can sound as expressive and distinct as a human voice. Unlike other more quantised instruments where pitch is a discrete function, guitarists can incorporate micro-tonality and, as a result, vibrato and sting-bending are idiosyncratic hallmarks of a player. Similarly, a wide variety of techniques unique to the electric guitar have emerged. While the mechano-acoustics of stringed instruments and vibrating strings are well studied, there has been comparatively little work dedicated to the underlying physics of unique electric guitar techniques and strings, nor the mechanical factors influencing vibrato, string-bending, fretting force and whammy-bar dynamics. In this work, models for these processes are derived and the implications for guitar and string design discussed. The string-bending model is experimentally validated using a variety of strings and vibrato dynamics are simulated. The implications of these findings on the configuration and design of guitars is also discussed.

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

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)

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

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

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.

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.

21 CFR 184.1271 - L-Cysteine.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true L-Cysteine. 184.1271 Section 184.1271 Food and... Substances Affirmed as GRAS § 184.1271 L-Cysteine. (a) L-Cysteine is the chemical L-2-amino-3... of total L-cysteine per 100 parts of flour in dough as a dough strengthener as defined in § 170.3(o...

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 ...

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

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

Directory of Open Access Journals (Sweden)

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.

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.

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.)

The mitochondrial toxicity of cysteine-S-conjugates: Studies with pentachlorobutadienyl-L-cysteine

International Nuclear Information System (INIS)

Wallin, A.

1990-01-01

Nephrotoxic cysteine conjugates, arising from mercapturate biosynthesis, can perturb the mitochondrial membrane potential and calcium homeostasis in renal epithelial cells. Activation of these cysteine conjugates to reactive species by mitochondrial β-lyases results in covalent binding and mitochondrial damage. PCBC and related cysteine conjugates inhibit ADP-stimulated respiration in mitochondria respiring on alpha-ketoglutrate/malate and succinate indicating that both dehydrogenases may be targets. The respiratory inhibition is blocked by aminooxyacetic acid, an inhibitor of the β-lyase. Hence, metabolic activation is required implying that covalent binding of reactive intermediates may be important to the mitochondrial injury. Binding of 35 S-fragments has been found for 5 conjugates with varying degrees of mitochondrial toxicity. PCBC is more lipophilic and has a higher affinity for cellular membranes than other cysteine conjugates. PCBC rapidly depolarizes the inner membrane potential resulting in an inhibition of mitochondrial oxidative phosphorylation and calcium upon sequestration. Consequently, mitochondria and renal epithelial cells exposed to PCBC show a sudden release of calcium upon exposure to PCBC which is followed by a later increase in state 4 respiration leading to an inhibition of oxidative phosphorylation. The primary effect of other cysteine conjugates is an inhibition of the dehydrogenases, thus inhibiting state 3 respiration

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...

Electronic structures of the L-cysteine film on dental alloys

International Nuclear Information System (INIS)

Ogawa, K.; Tsujibayashi, T.; Takahashi, K.; Azuma, J.; Kakimoto, K.; Kamada, M.

2011-01-01

Research highlights: → The electronic structures of dental alloys and L-cysteine film were studied by PES. → The density of states in the dental alloy originates from Au and Cu as constituents. → The Cu-3d states contribute dominantly to the occupied states near the Fermi level. → The electronic structure of L-cysteine thin film is different from the thick film. → The bonding between Cu-3d and S-3sp states are formed at the interface. - Abstract: Metal-organic interfaces have been attracting continuous attention in many fields including basic biosciences. The surface of dental alloys could be one of such interfaces since they are used in a circumstance full of organic compounds such as proteins and bacteria. In this work, electronic structures of Au-dominant dental alloys, which have Ag and Cu besides Au, and those of L-cysteine on the dental alloys have been studied by photoelectron spectroscopy with synchrotron radiation. It was found that the density of states in the dental alloy originate from gold and copper as constituents, and the Cu-3d states contribute dominantly to the occupied states near the Fermi level. It was also found that the electronic structure of the L-cysteine thin film on the dental alloy is different from that of the L-cysteine thick film. The result indicates the formation of the orbital bonding between Cu-3d and S-3sp states in the thin film on the dental alloy.

Electronic structures of the L-cysteine film on dental alloys

Energy Technology Data Exchange (ETDEWEB)

Ogawa, K., E-mail: e7141@cc.saga-u.ac.jp [Synchrotron Light Application Center, Saga University, Saga 840-8502 (Japan); Tsujibayashi, T. [Department of Physics, Osaka Dental University, Osaka 573-1121 (Japan); Takahashi, K.; Azuma, J. [Synchrotron Light Application Center, Saga University, Saga 840-8502 (Japan); Kakimoto, K. [Department of Geriatric Dentistry, Osaka Dental University, Osaka 573-1121 (Japan); Kamada, M. [Synchrotron Light Application Center, Saga University, Saga 840-8502 (Japan)

2011-04-15

Research highlights: {yields} The electronic structures of dental alloys and L-cysteine film were studied by PES. {yields} The density of states in the dental alloy originates from Au and Cu as constituents. {yields} The Cu-3d states contribute dominantly to the occupied states near the Fermi level. {yields} The electronic structure of L-cysteine thin film is different from the thick film. {yields} The bonding between Cu-3d and S-3sp states are formed at the interface. - Abstract: Metal-organic interfaces have been attracting continuous attention in many fields including basic biosciences. The surface of dental alloys could be one of such interfaces since they are used in a circumstance full of organic compounds such as proteins and bacteria. In this work, electronic structures of Au-dominant dental alloys, which have Ag and Cu besides Au, and those of L-cysteine on the dental alloys have been studied by photoelectron spectroscopy with synchrotron radiation. It was found that the density of states in the dental alloy originate from gold and copper as constituents, and the Cu-3d states contribute dominantly to the occupied states near the Fermi level. It was also found that the electronic structure of the L-cysteine thin film on the dental alloy is different from that of the L-cysteine thick film. The result indicates the formation of the orbital bonding between Cu-3d and S-3sp states in the thin film on the dental alloy.

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.

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...

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

Surface-modified CdS nanoparticles as a fluorescent probe for the selective detection of cysteine

International Nuclear Information System (INIS)

Negi, Devendra P S; Chanu, T Inakhunbi

2008-01-01

We present a novel method for the selective detection of cysteine, a sulfur-containing amino acid, which plays a crucial role in many important biological functions such as protein folding. Surface-modified colloidal CdS nanoparticles have been used as a fluorescent probe to selectively detect cysteine in the presence of other amino acids in the micromolar concentration range. Cysteine quenches the emission of CdS in the 0.5-10 μM concentration range, whereas the other amino acids do not affect its emission. Among the other amino acids, histidine is most efficient in quenching the emission of the CdS nanoparticles. The sulfur atom of cysteine plays a crucial role in the quenching process in the 0.5-10 μM concentration range. Cysteine is believed to quench the emission of the CdS nanoparticles by binding to their surface via its negatively charged sulfur atom. This method can potentially be applied for its detection in biological samples.

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

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

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.)

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...

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

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)

Increasing stringiness of low-fat mozzarella string cheese using polysaccharides.

Science.gov (United States)

Oberg, E N; Oberg, C J; Motawee, M M; Martini, S; McMahon, D J

2015-07-01

When fat content of pasta filata cheese is lowered, a loss of fibrous texture occurs and low-fat (LF) mozzarella cheese loses stringiness, making it unsuitable for the manufacture of string cheese. We investigated the use of various polysaccharides that could act as fat mimetics during the stretching and extruding process to aid in protein strand formation and increase stringiness. Low-fat mozzarella cheese curd was made, salted, and then 3.6-kg batches were heated in hot (80°) 5% brine, stretched, and formed into a homogeneous mass. Hot (80°C) slurries of various polysaccharides were then mixed with the hot cheese and formed into LF string cheese using a small piston-driven extruder. Polysaccharides used included waxy corn starch, waxy rice starch, instant tapioca starch, polydextrose, xanthan gum, and guar gum. Adding starch slurries increased cheese moisture content by up to 1.6% but was not effective at increasing stringiness. Xanthan gum functioned best as a fat mimetic and produced LF string cheese that most closely visually resembled commercial string cheese made using low-moisture part skim (LMPS) mozzarella cheese without any increase in moisture content. Extent of stringiness was determined by pulling apart the cheese longitudinally and observing size, length, and appearance of individual cheese strings. Hardness was determined using a modified Warner-Bratzler shear test. When LF string cheese was made using a 10% xanthan gum slurry added at ~1%, increased consumer flavor liking was observed, with scores after 2wk of storage of 6.44 and 6.24 compared with 5.89 for the LF control cheese; although this was lower than an LMPS string cheese that scored 7.27. The 2-wk-old LF string cheeses containing xanthan gum were considered still slightly too firm using a just-about-right (JAR) test, whereas the LMPS string cheese was considered as JAR for texture. With further storage up to 8wk, all of the LF string cheeses softened (JAR score was closer to 3

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.

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

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)

Conservation of Oxidative Protein Stabilization in an Insect Homologue of Parkinsonism-Associated Protein DJ-1

Energy Technology Data Exchange (ETDEWEB)

Lin, Jiusheng; Prahlad, Janani; Wilson, Mark A. (UNL)

2012-08-21

DJ-1 is a conserved, disease-associated protein that protects against oxidative stress and mitochondrial damage in multiple organisms. Human DJ-1 contains a functionally essential cysteine residue (Cys106) whose oxidation is important for regulating protein function by an unknown mechanism. This residue is well-conserved in other DJ-1 homologues, including two (DJ-1{alpha} and DJ-1{beta}) in Drosophila melanogaster. Because D. melanogaster is a powerful model system for studying DJ-1 function, we have determined the crystal structure and impact of cysteine oxidation on Drosophila DJ-1{beta}. The structure of D. melanogaster DJ-1{beta} is similar to that of human DJ-1, although two important residues in the human protein, Met26 and His126, are not conserved in DJ-1{beta}. His126 in human DJ-1 is substituted with a tyrosine in DJ-1{beta}, and this residue is not able to compose a putative catalytic dyad with Cys106 that was proposed to be important in the human protein. The reactive cysteine in DJ-1 is oxidized readily to the cysteine-sulfinic acid in both flies and humans, and this may regulate the cytoprotective function of the protein. We show that the oxidation of this conserved cysteine residue to its sulfinate form (Cys-SO{sub 2{sup -}}) results in considerable thermal stabilization of both Drosophila DJ-1{beta} and human DJ-1. Therefore, protein stabilization is one potential mechanism by which cysteine oxidation may regulate DJ-1 function in vivo. More generally, most close DJ-1 homologues are likely stabilized by cysteine-sulfinic acid formation but destabilized by further oxidation, suggesting that they are biphasically regulated by oxidative modification.

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.

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.)

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.)

Significance of Cuscutain, a cysteine protease from Cuscuta reflexa, in host-parasite interactions.

Science.gov (United States)

Bleischwitz, Marc; Albert, Markus; Fuchsbauer, Hans-Lothar; Kaldenhoff, Ralf

2010-10-22

Plant infestation with parasitic weeds like Cuscuta reflexa induces morphological as well as biochemical changes in the host and the parasite. These modifications could be caused by a change in protein or gene activity. Using a comparative macroarray approach Cuscuta genes specifically upregulated at the host attachment site were identified. One of the infestation specific Cuscuta genes encodes a cysteine protease. The protein and its intrinsic inhibitory peptide were heterologously expressed, purified and biochemically characterized. The haustoria specific enzyme was named cuscutain in accordance with similar proteins from other plants, e.g. papaya. The role of cuscutain and its inhibitor during the host parasite interaction was studied by external application of an inhibitor suspension, which induced a significant reduction of successful infection events. The study provides new information about molecular events during the parasitic plant--host interaction. Inhibition of cuscutain cysteine proteinase could provide means for antagonizing parasitic plants.

Hagedorn Behavior of Little String Theories from string corrections to NS5-branes

DEFF Research Database (Denmark)

Harmark, Troels; Obers, N. A.

2000-01-01

We examine the Hagedorn behavior of little string theory using its conjectured duality with near-horizon NS5-branes. In particular, by studying the string-corrected NS5-brane supergravity solution, it is shown that tree-level corrections to the temperature vanish, while the leading one-loop string...... correction generates the correct temperature dependence of the entropy near the Hagedorn temperature. Finally, the Hagedorn behavior of ODp-brane theories, which are deformed versions of little string theory, is considered via their supergravity duals....

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)

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.

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.)

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.

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...

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

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.

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

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

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.

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.

Observation of Motion of Bowed Strings and Resonant Strings in Violin Performances

Science.gov (United States)

Matsutani, Akihiro

2013-10-01

The motion of a bowed string and a resonant string of a violin were simultaneously observed for the first time. The results of the direct observation of string motion in double stops and harmonics are also presented. The importance of the resonance was experimentally demonstrated from these observations. It is suggested that players should take account of the resonance and ideal Helmholtz motion in violin performances.

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...

Non-critical Poincare invariant bosonic string backgrounds and closed string tachyons

International Nuclear Information System (INIS)

Alvarez, Enrique; Gomez, Cesar; Hernandez, Lorenzo

2001-01-01

A new family of non critical bosonic string backgrounds in arbitrary space-time dimension D and with ISO(1,D-2) Poincare invariance are presented. The metric warping factor and dilaton agree asymptotically with the linear dilaton background. The closed string tachyon equation of motion enjoys, in the linear approximation, an exact solution of 'kink' type interpolating between different expectation values. A renormalization group flow interpretation, based on a closed string tachyon potential of type -T 2 e -T , is suggested

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)

21 CFR 184.1272 - L-Cysteine monohydrochloride.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true L-Cysteine monohydrochloride. 184.1272 Section 184... Listing of Specific Substances Affirmed as GRAS § 184.1272 L-Cysteine monohydrochloride. (a) L-Cysteine... ingredient is used to supply up to 0.009 part of total L-cysteine per 100 parts of flour in dough as a dough...

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.)

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.

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

Open strings on AdS2 branes

International Nuclear Information System (INIS)

Lee, Peter; Ooguri, Hirosi.; Park, Jongwon; Tannenhauser, Jonathan

2001-01-01

We study the spectrum of open strings on AdS 2 branes in AdS 3 in an NS-NS background, using the SL(2,R) WZW model. When the brane carries no fundamental string charge, the open string spectrum is the holomorphic square root of the spectrum of closed strings in AdS 3 . It contains short and long strings, and is invariant under spectral flow. When the brane carries fundamental string charge, the open string spectrum again contains short and long strings in all winding sectors. However, branes with fundamental string charge break half the spectral flow symmetry. This has different implications for short and long strings. As the fundamental string charge increases, the brane approaches the boundary of AdS 3 . In this limit, the induced electric field on the worldvolume reaches its critical value, producing noncommutative open string theory on AdS 2

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.

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.

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.

Lifespan extension and increased resistance to environmental stressors by N-Acetyl-L-Cysteine in Caenorhabditis elegans

Directory of Open Access Journals (Sweden)

Seung-Il Oh

2015-05-01

Full Text Available OBJECTIVE: This study was performed to determine the effect of N-acetyl-L-cysteine, a modified sulfur-containing amino acid that acts as a strong cellular antioxidant, on the response to environmental stressors and on aging in C. elegans. METHOD: The survival of worms under oxidative stress conditions induced by paraquat was evaluated with and without in vivo N-acetyl-L-cysteine treatment. The effect of N-acetyl-L-cysteine on the response to other environmental stressors, including heat stress and ultraviolet irradiation (UV, was also monitored. To investigate the effect on aging, we examined changes in lifespan, fertility, and expression of age-related biomarkers in C. elegans after N-acetyl-L-cysteine treatment. RESULTS: Dietary N-acetyl-L-cysteine supplementation significantly increased resistance to oxidative stress, heat stress, and UV irradiation in C. elegans. In addition, N-acetyl-L-cysteine supplementation significantly extended both the mean and maximum lifespan of C. elegans. The mean lifespan was extended by up to 30.5% with 5 mM N-acetyl-L-cysteine treatment, and the maximum lifespan was increased by 8 days. N-acetyl-L-cysteine supplementation also increased the total number of progeny produced and extended the gravid period of C. elegans. The green fluorescent protein reporter assay revealed that expression of the stress-responsive genes, sod-3 and hsp-16.2, increased significantly following N-acetyl-L-cysteine treatment. CONCLUSION: N-acetyl-L-cysteine supplementation confers a longevity phenotype in C. elegans, possibly through increased resistance to environmental stressors.

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.

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.

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

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.

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...

Significance of Cuscutain, a cysteine protease from Cuscuta reflexa, in host-parasite interactions

Directory of Open Access Journals (Sweden)

Fuchsbauer Hans-Lothar

2010-10-01

Full Text Available Abstract Background Plant infestation with parasitic weeds like Cuscuta reflexa induces morphological as well as biochemical changes in the host and the parasite. These modifications could be caused by a change in protein or gene activity. Using a comparative macroarray approach Cuscuta genes specifically upregulated at the host attachment site were identified. Results One of the infestation specific Cuscuta genes encodes a cysteine protease. The protein and its intrinsic inhibitory peptide were heterologously expressed, purified and biochemically characterized. The haustoria specific enzyme was named cuscutain in accordance with similar proteins from other plants, e.g. papaya. The role of cuscutain and its inhibitor during the host parasite interaction was studied by external application of an inhibitor suspension, which induced a significant reduction of successful infection events. Conclusions The study provides new information about molecular events during the parasitic plant - host interaction. Inhibition of cuscutain cysteine proteinase could provide means for antagonizing parasitic plants.

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

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

Directory of Open Access Journals (Sweden)

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.

SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity.

Directory of Open Access Journals (Sweden)

Tzong-Yi Lee

Full Text Available S-nitrosylation, the covalent attachment of a nitric oxide to (NO the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1 and human hemoglobin subunit beta (HBB. Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (http://csb.cse.yzu.edu.tw/SNOSite/, for identifying S-nitrosylation sites on the uncharacterized protein sequences.

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.

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...

Reduction of Guanosyl Radical by Cysteine and Cysteine-Glycine Studied by Time-Resolved CIDNP

NARCIS (Netherlands)

Morozova, O.B.; Kaptein, R.; Yurkovskaya, A.V.

2012-01-01

As a model for chemical DNA repair, reduction of guanosyl radicals in the reaction with cysteine or the dipeptide cysteine-glycine has been studied by time-resolved chemically induced dynamic nuclear polarization (CIDNP). Radicals were generated photochemically by pulsed laser irradiation of a

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

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)

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

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

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.

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.

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...

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

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.

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.

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

Constraints on cosmic strings due to black holes formed from collapsed cosmic string loops

International Nuclear Information System (INIS)

Caldwell, R.R.; Gates, E.

1993-05-01

The cosmological features of primordial black holes formed from collapsed cosmic string loops are studied. Observational restrictions on a population of primordial black holes are used to restrict f, the fraction of cosmic string loops which collapse to form black holes, and μ, the cosmic string mass-per-unit-length. Using a realistic model of cosmic strings, we find the strongest restriction on the parameters f and μ is due to the energy density in 100MeV photons radiated by the black holes. We also find that inert black hole remnants cannot serve as the dark matter. If earlier, crude estimates of f are reliable, our results severely restrict μ, and therefore limit the viability of the cosmic string large-scale structure scenario

String Chopping and Time-ordered Products of Linear String-localized Quantum Fields

Science.gov (United States)

Cardoso, Lucas T.; Mund, Jens; Várilly, Joseph C.

2018-03-01

For a renormalizability proof of perturbative models in the Epstein-Glaser scheme with string-localized quantum fields, one needs to know what freedom one has in the definition of time-ordered products of the interaction Lagrangian. This paper provides a first step in that direction. The basic issue is the presence of an open set of n-tuples of strings which cannot be chronologically ordered. We resolve it by showing that almost all such string configurations can be dissected into finitely many pieces which can indeed be chronologically ordered. This fixes the time-ordered products of linear field factors outside a nullset of string configurations. (The extension across the nullset, as well as the definition of time-ordered products of Wick monomials, will be discussed elsewhere).

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...

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.

On the null origin of the ambitwistor string

Energy Technology Data Exchange (ETDEWEB)

Casali, Eduardo [Mathematical Institute, University of Oxford,Woodstock Road, Oxford, OX2 6GG (United Kingdom); Tourkine, Piotr [Department of Applied Mathematics and Theoretical Physics,Wilberforce Road, Cambridge, CB3 0WA (United Kingdom)

2016-11-07

In this paper we present the null string origin of the ambitwistor string. Classically, the null string is the tensionless limit of string theory, and so too is the ambitwistor string. Both have as constraint algebra the Galilean Conformal Algebra in two dimensions. But something interesting happens in the quantum theory since there is an ambiguity in quantizing the null string. We show that, given a particular choice of quantization scheme and a particular gauge, the null string coincides with the ambitwistor string both classically and quantum mechanically. We also show that the same holds for the spinning versions of the null string and ambitwistor string. With these results we clarify the relationship between the ambitwistor string, the null string, the usual string and the Hohm-Siegel-Zwiebach theory.

Molecular and Functional Characterization of Mouse S5D-SRCRB: A New Group B Member of the Scavenger Receptor Cysteine-Rich Superfamily

DEFF Research Database (Denmark)

Miró-Julià, Cristina; Roselló, Sandra; Martínez, Vanesa G

2011-01-01

The scavenger receptor cysteine-rich superfamily (SRCR-SF) members are transmembrane and/or secreted receptors exhibiting one or several repeats of a cysteine-rich protein module of ∼100 aa, named scavenger receptor cysteine-rich (SRCR). Two types of SRCR domains (A or B) have been reported, which...... differ in the number of coding exons and intradomain cysteines. Although no unifying function has been reported for SRCR-SF members, recognition of pathogen-associated molecular patterns (PAMPs) was recently shown for some of them. In this article, we report the structural and functional characterization...

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)

Minimal string theories and integrable hierarchies

Science.gov (United States)

Iyer, Ramakrishnan

Well-defined, non-perturbative formulations of the physics of string theories in specific minimal or superminimal model backgrounds can be obtained by solving matrix models in the double scaling limit. They provide us with the first examples of completely solvable string theories. Despite being relatively simple compared to higher dimensional critical string theories, they furnish non-perturbative descriptions of interesting physical phenomena such as geometrical transitions between D-branes and fluxes, tachyon condensation and holography. The physics of these theories in the minimal model backgrounds is succinctly encoded in a non-linear differential equation known as the string equation, along with an associated hierarchy of integrable partial differential equations (PDEs). The bosonic string in (2,2m-1) conformal minimal model backgrounds and the type 0A string in (2,4 m) superconformal minimal model backgrounds have the Korteweg-de Vries system, while type 0B in (2,4m) backgrounds has the Zakharov-Shabat system. The integrable PDE hierarchy governs flows between backgrounds with different m. In this thesis, we explore this interesting connection between minimal string theories and integrable hierarchies further. We uncover the remarkable role that an infinite hierarchy of non-linear differential equations plays in organizing and connecting certain minimal 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 find 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 other string-like special points arise and are connected. In some cases, the framework endows the theories with a non

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.

Worldsheet factorization for twistor-strings

Energy Technology Data Exchange (ETDEWEB)

Adamo, Tim [Department of Applied Mathematics & Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom)

2014-04-10

We study the multiparticle factorization properties of two worldsheet theories which — at tree-level — describe the scattering of massless particles in four dimensions: the Berkovits-Witten twistor-string for N=4 super-Yang-Mills coupled to N=4 conformal supergravity, and the Skinner twistor-string for N=8 supergravity. By considering these string-like theories, we can study factorization at the level of the worldsheet before any Wick contractions or integrals have been performed; this is much simpler than considering the factorization properties of the amplitudes themselves. In Skinner’s twistor-string this entails the addition of worldsheet gravity as well as a formalism that represents all external states in a manifestly symmetric way, which we develop explicitly at genus zero. We confirm that the scattering amplitudes of Skinner’s theory, as well as the gauge theory amplitudes for the planar sector of the Berkovits-Witten theory, factorize appropriately at genus zero. In the non-planar sector, we find behavior indicative of conformal gravity in the Berkovits-Witten twistor-string. We contrast factorization in twistor-strings with the story in ordinary string theory, and also make some remarks on higher genus factorization and disconnected prescriptions.

Worldsheet factorization for twistor-strings

International Nuclear Information System (INIS)

Adamo, Tim

2014-01-01

We study the multiparticle factorization properties of two worldsheet theories which — at tree-level — describe the scattering of massless particles in four dimensions: the Berkovits-Witten twistor-string for N=4 super-Yang-Mills coupled to N=4 conformal supergravity, and the Skinner twistor-string for N=8 supergravity. By considering these string-like theories, we can study factorization at the level of the worldsheet before any Wick contractions or integrals have been performed; this is much simpler than considering the factorization properties of the amplitudes themselves. In Skinner’s twistor-string this entails the addition of worldsheet gravity as well as a formalism that represents all external states in a manifestly symmetric way, which we develop explicitly at genus zero. We confirm that the scattering amplitudes of Skinner’s theory, as well as the gauge theory amplitudes for the planar sector of the Berkovits-Witten theory, factorize appropriately at genus zero. In the non-planar sector, we find behavior indicative of conformal gravity in the Berkovits-Witten twistor-string. We contrast factorization in twistor-strings with the story in ordinary string theory, and also make some remarks on higher genus factorization and disconnected prescriptions

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...

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....

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.)

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.)

Geometric derivation of string field theory from first principles: Closed strings and modular invariance

International Nuclear Information System (INIS)

Kaku, M.

1988-01-01

We present an entirely new approach to closed-string field theory, called Igeometric string field theory R, which avoids the complications found in Becchi-Rouet-Stora-Tyutin string field theory (e.g., ghost counting, infinite overcounting of diagrams, midpoints, lack of modular invariance). Following the analogy with general relativity and Yang-Mills theory, we define a new infinite-dimensional local gauge group, called the unified string group, which uniquely specifies the connection fields, the curvature tensor, the measure and tensor calculus, and finally the action itself. Geometric field theory, when gauge fixed, yields an entirely new class of gauges called the interpolating gauge which allows us to smoothly interpolate between the midpoint gauge and the end-point gauge (''covariantized light-cone gauge''). We can show that geometric string field theory reproduces one copy of the Shapiro-Virasoro model. Surprisingly, after the gauge is broken, a new Iclosed four-string interactionR emerges as the counterpart of the instantaneous four-fermion Coulomb term in QED. This term restores modular invariance and precisely fills the missing region of the complex plane

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.

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.

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

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

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...

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.)

The selenazal drug ebselen potently inhibits indoleamine 2,3-dioxygenase by targeting enzyme cysteine residues.

Science.gov (United States)

Terentis, Andrew C; Freewan, Mohammed; Sempértegui Plaza, Tito S; Raftery, Mark J; Stocker, Roland; Thomas, Shane R

2010-01-26

The heme enzyme indoleamine 2,3-dioxygenase (IDO) plays an important immune regulatory role by catalyzing the oxidative degradation of l-tryptophan. Here we show that the selenezal drug ebselen is a potent IDO inhibitor. Exposure of human macrophages to ebselen inhibited IDO activity in a manner independent of changes in protein expression. Ebselen inhibited the activity of recombinant human IDO (rIDO) with an apparent inhibition constant of 94 +/- 17 nM. Optical and resonance Raman spectroscopy showed that ebselen altered the active site heme of rIDO by inducing a transition of the ferric heme iron from the predominantly high- to low-spin form and by lowering the vibrational frequency of the Fe-CO stretch of the CO complex, indicating an opening of the distal heme pocket. Substrate binding studies showed that ebselen enhanced nonproductive l-tryptophan binding, while circular dichroism indicated that the drug reduced the helical content and protein stability of rIDO. Thiol labeling and mass spectrometry revealed that ebselen reacted with multiple cysteine residues of IDO. Removal of cysteine-bound ebselen with dithiothreitol reversed the effects of the drug on the heme environment and significantly restored enzyme activity. These findings indicate that ebselen inhibits IDO activity by reacting with the enzyme's cysteine residues that result in changes to protein conformation and active site heme, leading to an increase in the level of nonproductive substrate binding. This study highlights that modification of cysteine residues is a novel and effective means of inhibiting IDO activity. It also suggests that IDO is under redox control and that the enzyme represents a previously unrecognized in vivo target of ebselen.

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

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.

String fragmentation; La fragmentation des cordes

Energy Technology Data Exchange (ETDEWEB)

Drescher, H.J.; Werner, K. [Laboratoire de Physique Subatomique et des Technologies Associees - SUBATECH, Centre National de la Recherche Scientifique, 44 - Nantes (France)

1997-10-01

The classical string model is used in VENUS as a fragmentation model. For the soft domain simple 2-parton strings were sufficient, whereas for higher energies up to LHC, the perturbative regime of the QCD gives additional soft gluons, which are mapped on the string as so called kinks, energy singularities between the leading partons. The kinky string model is chosen to handle fragmentation of these strings by application of the Lorentz invariant area law. The `kinky strings` model, corresponding to the perturbative gluons coming from pQCD, takes into consideration this effect by treating the partons and gluons on the same footing. The decay law is always the Artru-Menessier area law which is the most realistic since it is invariant to the Lorentz and gauge transformations. For low mass strings a manipulation of the rupture point is necessary if the string corresponds already to an elementary particle determined by the mass and the flavor content. By means of the fragmentation model it will be possible to simulate the data from future experiments at LHC and RHIC 3 refs.

Querying and Mining Strings Made Easy

KAUST Repository

Sahli, Majed

2017-10-13

With the advent of large string datasets in several scientific and business applications, there is a growing need to perform ad-hoc analysis on strings. Currently, strings are stored, managed, and queried using procedural codes. This limits users to certain operations supported by existing procedural applications and requires manual query planning with limited tuning opportunities. This paper presents StarQL, a generic and declarative query language for strings. StarQL is based on a native string data model that allows StarQL to support a large variety of string operations and provide semantic-based query optimization. String analytic queries are too intricate to be solved on one machine. Therefore, we propose a scalable and efficient data structure that allows StarQL implementations to handle large sets of strings and utilize large computing infrastructures. Our evaluation shows that StarQL is able to express workloads of application-specific tools, such as BLAST and KAT in bioinformatics, and to mine Wikipedia text for interesting patterns using declarative queries. Furthermore, the StarQL query optimizer shows an order of magnitude reduction in query execution time.

First quantized noncritical relativistic Polyakov string

International Nuclear Information System (INIS)

Jaskolski, Z.; Meissner, K.A.

1994-01-01

The first quantization of the relativistic Brink-DiVecchia-Howe-Polyakov (BDHP) string in the range 1 < d 25 is considered. It is shown that using the Polyakov sum over bordered surfaces in the Feynman path integral quantization scheme one gets a consistent quantum mechanics of relativistic 1-dim extended objects in the range 1 < d < 25. In particular, the BDHP string propagator is exactly calculated for arbitrary initial and final string configurations and the Hilbert space of physical states of noncritical BDHP string is explicitly constructed. The resulting theory is equivalent to the Fairlie-Chodos-Thorn massive string model. In contrast to the conventional conformal field theory approach to noncritical string and random surfaces in the Euclidean target space the path integral formulation of the Fairlie-Chodos-Thorn string obtained in this paper does not rely on the principle of conformal invariance. Some consequences of this feature for constructing a consistent relativistic string theory based on the ''splitting-joining'' interaction are discussed. (author). 42 refs, 1 fig

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

Black string in dRGT massive gravity

Energy Technology Data Exchange (ETDEWEB)

Tannukij, Lunchakorn [Mahidol University, Department of Physics, Faculty of Science, Bangkok (Thailand); Hanyang University, Department of Physics, Seoul (Korea, Republic of); Naresuan University, The Institute for Fundamental Study, Phitsanulok (Thailand); Wongjun, Pitayuth [Naresuan University, The Institute for Fundamental Study, Phitsanulok (Thailand); Ministry of Education, Thailand Center of Excellence in Physics, Bangkok (Thailand); Ghosh, Suchant G. [Jamia Millia Islamia, Centre of Theoretical Physics, New Delhi (India); University of Kwazulu-Natal, Astrophysics and Cosmology Research Unit, School of Mathematical Sciences, Durban (South Africa)

2017-12-15

We present a cylindrically symmetric solution, both charged and uncharged, which is known as a black string solution to the nonlinear ghost-free massive gravity found by de Rham, Gabadadze, and Tolley (dRGT). This ''dRGT black string'' can be thought of as a generalization of the black string solution found by Lemos. Moreover, the dRGT black string solution includes other classes of black string solution such as the monopole-black string ones since the graviton mass contributes to the global monopole term as well as the cosmological-constant term. To investigate the solution, we compute mass, temperature, and entropy of the dRGT black string. We found that the existence of the graviton mass drastically affects the thermodynamics of the black string. Furthermore, the Hawking-Page phase transition is found to be possible for the dRGT black string as well as the charged dRGT black string. The dRGT black string solution is thermodynamically stable for r > r{sub c} with negative thermodynamical potential and positive heat capacity while it is unstable for r < r{sub c} where the potential is positive. (orig.)

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)

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

CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

Directory of Open Access Journals (Sweden)

Hamed Bostan

2012-01-01

Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

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

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.)

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

Treatment with the cysteine precursor l-2-oxothiazolidine-4-carboxylate (OTC) implicates taurine deficiency in severity of dystropathology in mdx mice.

Science.gov (United States)

Terrill, Jessica R; Boyatzis, Amber; Grounds, Miranda D; Arthur, Peter G

2013-09-01

Oxidative stress has been implicated in the pathology of the lethal skeletal muscle disease Duchenne muscular dystrophy (DMD), and various antioxidants have been investigated as a potential therapy. Recently, treatment of the mdx mouse model for DMD with the antioxidant and cysteine and glutathione (GSH) precursor n-acetylcysteine (NAC) was shown to decrease protein thiol oxidation and improve muscle pathology and ex vivo muscle strength. This study further investigates the mechanism for the benefits of NAC on dystrophic muscle by administering l-2-oxothiazolidine-4-carboxylate (OTC) which also upregulates intracellular cysteine and GSH, but does not directly function as an antioxidant. We observed that OTC, like NAC, decreases protein thiol oxidation, decreases pathology and increases strength, suggesting that the both NAC and OTC function via increasing cysteine and GSH content of dystrophic muscle. We demonstrate that mdx muscle is not deficient in either cysteine or GSH and that these are not increased by OTC treatment. However, we show that dystrophic muscle of 12 week old mdx mice is deficient in taurine, a by-product of disposal of excess cysteine, a deficiency that is ameliorated by OTC treatment. These data suggest that in dystrophic muscles, apart from the strong association of increased oxidative stress and protein thiol oxidation with dystropathology, another major issue is an insufficiency in taurine that can be corrected by increasing the availability of cysteine. This study provides new insight into the molecular mechanism underlying the benefits of NAC in muscular dystrophy and supports the use of OTC as an alternative drug for potential clinical applications to DMD. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

A Note on Tensionless Strings in M-Theory

OpenAIRE

Davis, K.

1996-01-01

In this article we examine the appearance of tensionless strings in M-Theory. We subsequently interpret these tensionless strings in a String Theory context. In particular, we examine tensionless strings appearing in M-Theory on $S^{1}$, M-Theory on $S^{1} / {\\bf Z}_{2}$, and M-Theory on $T^{2}$; we then interpret the appearance of such strings in a String Theory context. Then we reverse this process and examine the appearance of some tensionless strings in String Theory. Subsequently we inte...

Open strings in the SL(2, R) WZWN model with solution for a rigidly rotating string

DEFF Research Database (Denmark)

Lomholt, Michael Andersen; Larsen, A.L.

2003-01-01

Boundary conditions and gluing conditions for open strings and D-branes in the SL(2, R) WZWN model, corresponding to AdS , are discussed. Some boundary conditions and gluing conditions previously considered in the literature are shown to be incompatible with the variation principle. We then consi......Boundary conditions and gluing conditions for open strings and D-branes in the SL(2, R) WZWN model, corresponding to AdS , are discussed. Some boundary conditions and gluing conditions previously considered in the literature are shown to be incompatible with the variation principle. We...... then consider open string boundary conditions corresponding to a certain field-dependent gluing condition. This allows us to consider open strings with constant energy and angular momentum. Classically, these open strings naturally generalize the open strings in flat Minkowski space. For rigidly rotating open...

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.

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.

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.

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.

String theory and quantum gravity '92

International Nuclear Information System (INIS)

Harvey, J.; Iengo, R.; Narain, K.S.; Randjbar Daemi, S.; Verlinde, H.

1993-01-01

These proceedings of the 1992 Trieste Spring School and Workshop on String Theory and Quantum Gravity contains introductions and overviews of recent work on the use of two-dimensional string inspired models in the study of black holes, a lecture on gravitational scattering at planckian energies, another on the physical properties of higher-dimensional black holes and black strings in string theory, a discussion on N=2 superconformal field theories, a lecture about the application of matrix model techniques to the study of string theory in two dimensions, and an overview of the current status and developments in string field theory. Connections with models in statistical mechanics are also discussed. These proceedings contain seven lectures and ten contributions. Refs and figs

Collisions of cosmic F- and D-strings

International Nuclear Information System (INIS)

Jones, N.

2004-01-01

Recent theoretical advances and upcoming experimental measurements make the testing of generic predictions of string theory models of cosmology feasible. Brane anti-brane models of inflation within superstring theory are promising as string theory descriptions of the physics of the early universe. While varied in their construction, these models can have the generic and observable consequence that cosmic strings will be abundant in the early universe. This leads to possible detectable effects in the cosmic microwave background, gravitational wave physics and gravitational lensing. Detailed calculations of cosmic string interactions within string theory are presented, in order to distinguish these cosmic strings from those in more conventional theories; these interaction probabilities can be very different from conventional 4-dimension strings, providing the possibility of experimental tests of string theory. (authors)

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

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

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...

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.

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.

A new approach to strings and superstrings

International Nuclear Information System (INIS)

Sparano, G.

1988-01-01

The subject of this thesis is a new, more general, action principle for strings, superstrings, and extended objects in any number of dimensions. The origin and motivations for this approach can be found in the context of the study of the symmetries of string theories and, more specifically, are related to the application of K.S.K. (Kirillov, Souriau, Kostant) construction to strings. The main results we find are: (A) A classification of string theories analogous to the classification of relativistic point particles as massive, massless and tachionic with or without spin. Nambu-Goto string and Schild null string emerge as special cases of a more general classification of strings. (B) A new method to introduce spin in strings by using a Wess-Zumino term in the action. (C) Several results are obtained through the study of the configuration space which shows a rich topological structure: for the Nambu-Goto string in any number of dimensions it is found the existence of theta states analogous to the theta-vacua of nonabelian gauge theories. For the closed Schild Null string, in four dimensions, this analysis shows Z2 solitons and the possibility of quantizing the system so that the states are spinorial (have half odd integral spin) even though the Lagrangian consists only of bosonic variables. (D) Unlike Nambu-Goto string, the quantization of Schild Null string is consistent in any number of space-time dimensions. Besides these concrete results, the formalism we introduce will hopefully give also new insights in the problem of the hidden symmetries of the string

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

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.)

Bmcystatin, a cysteine proteinase inhibitor characterized from the tick Boophilus microplus

International Nuclear Information System (INIS)

Lima, Cassia A.; Sasaki, Sergio D.; Tanaka, Aparecida S.

2006-01-01

The bovine tick Rhipicephalus (Boophilus) microplus is a blood-sucking animal, which is responsible for Babesia spp and Anaplasma marginale transmission for cattle. From a B. microplus fat body cDNA library, 465 selected clones were sequenced randomly and resulted in 60 Contigs. An open reading frame (ORF) contains 98 amino acids named Bmcystatin, due to 70% amino acid identity to a classical type 1 cystatin from Ixodes scapularis tick (GenBank Accession No. DQ066227). The Bmcystatin amino acid sequence analysis showed two cysteine residues, theoretical pI of 5.92 and M r of 11kDa. Bmcystatin gene was cloned in pET 26b vector and the protein expressed using bacteria Escherichia coli BL21 SI. Recombinant Bmcystatin (rBmcystatin) purified by affinity chromatography on Ni-NTA-agarose column and ionic exchange chromatography on HiTrap Q column presented molecular mass of 11kDa, by SDS-PAGE and the N-terminal amino acid sequenced revealed unprocessed N-terminal containing part of pelB signal sequence. Purified rBmcystatin showed to be a C1 cysteine peptidase inhibitor with K i value of 0.1 and 0.6nM for human cathepsin L and VTDCE (vitellin degrading cysteine endopeptidase), respectively. The rBmcystatin expression analyzed by semi-quantitative RT-PCR confirmed the amplification of a specific DNA sequence (294bp) in the fat body and ovary cDNA preparation. On the other hand, a protein band was detected in the fat body, ovary, and the salivary gland extracts using anti-Bmcystatin antibody by Western blot. The present results suggest a possible role of Bmcystatin in the ovary, even though the gene was cloned from the fat body, which could be another site of this protein synthesis

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.

One-loop masses of open-string scalar fields in string theory

International Nuclear Information System (INIS)

Kitazawa, Noriaki

2008-01-01

In phenomenological models with D-branes, there are in general open-string massless scalar fields, in addition to closed-string massless moduli fields corresponding to the compactification. It is interesting to focus on the fate of such scalar fields in models with broken supersymmetry, because no symmetry forbids their masses. The one-loop effect may give non-zero masses to them, and in some cases mass squared may become negative, which means the radiative gauge symmetry breaking. In this article we investigate and propose a simple method for calculating the one-loop corrections using the boundary state formalism. There are two categories of massless open-string scalar fields. One consists the gauge potential fields corresponding to compactified directions, which can be understood as scalar fields in uncompactified space-time (related with Wilson line degrees of freedom). The other consists 'gauge potential fields' corresponding to transverse directions of D-brane, which emerge as scalar fields in D-brane world-volume (related with brane moduli fields). The D-brane boundary states with constant backgrounds of these scalar fields are constructed, and one-loop scalar masses are calculated in the closed string picture. Explicit calculations are given in the following four concrete models: one D25-brane with a circle compactification in bosonic string theory, one D9-brane with a circle compactification in superstring theory, D3-branes at a supersymmetric C 3 /Z 3 orbifold singularity, and a model of brane supersymmetry breaking with D3-branes and anti-D7-branes at a supersymmetric C 3 /Z 3 orbifold singularity. We show that the sign of the mass squared has a strong correlation with the sign of the related open-string one-loop vacuum amplitude.

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.)

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....

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.

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.)

T-Duality Group for Open String Theory

OpenAIRE

Kajiura, Hiroshige

2001-01-01

We study T-duality for open strings on tori $\\T^d$. The general boundary conditions for the open strings are constructed, and it is shown that T-duality group, which preserves the mass spectrum of closed strings, preserves also the mass spectrum of the open strings. The open strings are transformed to those with different boundary conditions by T-duality. We also discuss the T-duality for D-brane mass spectrum, and show that the D-branes and the open strings with both ends on them are transfo...

Characterization of cysteine-degrading and H2S-releasing enzymes of higher plants - From the field to the test tube and back

DEFF Research Database (Denmark)

Jutta, Papenbrock; Anja, Riemenschneider; Kamp, Anja

2007-01-01

focussed mainly on the release of H2S as defence strategy. In field experiments using different Brassica napus genotypes it was shown that the genetic differ- ences among Brassica genotypes lead to differences in sulfur content and L-cysteine desulfhydrase activity. Another field ex- periment demonstrated...... that sulfur supply and infection with Pyrenopeziza brassica influenced L-cysteine desulfhydrase activity in Brassica napus. Cysteine-degrading enzymes such as cysteine desulfhydrases are hypothesized to be involved in H2S release. Several L- and D-cysteine-specific desulfhydrase candidates have been isolated...... in plants which might be involved in SIR, such as high levels of thiols, glucosinolates, cysteine-rich proteins, phytoalexins, elemental sulfur, or H2S. Probably more than one strategy is used by plants. Species- or even variety-dependent differences in the development of SIR are probably used. Our research...

Integrated hydraulic booster/tool string technology for unfreezing of stuck downhole strings in horizontal wells

Science.gov (United States)

Tian, Q. Z.

2017-12-01

It is common to use a jarring tool to unfreeze stuck downhole string. However, in a horizontal well, influenced by the friction caused by the deviated section, jarring effect is poor; on the other hand, the forcing point can be located in the horizontal section by a hydraulic booster and the friction can be reduced, but it is time-consuming and easy to break downhole string using a large-tonnage and constant pull force. A hydraulic booster - jar tool string has been developed for unfreezing operation in horizontal wells. The technical solution involves three elements: a two-stage parallel spring cylinder structure for increasing the energy storage capacity of spring accelerators; multiple groups of spring accelerators connected in series to increase the working stroke; a hydraulic booster intensifying jarring force. The integrated unfreezing tool string based on these three elements can effectively overcome the friction caused by a deviated borehole, and thus unfreeze a stuck string with the interaction of the hydraulic booster and the mechanical jar which form an alternatively dynamic load. Experimental results show that the jarring performance parameters of the hydraulic booster-jar unfreezing tool string for the horizontal wells are in accordance with original design requirements. Then field technical parameters were developed based on numerical simulation and experimental data. Field application shows that the hydraulic booster-jar unfreezing tool string is effective to free stuck downhole tools in a horizontal well, and it reduces hook load by 80% and lessens the requirement of workover equipment. This provides a new technology to unfreeze stuck downhole string in a horizontal well.

[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.

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

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.

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.

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.)

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)

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.)

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.)

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.

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.

Remarks on entanglement entropy in string theory

Science.gov (United States)

Balasubramanian, Vijay; Parrikar, Onkar

2018-03-01

Entanglement entropy for spatial subregions is difficult to define in string theory because of the extended nature of strings. Here we propose a definition for bosonic open strings using the framework of string field theory. The key difference (compared to ordinary quantum field theory) is that the subregion is chosen inside a Cauchy surface in the "space of open string configurations." We first present a simple calculation of this entanglement entropy in free light-cone string field theory, ignoring subtleties related to the factorization of the Hilbert space. We reproduce the answer expected from an effective field theory point of view, namely a sum over the one-loop entanglement entropies corresponding to all the particle-excitations of the string, and further show that the full string theory regulates ultraviolet divergences in the entanglement entropy. We then revisit the question of factorization of the Hilbert space by analyzing the covariant phase-space associated with a subregion in Witten's covariant string field theory. We show that the pure gauge (i.e., BRST exact) modes in the string field become dynamical at the entanglement cut. Thus, a proper definition of the entropy must involve an extended Hilbert space, with new stringy edge modes localized at the entanglement cut.

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.)

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.)

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.

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.)

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)

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.

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

The role of cysteine residues in the sulphate transporter, SHST1: construction of a functional cysteine-less transporter.

Science.gov (United States)

Howitt, Susan M

2005-05-20

We investigated the role of cysteine residues in the sulphate transporter, SHST1, with the aim of generating a functional cysteine-less variant. SHST1 contains five cysteine residues and none was essential for function. However, replacement of C421 resulted in a reduction in transport activity. Sulphate transport by C205 mutants was dependent on the size of the residue at this position. Alanine at position 205 resulted in a complete loss of function whereas leucine resulted in a 3-fold increase in sulphate transport relative to wild type SHST1. C205 is located in a putative intracellular loop and our results suggest that this loop may be important for sulphate transport. By replacing C205 with leucine and the other four cysteine residues with alanine, we constructed a cysteine-less variant of SHST1 that has transport characteristics indistinguishable from wild type. This construct will be useful for further structure and function studies of SHST1.

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

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.

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.)

Aspects of some dualities in string theory

Science.gov (United States)

Kim, Bom Soo

AdS/CFT correspondence in string theory has changed landscape of the theoretical physics. Through this celebrated duality between gravity theory and field theory, one can investigate analytically strongly coupled gauge theories such as Quantum Chromodynamics (QCD) in terms of weakly coupled string theory such as supergravity theory and vice versa. In the first part of this thesis we used this duality to construct a new type of nonlocal field theory, called Puff Field Theory, in terms of D3 branes in type IIB string theory with a geometric twist. In addition to the strong-weak duality of AdS/CFT, there also exists a weak-weak duality, called Twistor String Theory. Twistor technique is successfully used to calculate the SYM scattering amplitude in an elegant fashion. Yet, the progress in the string theory side was hindered by a non-unitary conformal gravity. We extend the Twistor string theory by introducing mass terms, in the second part of the thesis. A chiral mass term is identified as a vacuum expectation value of a conformal supergravity field and is tied with the breaking of the conformal symmetry of gravity. As a prime candidate for a quantum theory of gravity, string theory revealed many promising successes such as counting the number of microstates in supersymmetric Black Holes thermodynamics and resolution of timelike and null singularities, to name a few. Yet, the fundamental string and M-theroy formulations are not yet available. Various string theories without gravity, such as Non-Commutative Open String (NCOS) and Open Membrane (OM) theories, are very nice playground to investigate the fundamental structure of string and M-theory without the complication of gravity. In the last part of the thesis, simpler Non-Relativistic String Theories are constructed and investigated. One important motivation for those theories is related to the connection between Non-Relativistic String Theories and Non-critical String Theories through the bosonization of betagamma

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

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

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.

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.

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

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

Non-linear σ-models and string theories

International Nuclear Information System (INIS)

Sen, A.

1986-10-01

The connection between σ-models and string theories is discussed, as well as how the σ-models can be used as tools to prove various results in string theories. Closed bosonic string theory in the light cone gauge is very briefly introduced. Then, closed bosonic string theory in the presence of massless background fields is discussed. The light cone gauge is used, and it is shown that in order to obtain a Lorentz invariant theory, the string theory in the presence of background fields must be described by a two-dimensional conformally invariant theory. The resulting constraints on the background fields are found to be the equations of motion of the string theory. The analysis is extended to the case of the heterotic string theory and the superstring theory in the presence of the massless background fields. It is then shown how to use these results to obtain nontrivial solutions to the string field equations. Another application of these results is shown, namely to prove that the effective cosmological constant after compactification vanishes as a consequence of the classical equations of motion of the string theory. 34 refs

Boundary terms in Nambu-Goto string action

OpenAIRE

Hadasz, Leszek; Wegrzyn, Pawel

1994-01-01

We investigate classical strings defined by the Nambu-Goto action with the boundary term added. We demonstrate that the latter term has a significant bearing on the string dynamics. It is confirmed that new action terms that depend on higher order derivatives of string coordinates cannot be considered as continuous perturbations from the starting string functional. In the case the boundary term reduces to the Gauss-Bonnet term, a stability analysis is performed on the rotating rigid string so...

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

Cross-talk between malarial cysteine proteases and falstatin: the BC loop as a hot-spot target.

Directory of Open Access Journals (Sweden)

Srinivasan Sundararaj

Full Text Available Cysteine proteases play a crucial role in the development of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Our earlier studies demonstrated that these enzymes are equipped with specific domains for defined functions and further suggested the mechanism of activation of cysteine proteases. The activities of these proteases are regulated by a new class of endogenous inhibitors of cysteine proteases (ICPs. Structural studies of the ICPs of Trypanosoma cruzi (chagasin and Plasmodium berghei (PbICP indicated that three loops (termed BC, DE, and FG are crucial for binding to target proteases. Falstatin, an ICP of P. falciparum, appears to play a crucial role in invasion of erythrocytes and hepatocytes. However, the mechanism of inhibition of cysteine proteases by falstatin has not been established. Our study suggests that falstatin is the first known ICP to function as a multimeric protein. Using site-directed mutagenesis, hemoglobin hydrolysis assays and peptide inhibition studies, we demonstrate that the BC loop, but not the DE or FG loops, inhibits cysteine proteases of P. falciparum and P. vivax via hydrogen bonds. These results suggest that the BC loop of falstatin acts as a hot-spot target for inhibiting malarial cysteine proteases. This finding suggests new strategies for the development of anti-malarial agents based on protease-inhibitor interactions.

E(lementary) Strings in Six-Dimensional Heterotic F-Theory

OpenAIRE

Choi, Kang-Sin; Rey, Soo-Jong

2017-01-01

Using E-strings, we can analyze not only six-dimensional superconformal field theories but also probe vacua of non-perturabative heterotic string. We study strings made of D3-branes wrapped on various two-cycles in the global F-theory setup. We claim that E-strings are elementary in the sense that various combinations of E-strings can form M-strings as well as heterotic strings and new kind of strings, called G-strings. Using them, we show that emissions and combinations of heterotic small in...

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

Cysteine proteases and wheat (Triticum aestivum L) under drought: A still greatly unexplored association.

Science.gov (United States)

Botha, Anna-Maria; Kunert, Karl J; Cullis, Christopher A

2017-09-01

Bread wheat (Triticum aestivum L.) provides about 19% of global dietary energy. Environmental stress, such as drought, affects wheat growth causing premature plant senescence and ultimately plant death. A plant response to drought is an increase in protease-mediated proteolysis with rapid degradation of proteins required for metabolic processes. Among the plant proteases that are increased in their activity following stress, cysteine proteases are the best characterized. Very little is known about particular wheat cysteine protease sequences, their expression and also localization. The current knowledge on wheat cysteine proteases belonging to the five clans (CA, CD, CE, CF and CP) is outlined, in particular their expression and possible function under drought. The first successes in establishing an annotated wheat genome database are further highlighted which has allowed more detailed mining of cysteine proteases. We also share our thoughts on future research directions considering the growing availability of genomic resources of this very important food crop. Finally, we also outline future application of developed knowledge in transgenic wheat plants for environmental stress protection and also as senescence markers to monitor wheat growth under environmental stress conditions. © 2017 John Wiley & Sons Ltd.

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...

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.

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.

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…

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.)

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.)

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.

Cosmic strings in unified gauge theories

International Nuclear Information System (INIS)

Everett, A.E.

1981-01-01

Some spontaneously broken gauge theories can give rise to stringlike vacuum structures (vortices). It has been pointed out by Vilenkin that in grand unified theories these can be sufficiently massive to have cosmological implications, e.g., in explaining the formation of galaxies. The circumstances in which such structures occur are examined. They do not occur in the simplest grand unified theories, but can occur in some more elaborate models which have been proposed. The cross section for the scattering of elementary particles by strings is estimated. This is used to evaluate the effect of collisions on the dynamics of a collapsing circular string, with particular attention to the question of whether energy dissipation by collision can reduce the rate of formation of black holes by collapsed strings, which may be unacceptably large in models where strings occur. It is found that the effect of collisions is not important in the case of grand unified strings, although it can be important for lighter strings

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.

Probes of the catalytic site of cysteine dioxygenase.

Science.gov (United States)

Chai, Sergio C; Bruyere, John R; Maroney, Michael J

2006-06-09

The first major step of cysteine catabolism, the oxidation of cysteine to cysteine sulfinic acid, is catalyzed by cysteine dioxygenase (CDO). In the present work, we utilize recombinant rat liver CDO and cysteine derivatives to elucidate structural parameters involved in substrate recognition and x-ray absorption spectroscopy to probe the interaction of the active site iron center with cysteine. Kinetic studies using cysteine structural analogs show that most are inhibitors and that a terminal functional group bearing a negative charge (e.g. a carboxylate) is required for binding. The substrate-binding site has no stringent restrictions with respect to the size of the amino acid. Lack of the amino or carboxyl groups at the alpha-carbon does not prevent the molecules from interacting with the active site. In fact, cysteamine is shown to be a potent activator of the enzyme without being a substrate. CDO was also rendered inactive upon complexation with the metal-binding inhibitors azide and cyanide. Unlike many non-heme iron dioxygenases that employ alpha-keto acids as cofactors, CDO was shown to be the only dioxygenase known to be inhibited by alpha-ketoglutarate.

Rotating strings in confining AdS/CFT backgrounds

International Nuclear Information System (INIS)

Armoni, Adi; Barbon, Jose L.F.; Petkou, Anastasios C.

2002-01-01

We study semiclassical rotating strings in AdS/CFT backgrounds that exhibit both confinement and finite-size effects. The energy versus spin dispersion relation for short strings is the expected Regge trajectory behaviour, with the same string tension as is measured by the Wilson loop. Long strings probe the interplay between confinement and finite-size effects. In particular, the dispersion relation for long strings shows a characteristic dependence on the string tension and the finite-size scale. (author)

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.)

Sa’Unine String Orchestra, Orkes Geseknya Indonesia

Directory of Open Access Journals (Sweden)

Ranti - Rachmawanti

2012-04-01

Full Text Available ABSTRACT   This article explains the result of Sa’Unine String Orchestra as one of Indonesian orchestras in popular culture. Main idea of this research is to uncover and describe the characteristic, func- tion, and role of Sa’Unine String Orchestra within the popular culture in Indonesia. This research used qualitative method with ethnographical approaches to identify all facts that discovered during research. The conclusions of this research show that Sa’Unine String Orchestra moves in two ways, there are; the idealism which had a vision to create a real Indonesian string orchestra and a part of music industry. At the end, these two ways are connected to each other because of the earnings of those. Music industry becomes a support factor which create the idealism of Sa’Unine String Or- chestra to be an Indonesian String Orchestra.   Keywords: String Orchestra, Music, Popular Culture.

Crystallization and preliminary crystallographic studies of a cysteine protease inhibitor from the human nematode parasite Ascaris lumbricoides

International Nuclear Information System (INIS)

Liu, Sanling; Dong, Jianmei; Mei, Guoqiang; Liu, Guiyun; Xu, Wei; Su, Zhong; Liu, Jinsong

2011-01-01

A recombinant cysteine protease inhibitor from the human nematode parasite A. lumbricoides has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.1 Å resolution. The cysteine protease inhibitor from Ascaris lumbricoides, a roundworm that lives in the human intestine, may be involved in the suppression of human immune responses. Here, the molecular cloning, protein expression and purification, preliminary crystallization and crystallographic characterization of the cysteine protease inhibitor from A. lumbricoides are reported. The rod-shaped crystal belonged to space group C2, with unit-cell parameters a = 99.40, b = 37.52, c = 62.92 Å, β = 118.26°. The crystal diffracted to 2.1 Å resolution and contained two molecules in the asymmetric unit

On background-independent open-string field theory

International Nuclear Information System (INIS)

Witten, E.

1992-01-01

A framework for background-independent open-string field theory is proposed. The approach involves using the Batalin-Vilkovisky formalism, in a way suggested by recent developments in closed-string field theory, to implicitly define a gauge-invariant Lagrangian in a hypothetical ''space of all open-string world-sheet theories.'' It is built into the formalism that classical solutions of the string field theory are Becchi-Rouet-Stora-Tyutin- (BRST-) invariant open-string world-sheet theories and that, when expanding around a classical solution, the infinitesimal gauge transformations are generated by the world-sheet BRST operator

Deformation of the cubic open string field theory

Energy Technology Data Exchange (ETDEWEB)

Lee, Taejin, E-mail: taejin@kangwon.ac.kr

2017-05-10

We study a consistent deformation of the cubic open bosonic string theory in such a way that the non-planar world sheet diagrams of the perturbative string theory are mapped onto their equivalent planar diagrams of the light-cone string field theory with some length parameters fixed. An explicit evaluation of the cubic string vertex in the zero-slope limit yields the correct relationship between the string coupling constant and the Yang–Mills coupling constant. The deformed cubic open string field theory is shown to produce the non-Abelian Yang–Mills action in the zero-slope limit if it is defined on multiple D-branes. Applying the consistent deformation systematically to multi-string world sheet diagrams, we may be able to calculate scattering amplitudes with an arbitrary number of external open strings.

Deformation of the cubic open string field theory

International Nuclear Information System (INIS)

Lee, Taejin

2017-01-01

We study a consistent deformation of the cubic open bosonic string theory in such a way that the non-planar world sheet diagrams of the perturbative string theory are mapped onto their equivalent planar diagrams of the light-cone string field theory with some length parameters fixed. An explicit evaluation of the cubic string vertex in the zero-slope limit yields the correct relationship between the string coupling constant and the Yang–Mills coupling constant. The deformed cubic open string field theory is shown to produce the non-Abelian Yang–Mills action in the zero-slope limit if it is defined on multiple D-branes. Applying the consistent deformation systematically to multi-string world sheet diagrams, we may be able to calculate scattering amplitudes with an arbitrary number of external open strings.

Deformation of the cubic open string field theory

Directory of Open Access Journals (Sweden)

Taejin Lee

2017-05-01

Full Text Available We study a consistent deformation of the cubic open bosonic string theory in such a way that the non-planar world sheet diagrams of the perturbative string theory are mapped onto their equivalent planar diagrams of the light-cone string field theory with some length parameters fixed. An explicit evaluation of the cubic string vertex in the zero-slope limit yields the correct relationship between the string coupling constant and the Yang–Mills coupling constant. The deformed cubic open string field theory is shown to produce the non-Abelian Yang–Mills action in the zero-slope limit if it is defined on multiple D-branes. Applying the consistent deformation systematically to multi-string world sheet diagrams, we may be able to calculate scattering amplitudes with an arbitrary number of external open strings.

Subcellular distribution of glutathione and cysteine in cyanobacteria.

Science.gov (United States)

Zechmann, Bernd; Tomasić, Ana; Horvat, Lucija; Fulgosi, Hrvoje

2010-10-01

Glutathione plays numerous important functions in eukaryotic and prokaryotic cells. Whereas it can be found in virtually all eukaryotic cells, its production in prokaryotes is restricted to cyanobacteria and proteobacteria and a few strains of gram-positive bacteria. In bacteria, it is involved in the protection against reactive oxygen species (ROS), osmotic shock, acidic conditions, toxic chemicals, and heavy metals. Glutathione synthesis in bacteria takes place in two steps out of cysteine, glutamate, and glycine. Cysteine is the limiting factor for glutathione biosynthesis which can be especially crucial for cyanobacteria, which rely on both the sufficient sulfur supply from the growth media and on the protection of glutathione against ROS that are produced during photosynthesis. In this study, we report a method that allows detection and visualization of the subcellular distribution of glutathione in Synechocystis sp. This method is based on immunogold cytochemistry with glutathione and cysteine antisera and computer-supported transmission electron microscopy. Labeling of glutathione and cysteine was restricted to the cytosol and interthylakoidal spaces. Glutathione and cysteine could not be detected in carboxysomes, cyanophycin granules, cell walls, intrathylakoidal spaces, periplasm, and vacuoles. The accuracy of the glutathione and cysteine labeling is supported by two observations. First, preadsorption of the antiglutathione and anticysteine antisera with glutathione and cysteine, respectively, reduced the density of the gold particles to background levels. Second, labeling of glutathione and cysteine was strongly decreased by 98.5% and 100%, respectively, in Synechocystis sp. cells grown on media without sulfur. This study indicates a strong similarity of the subcellular distribution of glutathione and cysteine in cyanobacteria and plastids of plants and provides a deeper insight into glutathione metabolism in bacteria.

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.)

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.)

Revisiting the systemic lipopolysaccharide mediated neuroinflammation: Appraising the effect of l-cysteine mediated hydrogen sulphide on it

Directory of Open Access Journals (Sweden)

Abdulaziz S. Al-Saeedan

2018-05-01

Full Text Available The present research was ventured to examine the effect of l-cysteine on neuro-inflammation persuaded by peripheral lipopolysaccharides (LPS, 125 μg/kg, i.p. administration. No behavioral, biochemical, and inflammatory abnormality was perceived in the brain tissues of experimental animals after LPS administration. l-cysteine precipitated marginal symptoms of toxicity in the brain tissue. Similar pattern of wholesome effect of LPS were perceived when evaluated through the brain tissue fatty acid profile, histopathologically and NF-ĸBP65 protein expression. LPS was unsuccessful to alter the levels of hydrogen sulphide (H2S, cyclooxygenase (COX and lipoxygenase (LOX enzyme in brain tissue. LPS afforded significant peripheral toxicity, when figured out through inflammatory markers (COX, LOX, gaseous signaling molecules nitric oxide (NO, H2S, liver toxicity (SGOT, SGPT, and inflammatory transcription factor (NF-ĸBP65 and l-cysteine also provided a momentous protection against the same as well. The study inculcated two major finding, firstly LPS (i.p. cannot impart inflammatory changes to brain and secondly, l-cysteine can afford peripheral protection against deleterious effect of LPS (i.p. Keywords: Hydrogen sulphide, l-cysteine, Inflammation, Lipopolysaccharide, Neuroinflammation

Cosmological horizons, quintessence and string theory

International Nuclear Information System (INIS)

Kaloper, Nemanja

2003-01-01

String theory is presently the best candidate for a quantum theory of gravity unified with other forces. It is natural to hope that applications of string theory to cosmology may shed new light on the cosmological conundra, such as singularities, initial conditions, cosmological constant problem and the origin of inflation. Before we can apply string theory to cosmology, there are important conceptual and practical problems which must be addressed. We have reviewed here some of these problems, related to how one defines string theory in a cosmological setting. (author)

Gauge invariant actions for string models

International Nuclear Information System (INIS)

Banks, T.

1986-06-01

String models of unified interactions are elegant sets of Feynman rules for the scattering of gravitons, gauge bosons, and a host of massive excitations. The purpose of these lectures is to describe the progress towards a nonperturbative formulation of the theory. Such a formulation should make the geometrical meaning of string theory manifest and explain the many ''miracles'' exhibited by the string Feynman rules. There are some new results on gauge invariant observables, on the cosmological constant, and on the symmetries of interacting string field theory. 49 refs

Joining-Splitting Interaction of Noncritical String

Science.gov (United States)

Hadasz, Leszek; Jaskólski, Zbigniew

The joining-splitting interaction of noncritical bosonic string is analyzed in the light-cone formulation. The Mandelstam method of constructing tree string amplitudes is extended to the bosonic massive string models of the discrete series. The general properties of the Liouville longitudinal excitations which are necessary and sufficient for the Lorentz covariance of the light-cone amplitudes are derived. The results suggest that the covariant and the light-cone approach are equivalent also in the noncritical dimensions. Some aspects of unitarity of interacting noncritical massive string theory are discussed.

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.)

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.

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.

Highly excited strings I: Generating function

Directory of Open Access Journals (Sweden)

Dimitri P. Skliros

2017-03-01

Full Text Available This is the first of a series of detailed papers on string amplitudes with highly excited strings (HES. In the present paper we construct a generating function for string amplitudes with generic HES vertex operators using a fixed-loop momentum formalism. We generalise the proof of the chiral splitting theorem of D'Hoker and Phong to string amplitudes with arbitrary HES vertex operators (with generic KK and winding charges, polarisation tensors and oscillators in general toroidal compactifications E=RD−1,1×TDcr−D (with generic constant Kähler and complex structure target space moduli, background Kaluza–Klein (KK gauge fields and torsion. We adopt a novel approach that does not rely on a “reverse engineering” method to make explicit the loop momenta, thus avoiding a certain ambiguity pointed out in a recent paper by Sen, while also keeping the genus of the worldsheet generic. This approach will also be useful in discussions of quantum gravity and in particular in relation to black holes in string theory, non-locality and breakdown of local effective field theory, as well as in discussions of cosmic superstrings and their phenomenological relevance. We also discuss the manifestation of wave/particle (or rather wave/string duality in string theory.

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.)

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 ...

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

The status and future prospects of string theory

International Nuclear Information System (INIS)

Gross, D.J.

1990-01-01

After a general introduction to the description of the fundamental forces by gauge theories and the difficulties occurring in the attemps of unifying these theories with gravity the reasons for the introduction of string theory are explained. After a description of the construction of a string theory the string theory of gravity is considered. Then the problems of string theory are described. Thereafter elastic scattering in string theory at energies comparable with the Planck mass is considered. Finally some prospects for string theory are discussed. (HSI)

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

A novel potentiometric biosensor for selective L-cysteine determination using L-cysteine-desulfhydrase producing Trichosporon jirovecii yeast cells coupled with sulfide electrode

International Nuclear Information System (INIS)

Hassan, Saad S.M.; El-Baz, Ashraf F.; Abd-Rabboh, Hisham S.M.

2007-01-01

Trichosporon jirovecii yeast cells are used for the first time as a source of L-cysteine desulfhydrase enzyme (EC 4.4.1.1) and incorporated in a biosensor for determining L-cysteine. The cells are grown under cadmium stress conditions to increase the expression level of the enzyme. The intact cells are immobilized on the membrane of a solid-state Ag 2 S electrode to provide a simple L-cysteine responsive biosensor. Upon immersion of the sensor in L-cysteine containing solutions, L-cysteine undergoes enzymatic hydrolysis into pyruvate, ammonia and sulfide ion. The rate of sulfide ion formation is potentiometrically measured as a function of L-cysteine concentration. Under optimized conditions (phosphate buffer pH 7, temperature 37 ± 1 deg. C and actual weight of immobilized yeast cells 100 mg), a linear relationship between L-cysteine concentration and the initial rate of sulfide liberation (dE/dt) is obtained. The sensor response covers the concentration range of 0.2-150 mg L -1 (1.7-1250 μmol L -1 ) L-cysteine. Validation of the assay method according to the quality control/quality assurance standards (precision, accuracy, between-day variability, within-day reproducibility, range of measurements and lower limit of detection) reveals remarkable performance characteristics of the proposed biosensor. The sensor is satisfactorily utilized for determination of L-cysteine in some pharmaceutical formulations. The lower limit of detection is ∼1 μmol L -1 and the accuracy and precision of the method are 97.5% and ±1.1%, respectively. Structurally similar sulfur containing compounds such as glutathione, cystine, methionine, and D-cysteine do no interfere

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)

Drill-string design for directional wells

Energy Technology Data Exchange (ETDEWEB)

Dawson, R; Corbett, K T [Exxon Production Research Co., Houston, TX (USA)

1983-01-01

This paper is concerned with predicting the tension and torsion loads on drill strings in directional wells and with adjusting the string design or well plan to provide adequate strength. Drill-string drag is the incremental force that is required to move the pipe up or down in the hole; torque is the moment required to rotate the pipe. Drag forces are usually given relative to the string weight measured with the string roating but not reciprocating. Measured from the roating string weight, the pick-up drag is usually slightly greater than the slack-off drag. The magnitudes of torque and drag are related in any particular well; high drag forced and exessive torque loads normally occur together. There are a number of phenomena wich contribute to torque and drag. Included are tight hole conditions, sloughing hole, keyseats, differential sticking, cuttings build up due to poor hole cleaning and sliding wellbore friction. With the exception of sliding friction, these causes are associated with problem conditions in the wellbore. Conversely, in wells with good hole conditions, the primary source of torque and drag is sliding friction. This paper is only concerned with the torque and drag caused by sliding friction. The cabability to predict frictional loads on drill pipe has two main benefits. First, more complete knowledge of drill-string loading allows use of improved drill-string design techniques. Drill-string components can be chosen using a systematic approach considering the force involved. Second, deep, highly-deviated wells can be planned to minimize torque and drag. Use of torque and drag as a criteria to select the most appropriate well path will help ensure successful drilling operations to total depth. 1 fig., 2 tabs. (Author).

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

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.)

Identification of arsenite-and arsenic diglutathione-binding proteins in human hepatocarcinoma cells

Energy Technology Data Exchange (ETDEWEB)

Mizumura, Ayano; Watanabe, Takayuki [Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi, Inage, Chiba 263-8522 (Japan); Kobayashi, Yayoi [Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi, Inage, Chiba 263-8522 (Japan); Environmental Health Sciences Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan); Hirano, Seishiro [Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi, Inage, Chiba 263-8522 (Japan); Research Center for Environmental Risk, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan)

2010-01-15

It is generally accepted that trivalent arsenicals are more toxic than the corresponding pentavalent arsenicals, since trivalent arsenicals bind the thiol groups of biomolecules, leading to a deterioration in cellular functions. In the present study, we prepared three different arsenic-bound sepharoses and investigated the binding of hepatic cytosolic proteins to pentavalent, trivalent, and glutathione-conjugated trivalent arsenicals. SDS-PAGE showed no proteins bound to pentavalent arsenic specifically. In contrast, we found a number of proteins that have specific and high affinity for trivalent arsenic. Two of those proteins were identified: protein disulfide isomerase-related protein 5 (PDSIRP5) and peroxiredoxin 1/enhancer protein (PRX1/EP). These proteins have vicinal cysteines, as previously reported. In contrast, one of the prominent proteins that did not bind to trivalent arsenic was identified as calreticulin precursor. Although there are 3 cysteines in calreticulin precursor, two of the cysteines are spaced more than 25 amino acids apart. Five synthetic peptides containing 2 vicinal cysteines were prepared to study whether they would inhibit the binding of PDSIRP5, PRX1/EP, and other arsenic-binding proteins to trivalent arsenicals. Only two of the five peptides effectively inhibited binding, suggesting that other amino acids besides the 2 vicinal cysteines may modulate the affinity of cysteine-rich proteins for trivalent arsenicals. We further investigated hepatic cytosolic proteins that bound specifically to glutathione-conjugated trivalent arsenic, which is the most abundant form of arsenical in bile fluid. Four proteins that bound specifically to glutathione-conjugated trivalent arsenic were identified; interestingly, these proteins were different from the trivalent arsenic-binding proteins. These results suggest that although glutathione-conjugation is an important process in the metabolism, excretion, and detoxification of arsenicals, glutathione

Mechanical Properties of Nylon Harp Strings

Science.gov (United States)

Lynch-Aird, Nicolas; Woodhouse, Jim

2017-01-01

Monofilament nylon strings with a range of diameters, commercially marketed as harp strings, have been tested to establish their long-term mechanical properties. Once a string had settled into a desired stress state, the Young’s modulus was measured by a variety of methods that probe different time-scales. The modulus was found to be a strong function of testing frequency and also a strong function of stress. Strings were also subjected to cyclical variations of temperature, allowing various thermal properties to be measured: the coefficient of linear thermal expansion and the thermal sensitivities of tuning, Young’s modulus and density. The results revealed that the particular strings tested are divided into two groups with very different properties: stress-strain behaviour differing by a factor of two and some parametric sensitivities even having the opposite sign. Within each group, correlation studies allowed simple functional fits to be found to the key properties, which have the potential to be used in automated tuning systems for harp strings. PMID:28772858

Mechanical Properties of Nylon Harp Strings

Directory of Open Access Journals (Sweden)

Nicolas Lynch-Aird

2017-05-01

Full Text Available Monofilament nylon strings with a range of diameters, commercially marketed as harp strings, have been tested to establish their long-term mechanical properties. Once a string had settled into a desired stress state, the Young’s modulus was measured by a variety of methods that probe different time-scales. The modulus was found to be a strong function of testing frequency and also a strong function of stress. Strings were also subjected to cyclical variations of temperature, allowing various thermal properties to be measured: the coefficient of linear thermal expansion and the thermal sensitivities of tuning, Young’s modulus and density. The results revealed that the particular strings tested are divided into two groups with very different properties: stress-strain behaviour differing by a factor of two and some parametric sensitivities even having the opposite sign. Within each group, correlation studies allowed simple functional fits to be found to the key properties, which have the potential to be used in automated tuning systems for harp strings.

Perturbation theory for quantized string fields

International Nuclear Information System (INIS)

Thorn, C.B.; Florida Univ., Gainesville

1987-01-01

We discuss the problem of gauge fixing in string field theory. We show that BRST invariance requires the gauge-fixed action to contain terms cubic in the ghost... of ghost of ghost fields. The final BRST invariant gauge-fixed action for the gauge b 0 A=0 is extremely simple: with the proper interpretation (as given in this article), it is essentially the one anticipated earlier in the work of Giddings, Martinec, and Witten in their analysis of the BRST invariant world-sheet approach to string theory. We derive the Feynman rules from this action and explain in detail how the sum over sufaces of the BRST first-quantized string is reproduced. This result depends crucially on the correct assignment for the Grassmann character of the string field and its ghost... of ghost of ghost string fields. If all these fields are unified in a single string field Φ containing all ghost numbers, the requirements is that Φ be uniformly Grassmann odd. Finally, we do some sample calculations which provide some simple checks on our general results. (orig.)

Multi-branes boundary states with open string interactions

International Nuclear Information System (INIS)

Pesando, Igor

2008-01-01

We derive boundary states which describe configurations of multiple parallel branes with arbitrary open string states interactions in bosonic string theory. This is obtained by a careful discussion of the factorization of open/closed string states amplitudes taking care of cycles needed by ensuring vertices commutativity: in particular the discussion reveals that already at the tree level open string knows of the existence of closed string

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...

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.)

The stability of D-term cosmic strings

International Nuclear Information System (INIS)

Collinucci, A.; Smyth, P.; Van Proeyen, A.

2007-01-01

In this article, we discuss the semi-classical stability of the D-term string solution of D=4, N=1 supergravity with a constant Fayet-Iliopoulos term. Regardless of the particular theory one is interested in, the stability of cosmic strings is necessary if we hope to observe them. We apply the spinorial Witten-Nester method to prove a positive energy theorem for the D-term cosmic string background with positive deficit angle. We also pay particular attention to the negative deficit angle D-term string, which is known to violate the dominant energy condition. Within the class of string solutions we consider, this violation implies that the negative deficit angle D-term string must have a naked pathology and therefore the positive energy theorem we prove does not apply to it. (orig.)

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

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.)

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

Pulse photolysis of NADH in the presence of cysteine

International Nuclear Information System (INIS)

Scheel, H.E.

1976-01-01

In the UV irradiation of NADH under anaerobic conditions, cysteine, which often acts as a radioprotective substance, has a sensitizing effect. With the aid of pulse photolysis, it was studied which reaction mechanisms in the presence or absence of cysteine are responsible for the damage to NADH in aqueous solution. In the absence of cysteine, the characteristic NADH absorption at 340 nm is reduced immediately after UV quanta have been absorbed by the adenine fraction of the molecules; in the presence of cysteine, a secondary reaction causes additional damage. The spectra of the intermediate products of NADH and cysteine have been recorded for different cysteine concentrations, and the reaction constants have been determined. These values suggest that the sensitizing effect is due to a reaction of NADH with radical anions produced by photolysis. (orig.) [de

Effect of (L)-cysteine on acetaldehyde self-administration.

Science.gov (United States)

Peana, Alessandra T; Muggironi, Giulia; Fois, Giulia R; Zinellu, Manuel; Sirca, Donatella; Diana, Marco

2012-08-01

Acetaldehyde (ACD), the first metabolite of ethanol, has been implicated in several behavioural actions of alcohol, including its reinforcing effects. Recently, we reported that l-cysteine, a sequestrating agent of ACD, reduced oral ethanol self-administration and that ACD was orally self-administered. This study examined the effects of l-cysteine pre-treatment during the acquisition and maintenance phases of ACD (0.2%) self-administration as well as on the deprivation effect after ACD extinction and on a progressive ratio (PR) schedule of reinforcement. In a separate PR schedule of reinforcement, the effect of l-cysteine was assessed on the break-point produced by ethanol (10%). Furthermore, we tested the effect of l-cysteine on saccharin (0.2%) reinforcement. Wistar rats were trained to self-administer ACD by nose poking on a fixed ratio (FR1) schedule in 30-min daily sessions. Responses on an active nose-poke caused delivery of ACD solution, whereas responses on an inactive nose-poke had no consequences. l-cysteine reduced the acquisition (40 mg/kg), the maintenance and the deprivation effect (100 mg/kg) of ACD self-administration. Furthermore, at the same dose, l-cysteine (120 mg/kg) decreased both ACD and ethanol break point. In addition, l-cysteine was unable to suppress the different responses for saccharin, suggesting that its effect did not relate to an unspecific decrease in a general motivational state. Compared to saline, l-cysteine did not modify responses on inactive nose-pokes, suggesting an absence of a non-specific behavioural activation. Taken together, these results could support the hypotheses that ACD possesses reinforcing properties and l-cysteine reduces motivation to self-administer ACD. Copyright © 2012 Elsevier Inc. All rights reserved.

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

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

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.

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

Document retrieval on repetitive string collections.

Science.gov (United States)

Gagie, Travis; Hartikainen, Aleksi; Karhu, Kalle; Kärkkäinen, Juha; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2017-01-01

Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their repetitiveness, which can reduce their space usage by orders of magnitude. We study the problem of indexing repetitive string collections in order to perform efficient document retrieval operations on them. Document retrieval problems are routinely solved by search engines on large natural language collections, but the techniques are less developed on generic string collections. The case of repetitive string collections is even less understood, and there are very few existing solutions. We develop two novel ideas, interleaved LCPs and precomputed document lists , that yield highly compressed indexes solving the problem of document listing (find all the documents where a string appears), top- k document retrieval (find the k documents where a string appears most often), and document counting (count the number of documents where a string appears). We also show that a classical data structure supporting the latter query becomes highly compressible on repetitive data. Finally, we show how the tools we developed can be combined to solve ranked conjunctive and disjunctive multi-term queries under the simple [Formula: see text] model of relevance. We thoroughly evaluate the resulting techniques in various real-life repetitiveness scenarios, and recommend the best choices for each case.

Boundary terms in the Nambu-Goto string action

Science.gov (United States)

Hadasz, Leszek; Wȩgrzyn, Paweł

1995-03-01

We investigate classical strings defined by the Nambu-Goto action with the boundary term added. We demonstrate that the latter term has a significant bearing on the string dynamics. It is confirmed that new action terms that depend on higher order derivatives of string coordinates cannot be considered as continuous perturbations from the starting string functional. In the case when the boundary term reduces to the Gauss-Bonnet term, a stability analysis is performed on the rotating rigid string solution. We determine the most generic solution that the fluctuations grow to. Longitudinal string excitations are found. The Regge trajectories are nonlinear.