Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

Science.gov (United States)

Takahashi, Shuntaro; Sugimoto, Naoki

2017-12-01

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆V tr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm 3 mol -1 , which was larger than that of TBA (54.6cm 3 mol -1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆V tr of 41.1cm 3 mol -1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆V tr values were 14.7cm 3 mol -1 for TBA T3A and 13.2cm 3 mol -1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro

Science.gov (United States)

Williams, Jonathan D.; Fleetwood, Sara; Berroyer, Alexandra; Kim, Nayun; Larson, Erik D.

2015-01-01

The formation of highly stable four-stranded DNA, called G-quadruplex (G4), promotes site-specific genome instability. G4 DNA structures fold from repetitive guanine sequences, and increasing experimental evidence connects G4 sequence motifs with specific gene rearrangements. The human transcription factor 3 (TCF3) gene (also termed E2A) is subject to genetic instability associated with severe disease, most notably a common translocation event t(1;19) associated with acute lymphoblastic leukemia. The sites of instability in TCF3 are not randomly distributed, but focused to certain sequences. We asked if G4 DNA formation could explain why TCF3 is prone to recombination and mutagenesis. Here we demonstrate that sequences surrounding the major t(1;19) break site and a region associated with copy number variations both contain G4 sequence motifs. The motifs identified readily adopt G4 DNA structures that are stable enough to interfere with DNA synthesis in physiological salt conditions in vitro. When introduced into the yeast genome, TCF3 G4 motifs promoted gross chromosomal rearrangements in a transcription-dependent manner. Our results provide a molecular rationale for the site-specific instability of human TCF3, suggesting that G4 DNA structures contribute to oncogenic DNA breaks and recombination. PMID:26029241

Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

Energy Technology Data Exchange (ETDEWEB)

Pegan, Scott D. [Univ. of Denver, CO (United States); Rukseree, Kamolchanok [National Center for Genetic Engineering and Biotechnology (BIOTEC), Tha Khlong (Thailand); Capodagli, Glenn C. [Univ. of Denver, CO (United States); Baker, Erica A. [Univ. of Denver, CO (United States); Krasnykh, Olga [Univ. of Illinois, Chicago, IL (United States); Franzblau, Scott G. [Univ. of Illinois, Chicago, IL (United States); Mesecar, Andrew D. [Purdue Univ., West Lafayette, IN (United States)

2013-01-08

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

Energetic molecular outflow near AFGL 961: millimeter-wave and infrared observations

International Nuclear Information System (INIS)

Lada, C.J.; Gautier, T.N. III

1982-01-01

We report detailed millimeter-wave and near-infrared spectroscopy of the dynamically active region around the infrared source AFGL 961, near the Rosette nebula. Millimeter-wave 12 CO observations are used to study the high-velocity molecular flow around AFGL 961. These observations show that the high-velocity flow has a maximum extent of at least 6' or 2.9 pc at the distance of AFGL 961. The flow is found to be anisotropic, with redshifted high-velocity emission considerably more extended than blueshifted high-velocity emission. However, the flow does not appear to be as highly collimated as some other sources of high-velocity bipolar outflow. We also find the emission profiles to be asymmetric in velocity such that the integrated intensity of the redshifted high-velocity emission is on average 2.5 times greater than that of the blueshifted emission. The mass of the gas involved in the flow is determined to be approximately 19 M/sub sun/, and the kinetic energy of this gas is estimated to be about 8 x 10 46 ergs. These observations are interpreted as evidence that an energetic bipolar outflow of molecular gas is occurring near AFGL 961. The momentum of the outflowing molecular gas is large, and it is shown that this places strong constraints on possible physical mechanisms which may be driving the outflow. The near-infrared spectrum of AFGL 961 from 1.4-2.4 μm was obtained in order to study the conditions immediately around the infrared source which may be driving the molecular outflow

Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops.

Directory of Open Access Journals (Sweden)

Giovanna Sattin

Full Text Available Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules.

Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox.

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Julien Hiblot

Full Text Available Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263 that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.

7 CFR 28.961 - False and misleading information.

Science.gov (United States)

2010-01-01

....961 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE COMMODITY STANDARDS AND STANDARD CONTAINER... or misleading information concerning the results of tests as reported by laboratories under the...

Full O(α) electroweak radiative corrections to e+e- → t anti t γ with GRACE-Loop

International Nuclear Information System (INIS)

Khiem, P.H.; Fujimoto, J.; Ishikawa, T.; Kaneko, T.; Kurihara, Y.; Shimizu, Y.; Kato, K.; Ueda, T.; Vermaseren, J.A.M.; Yasui, Y.

2013-01-01

We present the full O(α) electroweak radiative corrections to the process e + e - → t anti t γ at the International Linear Collider (ILC). The computation is performed with the help of the GRACE-Loop system. We present the total cross-section and the top quark forward-backward asymmetry (A FB ) as a function of the center-of-mass energy and compare them with the process e + e - → t anti t γ. We find that the value of A FB in t anti t γ production is larger than A FB in t anti t production. It is an important result for the measurement of the top quark forward-backward asymmetry at the ILC. Applying a structure function method, we also subtract the QED correction to gain the genuine weak correction in both the α scheme and the G μ scheme (δ W G μ ). We obtain numerical values for δ W G μ which are changing from 2 % to -24 % when we vary the center-of-mass energy from 360 GeV to 1 TeV. (orig.)

Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

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Marius Rutkauskas

2015-03-01

Full Text Available CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM. Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.

Water loop for training

International Nuclear Information System (INIS)

Moeller, S.V.

1983-02-01

The procedures used to operate the water loop of the Institute of Nuclear Enginering (IEN) in Brazil are presented. The aim is to help future operators of the training water loop in the operation technique and in a better comprehension of the phenomena occured during the execution of an experience. (E.G.) [pt

S961, an insulin receptor antagonist causes hyperinsulinemia, insulin-resistance and depletion of energy stores in rats

Energy Technology Data Exchange (ETDEWEB)

Vikram, Ajit [Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Mohali, Punjab 160 062 (India); Jena, Gopabandhu, E-mail: gbjena@gmail.com [Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Mohali, Punjab 160 062 (India)

2010-07-23

Research highlights: {yields}Insulin receptor antagonist S961 causes hyperglycemia, hyperinsulinemia and insulin resistance in rats. {yields}Peroxysome-proliferator-activated-receptor-gamma agonist pioglitazone improves S961 induced hyperglycemia and glucose intolerance. {yields}Long term treatment with insulin receptor antagonist S961 results in the decreased adiposity and hepatic glycogen content. {yields}Improvement in the hyperglycemia and glucose intolerance by pioglitazone clearly demonstrates that S961 treated rats can be successfully used to screen the novel therapeutic interventions having potential to improve glucose disposal through receptor independent mechanisms. -- Abstract: Impairment in the insulin receptor signaling and insulin mediated effects are the key features of type 2 diabetes. Here we report that S961, a peptide insulin receptor antagonist induces hyperglycemia, hyperinsulinemia ({approx}18-fold), glucose intolerance and impairment in the insulin mediated glucose disposal in the Sprague-Dawley rats. Further, long-term S961 treatment (15 day, 10 nM/kg/day) depletes energy storage as evident from decrease in the adiposity and hepatic glycogen content. However, peroxysome-proliferator-activated-receptor-gamma (PPAR{gamma}) agonist pioglitazone significantly (P < 0.001) restored S961 induced hyperglycemia (196.73 {+-} 16.32 vs. 126.37 {+-} 27.07 mg/dl) and glucose intolerance ({approx}78%). Improvement in the hyperglycemia and glucose intolerance by pioglitazone clearly demonstrates that S961 treated rats can be successfully used to screen the novel therapeutic interventions having potential to improve glucose disposal through receptor independent mechanisms. Further, results of the present study reconfirms and provide direct evidence to the crucial role of insulin receptor signaling in the glucose homeostasis and fuel metabolism.

Variation of wave speed determined by the PU-loop with proximity to a reflection site.

Science.gov (United States)

Li, Ye; Borlotti, Alessandra; Parker, Kim H; Khir, Ashraf W

2011-01-01

Wave speed is directly related to arterial distensibility and is widely used by clinicians to assess arterial stiffness. The PU-loop method for determining wave speed is based on the water hammer equation for flow in flexible tubes and artery using the method of characteristics. This technique determines wave speed using simultaneous measurements of pressure and velocity at a single point. The method shows that during the early part of systole, the relationship between pressure and velocity is generally linear, and the initial slope of the PU-loop is proportional to wave speed. In this work, we designed an in-vitro experiment to investigate the effect of proximity to a reflection site on the wave speed determined by the PU-loop through varying the distance between the measurement and reflection sites. Measurements were made in a flexible tube with a reflection site at the distal end formed by joining the tube to another tube with a different diameter and material properties. Six different flexible tubes were used to generate both positive and negative reflection coefficients of different magnitudes. We found that the wave speed determined by the PU-loop did not change when the measurement site was far from the reflection site but did change as the distance to the reflection site decreased. The calculated wave speed increased with positive reflections and decreased with negative reflections. The magnitude of the change in wave speed at a fixed distance from the reflection site increased with increasing the value of the reflection coefficient.

S961, an insulin receptor antagonist causes hyperinsulinemia, insulin-resistance and depletion of energy stores in rats

International Nuclear Information System (INIS)

Vikram, Ajit; Jena, Gopabandhu

2010-01-01

Research highlights: →Insulin receptor antagonist S961 causes hyperglycemia, hyperinsulinemia and insulin resistance in rats. →Peroxysome-proliferator-activated-receptor-gamma agonist pioglitazone improves S961 induced hyperglycemia and glucose intolerance. →Long term treatment with insulin receptor antagonist S961 results in the decreased adiposity and hepatic glycogen content. →Improvement in the hyperglycemia and glucose intolerance by pioglitazone clearly demonstrates that S961 treated rats can be successfully used to screen the novel therapeutic interventions having potential to improve glucose disposal through receptor independent mechanisms. -- Abstract: Impairment in the insulin receptor signaling and insulin mediated effects are the key features of type 2 diabetes. Here we report that S961, a peptide insulin receptor antagonist induces hyperglycemia, hyperinsulinemia (∼18-fold), glucose intolerance and impairment in the insulin mediated glucose disposal in the Sprague-Dawley rats. Further, long-term S961 treatment (15 day, 10 nM/kg/day) depletes energy storage as evident from decrease in the adiposity and hepatic glycogen content. However, peroxysome-proliferator-activated-receptor-gamma (PPARγ) agonist pioglitazone significantly (P < 0.001) restored S961 induced hyperglycemia (196.73 ± 16.32 vs. 126.37 ± 27.07 mg/dl) and glucose intolerance (∼78%). Improvement in the hyperglycemia and glucose intolerance by pioglitazone clearly demonstrates that S961 treated rats can be successfully used to screen the novel therapeutic interventions having potential to improve glucose disposal through receptor independent mechanisms. Further, results of the present study reconfirms and provide direct evidence to the crucial role of insulin receptor signaling in the glucose homeostasis and fuel metabolism.

20 CFR 404.961 - Prehearing and posthearing conferences.

Science.gov (United States)

2010-04-01

... and Decisions Administrative Law Judge Hearing Procedures § 404.961 Prehearing and posthearing conferences. The administrative law judge may decide on his or her own, or at the request of any party to the.... The administrative law judge shall tell the parties of the time, place and purpose of the conference...

RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity.

Science.gov (United States)

Vannier, Jean-Baptiste; Pavicic-Kaltenbrunner, Visnja; Petalcorin, Mark I R; Ding, Hao; Boulton, Simon J

2012-05-11

T loops and telomeric G-quadruplex (G4) DNA structures pose a potential threat to genome stability and must be dismantled to permit efficient telomere replication. Here we implicate the helicase RTEL1 in the removal of telomeric DNA secondary structures, which is essential for preventing telomere fragility and loss. In the absence of RTEL1, T loops are inappropriately resolved by the SLX4 nuclease complex, resulting in loss of the telomere as a circle. Depleting SLX4 or blocking DNA replication abolished telomere circles (TCs) and rescued telomere loss in RTEL1(-/-) cells but failed to suppress telomere fragility. Conversely, stabilization of telomeric G4-DNA or loss of BLM dramatically enhanced telomere fragility in RTEL1-deficient cells but had no impact on TC formation or telomere loss. We propose that RTEL1 performs two distinct functions at telomeres: it disassembles T loops and also counteracts telomeric G4-DNA structures, which together ensure the dynamics and stability of the telomere. Copyright © 2012 Elsevier Inc. All rights reserved.

Use of helicity methods in evaluating loop integrals: a QCD example

International Nuclear Information System (INIS)

Koerner, J.G.; Sieben, P.

1991-01-01

We discuss the use of helicity methods in evaluating loop diagrams by analyzing a specific example: the one-loop concentration to e + e - → qanti qg in massless QCD. By using covariant helicity representations for the spinor and vector wave functins we obtain the helicity amplitudes directly from the Feynman loop diagrams by covariant contraction. The necessary loop integrations are considerably simplified since one encounters only scalar loop integrals after contraction. We discuss crossing relations that allow one to obtain the corresponding one-loop helicity amplitudes for the crossed processes as e.g. qanti q → (W, Z, γ * ) + g including the real photon cases. As we treat the spin degrees of freedom in four dimensions and only continue momenta to n dimensions (dimensional reduction scheme) we explicate how our results are related to the usual dimensional regularization results. (orig.)

Bela Lugosi´s not dead: o discurso e a representação de góticos no site de Rede Social Facebbok

OpenAIRE

Borges, Camila Dias

2014-01-01

O escopo deste estudo é o de investigar de que forma acontece a representação e a manifestação do discurso da subcultura gótica em perfis no site de rede social Facebook. No decorrer da história, o termo gótico esteve atrelado ao específico entrecruzamento de significações discursivas, sendo assim, buscaremos resgatar suas principais contribuições na literatura, no cinema e na música e suas implicações na moda e no estilo visual dos adeptos da subcultura gótica. Para a composiç...

Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids.

Directory of Open Access Journals (Sweden)

Gonzalo E Yévenes

Full Text Available Glycine receptors (GlyRs are transmitter-gated anion channels of the Cys-loop superfamily which mediate synaptic inhibition at spinal and selected supraspinal sites. Although they serve pivotal functions in motor control and sensory processing, they have yet to be exploited as drug targets partly because of hitherto limited possibilities for allosteric control. Endocannabinoids (ECs have recently been characterized as direct allosteric GlyR modulators, but the underlying molecular sites have remained unknown. Here, we show that chemically neutral ECs (e.g. anandamide, AEA are positive modulators of α(1, α(2 and α(3 GlyRs, whereas acidic ECs (e.g. N-arachidonoyl-glycine; NA-Gly potentiate α(1 GlyRs but inhibit α(2 and α(3. This subunit-specificity allowed us to identify the underlying molecular sites through analysis of chimeric and mutant receptors. We found that alanine 52 in extracellular loop 2, glycine 254 in transmembrane (TM region 2 and intracellular lysine 385 determine the positive modulation of α(1 GlyRs by NA-Gly. Successive substitution of non-conserved extracellular and TM residues in α(2 converted NA-Gly-mediated inhibition into potentiation. Conversely, mutation of the conserved lysine within the intracellular loop between TM3 and TM4 attenuated NA-Gly-mediated potentiation of α(1 GlyRs, without affecting inhibition of α(2 and α(3. Notably, this mutation reduced modulation by AEA of all three GlyRs. These results define molecular sites for allosteric control of GlyRs by ECs and reveal an unrecognized function for the TM3-4 intracellular loop in the allosteric modulation of Cys-loop ion channels. The identification of these sites may help to understand the physiological role of this modulation and facilitate the development of novel therapeutic approaches to diseases such as spasticity, startle disease and possibly chronic pain.

Description of the two-loop RELAP5 model of the L-Reactor at the Savannah River Site

International Nuclear Information System (INIS)

Cozzuol, J.M.; Davis, C.B.

1989-12-01

A two-loop RELAP5 input model of the L-Reactor at the Savannah River Site (SRS) was developed to support thermal-hydraulic analysis of SRS reactors. The model was developed to economically evaluate potential design changes. The primary simplifications in the model were in the number of loops and the detail in the moderator tank. The six loops in the reactor were modeled with two loops, one representing a single loop and the other representing five combined loops. The model has undergone a quality assurance review. This report describes the two-loop model, its limitations, and quality assurance. 29 refs., 18 figs., 10 tabs

Astrocytic autoantibody of neuromyelitis optica (NMO-IgG) binds to aquaporin-4 extracellular loops, monomers, tetramers and high order arrays

Science.gov (United States)

Iorio, Raffaele; Fryer, James P.; Hinson, Shannon R.; Fallier-Becker, Petra; Wolburg, Hartwig; Pittock, Sean J.; Lennon, Vanda A.

2012-01-01

The principal central nervous system (CNS) water channel, aquaporin-4 (AQP4), is confined to astrocytic and ependymal membranes and is the target of a pathogenic autoantibody, neuromyelitis optica (NMO)-IgG. This disease-specific autoantibody unifies a spectrum of relapsing CNS autoimmune inflammatory disorders of which NMO exemplifies the classic phenotype. Multiple sclerosis and other immune-mediated demyelinating disorders of the CNS lack a distinctive biomarker. Two AQP4 isoforms, M1 and M23, exist as homotetrameric and heterotetrameric intramembranous particles (IMPs). Orthogonal arrays of predominantly M23 particles (OAPs) are an ultrastructural characteristic of astrocytic membranes. We used high-titered serum from 32 AQP4-IgG-seropositive patients and 85 controls to investigate the nature and molecular location of AQP4 epitopes that bind NMO-IgG, and the influence of supramolecular structure. NMO-IgG bound to denatured AQP4 monomers (68% of cases), to native tetramers and high order arrays (90% of cases), and to AQP4 in live cell membranes (100% of cases). Disease-specific epitopes reside in extracellular loop C more than in loops A or E. IgG binding to intracellular epitopes lacks disease specificity. These observations predict greater disease specificity and sensitivity for tissue-based and cell-based serological assays employing “native” AQP4 than assays employing denatured AQP4 and fragments. NMO-IgG binds most avidly to plasma membrane surface AQP4 epitopes formed by loop interactions within tetramers and by intermolecular interactions within high order structures. The relative abundance and localization of AQP4 high order arrays in distinct CNS regions may explain the variability in clinical phenotype of NMO spectrum disorders. PMID:22906356

Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

DEFF Research Database (Denmark)

Mikkelsen, J G; Lund, Anders Henrik; Duch, M

2000-01-01

synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

In pile helium loop ''COMEDIE''

International Nuclear Information System (INIS)

Abassin, J.J.; Blanchard, R.J.; Gentil, J.

1981-01-01

The SR1 test in the COMEDIE loop has permitted to demonstrate particularly the device operation reliability with a fuel loading. The post-irradiation examinations have pointed out the good filter efficiency and have enabled to determine the deposition profiles either for the activation products (e.g.: 51 Cr, 60 Co) or for the fission products (e.g.: sup(110m)Ag, 131 I, 134 Cs, 137 Cs). (author)

The Triticum Mosaic Virus 5' Leader Binds to Both eIF4G and eIFiso4G for Translation.

Directory of Open Access Journals (Sweden)

Robyn Roberts

Full Text Available We recently identified a remarkably strong (739 nt-long IRES-like element in the 5' untranslated region (UTR of Triticum mosaic virus (TriMV, Potyviridae. Here, we define the components of the cap-binding translation initiation complex that are required for TriMV translation. Using bio-layer interferometry and affinity capture of the native translation apparatus, we reveal that the viral translation element has a ten-fold greater affinity for the large subunit eIF4G/eIFiso4G than to the cap binding protein eIF4E/eIFiso4E. This data supports a translation mechanism that is largely dependent on eIF4G and its isoform. The binding of both scaffold isoforms requires an eight base-pair-long hairpin structure located 270 nucleotides upstream of the translation initiation site, which we have previously shown to be crucial for IRES activity. Despite a weak binding affinity to the mRNA, eIFiso4G alone or in combination with eIFiso4E supports TriMV translation in a cap-binding factor-depleted wheat germ extract. Notably, TriMV 5' UTR-mediated translation is dependent upon eIF4A helicase activity, as the addition of the eIF4A inhibitor hippuristanol inhibits 5' UTR-mediated translation. This inhibition is reversible with the addition of recombinant wheat eIF4A. These results and previous observations demonstrate a key role of eIF4G and eIF4A in this unique mechanism of cap-independent-translation. This work provides new insights into the lesser studied translation mechanisms of plant virus-mediated internal translation initiation.

One-loop corrections to the process e+e-→tt including hard bremsstrahlung

International Nuclear Information System (INIS)

Fleischer, J.; Riemann, T.; Werthenbach, A.; Leike, A.

2002-03-01

Radiative corrections to the process e + e - → t anti t are calculated in one-loop approximation of the Standard Model. There exist results from several groups. This talk provides further comparisons of the complete electroweak contributions, including hard bremsstrahlung. The excellent final agreement of the different groups allows to continue by working on a code for an event generator for TESLA and an extension to e + e - → 6 fermions. (orig.)

Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation.

Science.gov (United States)

Peeters, M C; van Westen, G J P; Li, Q; IJzerman, A P

2011-01-01

G protein-coupled receptors (GPCRs) are the major drug target of medicines on the market today. Therefore, much research is and has been devoted to the elucidation of the function and three-dimensional structure of this large family of membrane proteins, which includes multiple conserved transmembrane domains connected by intra- and extracellular loops. In the last few years, the less conserved extracellular loops have garnered increasing interest, particularly after the publication of several GPCR crystal structures that clearly show the extracellular loops to be involved in ligand binding. This review will summarize the recent progress made in the clarification of the ligand binding and activation mechanism of class-A GPCRs and the role of extracellular loops in this process. Copyright © 2010 Elsevier Ltd. All rights reserved.

N-point g-loop vertex for free bosonic theory with vacuum charge Q

International Nuclear Information System (INIS)

Di Vecchia, P.; Pezzella, F.; Frau, M.; Hornfeck, K.

1988-12-01

Starting from the N-Point Vertex on the sphere and using the sewing procedure we construct the N-Point g-Loop Vertex for a free bosonic theory with vacuum charge Q. We then show that, when this vertex is saturated with N highest weight states, it gives their correlation function on an arbitrary Riemann surface of genus g. We also extend our formalism to the case of a free scalar field compactified on a circle, which is related to the Coulomb gas description of minimal models. (orig.)

A 9.61-W, b-cut Tm,Ho:YAP laser in Q-switched mode operation

Science.gov (United States)

Li, Guoxing; Yang, Xining; Zhang, Ziqiu; Zhang, Hongda; Zhang, Liang

2018-02-01

A high energy of b-cut Tm, Ho:YAlO3 laser is reported in the paper. The laser operated in acousto-optical Qswitched mode at 2.12 μm. The output average power of 9.61 W was achieved at the pulse repetition frequency of 10 kHz ,and the power of 11.6 W was acquired in continuous wave mode. Moreover, the energy per pulse of 0.961 mJ in 64.4 ns was acquired at 10 kHz with a 14.92-kW peak power.

R-loops: targets for nuclease cleavage and repeat instability.

Science.gov (United States)

Freudenreich, Catherine H

2018-01-11

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

Two-Loop Effective Theory Analysis of π (K)→eνe[γ] Branching Ratios

International Nuclear Information System (INIS)

Cirigliano, Vincenzo; Rosell, Ignasi

2007-01-01

We study the ratios R e/μ (P) ≡Γ(P→eν e [γ])/Γ(P→μν μ [γ]) (P=π, K) in Chiral Perturbation Theory to order e 2 p 4 . We complement the two-loop effective theory results with a matching calculation of the counterterm, finding R e/μ (π) =(1.2352±0.0001)x10 -4 and R e/μ (K) =(2.477±0.001)x10 -5

Disease-associated extracellular loop mutations in the adhesion G protein-coupled receptor G1 (ADGRG1; GPR56) differentially regulate downstream signaling.

Science.gov (United States)

Kishore, Ayush; Hall, Randy A

2017-06-09

Mutations to the adhesion G protein-coupled receptor ADGRG1 (G1; also known as GPR56) underlie the neurological disorder bilateral frontoparietal polymicrogyria. Disease-associated mutations in G1 studied to date are believed to induce complete loss of receptor function through disruption of either receptor trafficking or signaling activity. Given that N-terminal truncation of G1 and other adhesion G protein-coupled receptors has been shown to significantly increase the receptors' constitutive signaling, we examined two different bilateral frontoparietal polymicrogyria-inducing extracellular loop mutations (R565W and L640R) in the context of both full-length and N-terminally truncated (ΔNT) G1. Interestingly, we found that these mutations reduced surface expression of full-length G1 but not G1-ΔNT in HEK-293 cells. Moreover, the mutations ablated receptor-mediated activation of serum response factor luciferase, a classic measure of Gα 12/13 -mediated signaling, but had no effect on G1-mediated signaling to nuclear factor of activated T cells (NFAT) luciferase. Given these differential signaling results, we sought to further elucidate the pathway by which G1 can activate NFAT luciferase. We found no evidence that ΔNT activation of NFAT is dependent on Gα q/11 -mediated or β-arrestin-mediated signaling but rather involves liberation of Gβγ subunits and activation of calcium channels. These findings reveal that disease-associated mutations to the extracellular loops of G1 differentially alter receptor trafficking, depending on the presence of the N terminus, and differentially alter signaling to distinct downstream pathways. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

R-loops and initiation of DNA replication in human cells: a missing link?

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Rodrigo eLombraña

2015-04-01

Full Text Available The unanticipated widespread occurrence of stable hybrid DNA/RNA structures (R-loops in human cells and the increasing evidence of their involvement in several human malignancies have invigorated the research on R-loop biology in recent years. Here we propose that physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. Quite likely, this occurs by the strand-displacement reaction activating the formation of G-quadruplex structures that target the Origin Recognition Complex (ORC in the single-stranded conformation. In agreement with this, we found that R-loops co-localize with the ORC within the same CpG island region in a significant fraction of these efficient replication origins, precisely at the position displaying the highest density of G4 motifs. This scenario builds on the connection between transcription and replication in human cells and suggests that R-loop dysregulation at CpG island promoter-origins might contribute to the phenotype of DNA replication abnormalities and loss of genome integrity detected in cancer cells.

Identification of a Novel EF-Loop in the N-terminus of TRPM2 Channel Involved in Calcium Sensitivity

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Yuhuan Luo

2018-06-01

Full Text Available As an oxidative stress sensor, transient receptor potential melastatin 2 (TRPM2 channel is involved in many physiological and pathological processes including warmth sensing, ischemia injury, inflammatory diseases and diabetes. Intracellular calcium is critical for TRPM2 channel activation and the IQ-like motif in the N-terminus has been shown to be important by mediating calmodulin binding. Sequence analysis predicted two potential EF-loops in the N-terminus of TRPM2. Site-directed mutagenesis combining with functional assay showed that substitution with alanine of several residues, most of which are conserved in the typical EF-loop, including D267, D278, D288, and E298 dramatically reduced TRPM2 channel currents. By further changing the charges or side chain length of these conserved residues, our results indicate that the negative charge of D267 and the side chain length of D278 are critical for calcium-induced TRPM2 channel activation. G272I mutation also dramatically reduced the channel currents, suggesting that this site is critical for calcium-induced TRPM2 channel activation. Furthermore, D267A mutant dramatically reduced the currents induced by calcium alone compared with that by ADPR, indicating that D267 residue in D267–D278 motif is the most important site for calcium sensitivity of TRPM2. In addition, inside-out recordings showed that mutations at D267, G272, D278, and E298 had no effect on single-channel conductance. Taken together, our data indicate that D267–D278 motif in the N-terminus as a novel EF-loop is critical for calcium-induced TRPM2 channel activation.

Molecular landscape of the interaction between the urease accessory proteins UreE and UreG.

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Merloni, Anna; Dobrovolska, Olena; Zambelli, Barbara; Agostini, Federico; Bazzani, Micaela; Musiani, Francesco; Ciurli, Stefano

2014-09-01

Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9μM; Kd2=1.7±0.3μM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements.

Science.gov (United States)

Bretschneider, Nancy; Kangaspeska, Sara; Seifert, Martin; Reid, George; Gannon, Frank; Denger, Stefanie

2008-08-01

Estrogen receptor alpha (ERalpha) is a ligand dependent transcription factor that regulates the expression of target genes through interacting with cis-acting estrogen response elements (EREs). However, only a minority of ERalpha binding sites are located within the proximal promoter regions of responsive genes. Here we report the characterization of an ERE located 9kbp upstream of the TSS of the cathepsin D gene (CTSD) that up-regulates CTSD expression upon estrogen stimulation in MCF-7 cells. Using ChIP, we show recruitment of ERalpha and phosphorylated PolII at the CTSD distal enhancer region. Moreover, we determine the kinetics of transient CpG methylation on the promoter region of CTSD and for the first time, at a distal enhancer element. We show that ERalpha is crucial for long-distance regulation of CTSD expression involving a looping mechanism.

(g-2){sub μ} at four loops in QED

Energy Technology Data Exchange (ETDEWEB)

Marquard, Peter [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Smirnov, Alexander V. [Moscow State Univ. (Russian Federation). Research Computing Center; Smirnov, Vladimir A. [Moscow State Univ. (Russian Federation). Skobeltsyn Inst. of Nuclear Physics; Steinhauser, Matthias; Wellmann, David [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Theoretische Teilchenphysik

2017-08-15

We review the four-loop QED corrections to the anomalous magnetic moment of the muon. The fermionic contributions with closed electron and tau contributions are discussed. Furthermore, we report on a new independent calculation of the universal four-loop contribution and compare with existing results.

New polymorphic mtDNA restriction site in the 12S rRNA gene detected in Tunisian patients with non-syndromic hearing loss

International Nuclear Information System (INIS)

Mkaouar-Rebai, Emna; Tlili, Abdelaziz; Masmoudi, Saber; Charfeddine, Ilhem; Fakhfakh, Faiza

2008-01-01

The 12S rRNA gene was shown to be a hot spot for aminoglycoside-induced and non-syndromic hearing loss since several deafness-associated mtDNA mutations were identified in this gene. Among them, we distinguished the A1555G, the C1494T and the T1095C mutations and C-insertion or deletion at position 961. One hundred Tunisian patients with non-syndromic hearing loss and 100 hearing individuals were analysed in this study. A PCR-RFLP analysis with HaeIII restriction enzyme showed the presence of the A1555G mutation in the 12S rRNA gene in only one out of the 100 patients. In addition, PCR-RFLP and radioactive PCR revealed the presence of a new HaeIII polymorphic restriction site in the same gene of 12S rRNA site in 4 patients with non-syndromic hearing loss. UVIDOC-008-XD analyses showed the presence of this new polymorphic restriction site with a variable heteroplasmic rates at position +1517 of the human mitochondrial genome. On the other hand, direct sequencing of the entire mitochondrial 12S rRNA gene in the 100 patients and in 100 hearing individuals revealed the presence of the A750G and A1438G polymorphisms and the absence of the C1494T, T1095C and 961insC mutations in all the tested individuals. Sequencing of the whole mitochondrial genome in the 4 patients showing the new HaeIII polymorphic restriction site revealed only the presence of the A8860G transition in the MT-ATP6 gene and the A4769G polymorphism in the ND2 gene

Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities.

Science.gov (United States)

Attanayake, Gayanthi; Walter, Tyler; Walker, Kevin D

2018-05-30

Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.

CHARACTERIZING THE COOL KOIs. III. KOI 961: A SMALL STAR WITH LARGE PROPER MOTION AND THREE SMALL PLANETS

International Nuclear Information System (INIS)

Muirhead, Philip S.; Johnson, John Asher; Morton, Timothy D.; Pineda, John Sebastian; Bottom, Michael; Crepp, Justin R.; Kirby, Evan N.; Apps, Kevin; Carter, Joshua A.; Fabrycky, Daniel C.; Hamren, Katherine; Rojas-Ayala, Bárbara; Schlawin, Everett; Covey, Kevin R.; Stassun, Keivan G.; Pepper, Joshua; Hebb, Leslie; Howard, Andrew W.; Isaacson, Howard T.; Marcy, Geoffrey W.

2012-01-01

We characterize the star KOI 961, an M dwarf with transit signals indicative of three short-period exoplanets discovered by the Kepler mission. We proceed by comparing KOI 961 to Barnard's Star, a nearby, well-characterized mid-M dwarf. We compare colors, optical and near-infrared spectra, and find remarkable agreement between the two, implying similar effective temperatures and metallicities. Both are metal-poor compared to the Solar neighborhood, have low projected rotational velocity, high absolute radial velocity, large proper motion, and no quiescent Hα emission—all of which are consistent with being old M dwarfs. We combine empirical measurements of Barnard's Star and expectations from evolutionary isochrones to estimate KOI 961's mass (0.13 ± 0.05 M ☉ ), radius (0.17 ± 0.04 R ☉ ), and luminosity (2.40 × 10 –3.0±0.3 L ☉ ). We calculate KOI 961's distance (38.7 ± 6.3 pc) and space motions, which, like Barnard's Star, are consistent with a high scale-height population in the Milky Way. We perform an independent multi-transit fit to the public Kepler light curve and significantly revise the transit parameters for the three planets. We calculate the false-positive probability for each planet candidate, and find a less than 1% chance that any one of the transiting signals is due to a background or hierarchical eclipsing binary, validating the planetary nature of the transits. The best-fitting radii for all three planets are less than 1 R ⊕ , with KOI 961.03 being Mars-sized (R P = 0.57 ± 0.18 R ⊕ ), and they represent some of the smallest exoplanets detected to date.

Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

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Yu Zhang

Full Text Available Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL from Geobacillus kaustophilus HTA426 (GkaP exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Science.gov (United States)

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

PHOTOSPHERIC PROPERTIES OF WARM EUV LOOPS AND HOT X-RAY LOOPS

Energy Technology Data Exchange (ETDEWEB)

Kano, R. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ueda, K. [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Tsuneta, S., E-mail: ryouhei.kano@nao.ac.jp [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo, Sagamihara, Kanagawa 252-5210 (Japan)

2014-02-20

We investigate the photospheric properties (vector magnetic fields and horizontal velocity) of a well-developed active region, NOAA AR 10978, using the Hinode Solar Optical Telescope specifically to determine what gives rise to the temperature difference between ''warm loops'' (1-2 MK), which are coronal loops observed in EUV wavelengths, and ''hot loops'' (>3 MK), coronal loops observed in X-rays. We found that outside sunspots, the magnetic filling factor in the solar network varies with location and is anti-correlated with the horizontal random velocity. If we accept that the observed magnetic features consist of unresolved magnetic flux tubes, this anti-correlation can be explained by the ensemble average of flux-tube motion driven by small-scale random flows. The observed data are consistent with a flux tube width of ∼77 km and horizontal flow at ∼2.6 km s{sup –1} with a spatial scale of ∼120 km. We also found that outside sunspots, there is no significant difference between warm and hot loops either in the magnetic properties (except for the inclination) or in the horizontal random velocity at their footpoints, which are identified with the Hinode X-Ray Telescope and the Transition Region and Coronal Explorer. The energy flux injected into the coronal loops by the observed photospheric motion of the magnetic fields is estimated to be 2 × 10{sup 6} erg s{sup –1} cm{sup –2}, which is the same for both warm and hot loops. This suggests that coronal properties (e.g., loop length) play a more important role in giving rise to temperature differences of active-region coronal loops than photospheric parameters.

Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription.

Science.gov (United States)

Zheng, Ke-Wei; He, Yi-de; Liu, Hong-He; Li, Xin-Min; Hao, Yu-Hua; Tan, Zheng

2017-10-20

Transcription induces formation of intramolecular G-quadruplex structures at the upstream region of a DNA duplex by an upward transmission of negative supercoiling through the DNA. Currently the regulation of such G-quadruplex formation remains unclear. Using plasmid as a model, we demonstrate that while it is the dynamic negative supercoiling generated by a moving RNA polymerase that triggers a formation of a G-quadruplex, the constitutional superhelicity determines the potential and range of the formation of a G-quadruplex by constraining the propagation of the negative supercoiling. G-quadruplex formation is maximal in negatively supercoiled and nearly abolished in relaxed plasmids while being moderate in nicked and linear ones. The formation of a G-quadruplex strongly correlates with the presence of an R-loop. Preventing R-loop formation virtually abolished G-quadruplex formation even in the negatively supercoiled plasmid. Enzymatic action and protein binding that manipulate supercoiling or its propagation all impact the formation of G-quadruplexes. Because chromosomes and plasmids in cells in their natural form are maintained in a supercoiled state, our findings reveal a physical basis that justifies the formation and regulation of G-quadruplexes in vivo. The structural features involved in G-quadruplex formation may all serve as potential targets in clinical and therapeutic applications.

G1/S-regulated E2F-containing protein complexes bind to the mouse thymidine kinase gene promoter

DEFF Research Database (Denmark)

Dou, Q P; Zhao, S; Levin, A H

1994-01-01

report that MT2 includes an E2F-like binding site (GTTCGCGGGCAAA), as shown by the following evidence. (i) MT2 bound specifically to an affinity-purified fusion human E2F protein. (ii) Both MT2 and an authentic E2F site (TTTCGCGCGCTTT) bound specifically to similar or identical nuclear protein complexes...... complexes were also investigated. Studies using specific antibodies revealed that p107, a retinoblastoma-like protein, was present in both E2F-G0/G1 and E2F.S, whereas cyclin E.cyclin A.cdk2 were only present in E2F.S complex(es). These data suggest that removal of the p107-containing E2F.G0/G1 complex...

SU-E-J-85: Leave-One-Out Perturbation (LOOP) Fitting Algorithm for Absolute Dose Film Calibration

International Nuclear Information System (INIS)

Chu, A; Ahmad, M; Chen, Z; Nath, R; Feng, W

2014-01-01

Purpose: To introduce an outliers-recognition fitting routine for film dosimetry. It cannot only be flexible with any linear and non-linear regression but also can provide information for the minimal number of sampling points, critical sampling distributions and evaluating analytical functions for absolute film-dose calibration. Methods: The technique, leave-one-out (LOO) cross validation, is often used for statistical analyses on model performance. We used LOO analyses with perturbed bootstrap fitting called leave-one-out perturbation (LOOP) for film-dose calibration . Given a threshold, the LOO process detects unfit points (“outliers”) compared to other cohorts, and a bootstrap fitting process follows to seek any possibilities of using perturbations for further improvement. After that outliers were reconfirmed by a traditional t-test statistics and eliminated, then another LOOP feedback resulted in the final. An over-sampled film-dose- calibration dataset was collected as a reference (dose range: 0-800cGy), and various simulated conditions for outliers and sampling distributions were derived from the reference. Comparisons over the various conditions were made, and the performance of fitting functions, polynomial and rational functions, were evaluated. Results: (1) LOOP can prove its sensitive outlier-recognition by its statistical correlation to an exceptional better goodness-of-fit as outliers being left-out. (2) With sufficient statistical information, the LOOP can correct outliers under some low-sampling conditions that other “robust fits”, e.g. Least Absolute Residuals, cannot. (3) Complete cross-validated analyses of LOOP indicate that the function of rational type demonstrates a much superior performance compared to the polynomial. Even with 5 data points including one outlier, using LOOP with rational function can restore more than a 95% value back to its reference values, while the polynomial fitting completely failed under the same conditions

SU-E-J-85: Leave-One-Out Perturbation (LOOP) Fitting Algorithm for Absolute Dose Film Calibration

Energy Technology Data Exchange (ETDEWEB)

Chu, A; Ahmad, M; Chen, Z; Nath, R [Yale New Haven Hospital/School of Medicine Yale University, New Haven, CT (United States); Feng, W [New York Presbyterian Hospital, Tenafly, NJ (United States)

2014-06-01

Purpose: To introduce an outliers-recognition fitting routine for film dosimetry. It cannot only be flexible with any linear and non-linear regression but also can provide information for the minimal number of sampling points, critical sampling distributions and evaluating analytical functions for absolute film-dose calibration. Methods: The technique, leave-one-out (LOO) cross validation, is often used for statistical analyses on model performance. We used LOO analyses with perturbed bootstrap fitting called leave-one-out perturbation (LOOP) for film-dose calibration . Given a threshold, the LOO process detects unfit points (“outliers”) compared to other cohorts, and a bootstrap fitting process follows to seek any possibilities of using perturbations for further improvement. After that outliers were reconfirmed by a traditional t-test statistics and eliminated, then another LOOP feedback resulted in the final. An over-sampled film-dose- calibration dataset was collected as a reference (dose range: 0-800cGy), and various simulated conditions for outliers and sampling distributions were derived from the reference. Comparisons over the various conditions were made, and the performance of fitting functions, polynomial and rational functions, were evaluated. Results: (1) LOOP can prove its sensitive outlier-recognition by its statistical correlation to an exceptional better goodness-of-fit as outliers being left-out. (2) With sufficient statistical information, the LOOP can correct outliers under some low-sampling conditions that other “robust fits”, e.g. Least Absolute Residuals, cannot. (3) Complete cross-validated analyses of LOOP indicate that the function of rational type demonstrates a much superior performance compared to the polynomial. Even with 5 data points including one outlier, using LOOP with rational function can restore more than a 95% value back to its reference values, while the polynomial fitting completely failed under the same conditions

A bag model calculation of the electroweak s → dγ loop

International Nuclear Information System (INIS)

Eeg, J.O.; Ruud, J.Aa.

1990-10-01

The CP-conservering electroweak transitions s → dγ have been considered. In order to include confinement effects below the charm scale, the loop calculations within the bag model were performed. According to the calculations, confinement effects are rather important and give amplitudes three orders of magnitude larger than those obtained from the free quark loop, which is ∼eG F m c 2 /M W 2 . Moreover, the amplitude is of the same order of magnitude as the perturbative two-loop amplitude ∼eG F α s ln(m c /μ). For the decay mode Ω - → γΞ - , a branching ratio 4.4 x 10 -5 was obtained. Other radiative decays of strange baryons are known to be dominated by pole diagrams. 14 refs., 1 fig

Thermodynamic analysis of in situ gasification-chemical looping combustion (iG-CLC) of Indian coal.

Science.gov (United States)

Suresh, P V; Menon, Kavitha G; Prakash, K S; Prudhvi, S; Anudeep, A

2016-10-01

Chemical looping combustion (CLC) is an inherent CO 2 capture technology. It is gaining much interest in recent years mainly because of its potential in addressing climate change problems associated with CO 2 emissions from power plants. A typical chemical looping combustion unit consists of two reactors-fuel reactor, where oxidation of fuel occurs with the help of oxygen available in the form of metal oxides and, air reactor, where the reduced metal oxides are regenerated by the inflow of air. These oxides are then sent back to the fuel reactor and the cycle continues. The product gas from the fuel reactor contains a concentrated stream of CO 2 which can be readily stored in various forms or used for any other applications. This unique feature of inherent CO 2 capture makes the technology more promising to combat the global climate changes. Various types of CLC units have been discussed in literature depending on the type of fuel burnt. For solid fuel combustion three main varieties of CLC units exist namely: syngas CLC, in situ gasification-CLC (iG-CLC) and chemical looping with oxygen uncoupling (CLOU). In this paper, theoretical studies on the iG-CLC unit burning Indian coal are presented. Gibbs free energy minimization technique is employed to determine the composition of flue gas and oxygen carrier of an iG-CLC unit using Fe 2 O 3 , CuO, and mixed carrier-Fe 2 O 3 and CuO as oxygen carriers. The effect of temperature, suitability of oxygen carriers, and oxygen carrier circulation rate on the performance of a CLC unit for Indian coal are studied and presented. These results are analyzed in order to foresee the operating conditions at which economic and smooth operation of the unit is expected.

G-quadruplex recognition activities of E. Coli MutS

Directory of Open Access Journals (Sweden)

Ehrat Edward A

2012-07-01

Full Text Available Abstract Background Guanine quadruplex (G4 DNA is a four-stranded structure that contributes to genome instability and site-specific recombination. G4 DNA folds from sequences containing tandemly repetitive guanines, sequence motifs that are found throughout prokaryote and eukaryote genomes. While some cellular activities have been identified with binding or processing G4 DNA, the factors and pathways governing G4 DNA metabolism are largely undefined. Highly conserved mismatch repair factors have emerged as potential G4-responding complexes because, in addition to initiating heteroduplex correction, the human homologs bind non-B form DNA with high affinity. Moreover, the MutS homologs across species have the capacity to recognize a diverse range of DNA pairing variations and damage, suggesting a conserved ability to bind non-B form DNA. Results Here, we asked if E. coli MutS and a heteroduplex recognition mutant, MutS F36A, were capable of recognizing and responding to G4 DNA structures. We find by mobility shift assay that E. coli MutS binds to G4 DNA with high affinity better than binding to G-T heteroduplexes. In the same assay, MutS F36A failed to recognize G-T mismatched oligonucleotides, as expected, but retained an ability to bind to G4 DNA. Association with G4 DNA by MutS is not likely to activate the mismatch repair pathway because nucleotide binding did not promote release of MutS or MutS F36A from G4 DNA as it does for heteroduplexes. G4 recognition activities occur under physiological conditions, and we find that M13 phage harboring G4-capable DNA poorly infected a MutS deficient strain of E. coli compared to M13mp18, suggesting functional roles for mismatch repair factors in the cellular response to unstable genomic elements. Conclusions Taken together, our findings demonstrate that E. coli MutS has a binding activity specific for non-B form G4 DNA, but such binding appears independent of canonical heteroduplex repair activation.

Chemical-Looping Combustion and Gasification of Coals and Oxygen Carrier Development: A Brief Review

Directory of Open Access Journals (Sweden)

Ping Wang

2015-09-01

Full Text Available Chemical-looping technology is one of the promising CO2 capture technologies. It generates a CO2 enriched flue gas, which will greatly benefit CO2 capture, utilization or sequestration. Both chemical-looping combustion (CLC and chemical-looping gasification (CLG have the potential to be used to generate power, chemicals, and liquid fuels. Chemical-looping is an oxygen transporting process using oxygen carriers. Recently, attention has focused on solid fuels such as coal. Coal chemical-looping reactions are more complicated than gaseous fuels due to coal properties (like mineral matter and the complex reaction pathways involving solid fuels. The mineral matter/ash and sulfur in coal may affect the activity of oxygen carriers. Oxygen carriers are the key issue in chemical-looping processes. Thermogravimetric analysis (TGA has been widely used for the development of oxygen carriers (e.g., oxide reactivity. Two proposed processes for the CLC of solid fuels are in-situ Gasification Chemical-Looping Combustion (iG-CLC and Chemical-Looping with Oxygen Uncoupling (CLOU. The objectives of this review are to discuss various chemical-looping processes with coal, summarize TGA applications in oxygen carrier development, and outline the major challenges associated with coal chemical-looping in iG-CLC and CLOU.

Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro.

Science.gov (United States)

Jing, N; Marchand, C; Liu, J; Mitra, R; Hogan, M E; Pommier, Y

2000-07-14

The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.

Charged Higgs Boson production at e{sup +}e{sup -} colliders in the complex MSSM: a full one-loop analysis

Energy Technology Data Exchange (ETDEWEB)

Heinemeyer, S. [Campus of International Excellence UAM+CSIC, Madrid (Spain); Universidad Autonoma de Madrid, Instituto de Fisica Teorica (UAM/CSIC), Madrid (Spain); Instituto de Fisica de Cantabria (CSIC-UC), Santander (Spain); Schappacher, C. [Karlsruhe Institute of Technology, Institut fuer Theoretische Physik, Karlsruhe (Germany)

2016-10-15

For the search for additional Higgs bosons in the Minimal Supersymmetric Standard Model (MSSM) as well as for future precision analyses in the Higgs sector precise knowledge of their production properties is mandatory. We evaluate the cross sections for the charged Higgs boson production at e{sup +}e{sup -} colliders in the MSSM with complex parameters (cMSSM). The evaluation is based on a full one-loop calculation of the production mechanism e{sup +}e{sup -} → H{sup +}H{sup -} and e{sup +}e{sup -} → H{sup ±}W{sup -+}, including soft and hard QED radiation. The dependence of the Higgs boson production cross sections on the relevant cMSSM parameters is analyzed numerically. We find sizable contributions to many cross sections. They are, depending on the production channel, roughly of 5-10 % of the tree-level results, but can go up to 20 % or higher. The full one-loop contributions are important for a future linear e{sup +}e{sup -} collider such as the ILC or CLIC. (orig.)

Field campaign LINEX 96/1 - possibilities of water vapor observation in the free atmosphere

Energy Technology Data Exchange (ETDEWEB)

Steinhagen, H.; Dier, H.; Engelbart, D.; Goersdorf, U.; Lehmann, V.; Leiterer, U.; Neisser, J. [Deutscher Wetterdienst, Lindenberg (Germany). Meteorologisches Observatorium; Bakan, S. [Hamburg Univ. (Germany). Meteorologisches Inst.; Boesenberg, J.; Jansen, F.; Wulfmeyer, V. [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); Fischer, J. [Freie Univ. Berlin (Germany). Inst. fuer Weltraumwissenschaften; Gendt, G. [GeoForschungsZentrum Potsdam (Germany); Gueldner, J. [Deutscher Wetterdienst, Potsdam (Germany). Meteorologisches Observatorium

1998-12-01

LINEX 96/1 was a field experiment to assess information content, accuracy, and availability for different remote sensing techniques measuring water vapor. An important goal of LINEX 96/1 was the test of a new differential absorption lidar (DIAL) developed by the MPI fuer meteorologie Hamburg. Comparisons of DIAL with rawinsonde and tethersonde measurements showed an excellent accuracy of the DIAL method in the determination of water vapor with high vertical and temporal resolution. The operation of the microwave radiometer WVR-1100 showed a high availability of water vapor and liquid water column content measurements except during rain. Microwave radiometers are reliable systems to measure the precipitable water vapor and liquid water content under unattended operational conditions with high accuracy and temporal resolution. Measurements of the water vapor column content by ground-based GPS receivers proved highly reliable. Comparisons with corresponding values of the microwave radiometer showed a bias less than 0.6 mm and a standard deviation less than 0.9 mm. The main problem of an operational use of this new information is that the evaluated data are not available in real-time because, at present, the data have to be postprocessed in a ground control center. During LINEX 96/1, possibilities for estimation of water vapor column content from sun and star photometer measurements were also demonstrated. The comparison of the precipitable water vapor content measurements of sun and star photometers, microwave radiometer, and rawinsondes RS 80 showed a good agreement. Unfortunately, the use of optical methods like sun and star photometers is restricted by cloudy conditions. 28 refs.

The fusion loops and membrane proximal region of Epstein-Barr virus glycoprotein B (gB) can function in the context of herpes simplex virus 1 gB when substituted individually but not in combination.

Science.gov (United States)

Zago, Anna; Connolly, Sarah A; Spear, Patricia G; Longnecker, Richard

2013-01-01

Among the herpesvirus glycoprotein B (gB) fusion proteins, the hydrophobic content of fusion loops and membrane proximal regions (MPRs) are inversely correlated with each other. We examined the functional importance of the hydrophobicity of these regions by replacing them in herpes simplex virus type 1 gB with corresponding regions from Epstein-Barr virus gB. We show that fusion activity is dependent on the structural context in which the specific loops and MPR sequences exist, rather than a simple hydrophobic relationship. Copyright © 2012 Elsevier B.V. All rights reserved.

Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans

International Nuclear Information System (INIS)

Gao, Xiong-Zhuo; Li, Lan-Fen; Su, Xiao-Dong; Zhao, XiaoJun; Liang, Yu-He

2007-01-01

The SMU.961 protein from S. mutans was crystallized and preliminary characterization of the crystals, which diffracted to 2.9 Å resolution, shows them to belong to space group C2. The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni 2+ -chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 Å resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 Å, β = 98.82°

Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans

Energy Technology Data Exchange (ETDEWEB)

Gao, Xiong-Zhuo [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Li, Lan-Fen; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Zhao, XiaoJun, E-mail: zhaoxj@scu.edu.cn [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Liang, Yu-He, E-mail: zhaoxj@scu.edu.cn [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China)

2007-10-01

The SMU.961 protein from S. mutans was crystallized and preliminary characterization of the crystals, which diffracted to 2.9 Å resolution, shows them to belong to space group C2. The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 Å resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 Å, β = 98.82°.

Mutational epitope analysis of Pru av 1 and Api g 1, the major allergens of cherry (Prunus avium) and celery (Apium graveolens): correlating IgE reactivity with three-dimensional structure.

Science.gov (United States)

Neudecker, Philipp; Lehmann, Katrin; Nerkamp, Jörg; Haase, Tanja; Wangorsch, Andrea; Fötisch, Kay; Hoffmann, Silke; Rösch, Paul; Vieths, Stefan; Scheurer, Stephan

2003-01-01

Birch pollinosis is often accompanied by adverse reactions to food due to pollen-allergen specific IgE cross-reacting with homologous food allergens. The tertiary structure of Pru av 1, the major cherry (Prunus avium) allergen, for example, is nearly identical with Bet v 1, the major birch (Betula verrucosa) pollen allergen. In order to define cross-reactive IgE epitopes, we generated and analysed mutants of Pru av 1 and Api g 1.0101, the major celery (Apium graveolens) allergen, by immunoblotting, EAST (enzyme allergosorbent test), CD and NMR spectroscopy. The mutation of Glu45 to Trp45 in the P-loop region, a known IgE epitope of Bet v 1, significantly reduced IgE binding to Pru av 1 in a subgroup of cherry-allergic patients. The backbone conformation of Pru av 1 wild-type is conserved in the three-dimensional structure of Pru av 1 Trp45, demonstrating that the side chain of Glu45 is involved in a cross-reactive IgE epitope. Accordingly, for a subgroup of celery-allergic patients, IgE binding to the homologous celery allergen Api g 1.0101 was enhanced by the mutation of Lys44 to Glu. The almost complete loss of IgE reactivity to the Pru av 1 Pro112 mutant is due to disruption of its tertiary structure. Neither the mutation Ala112 nor deletion of the C-terminal residues 155-159 influenced IgE binding to Pru av 1. In conclusion, the structure of the P-loop partially explains the cross-reactivity pattern, and modulation of IgE-binding by site-directed mutagenesis is a promising approach to develop hypo-allergenic variants for patient-tailored specific immunotherapy. PMID:12943529

Renormalization of loop functions for all loops

International Nuclear Information System (INIS)

Brandt, R.A.; Neri, F.; Sato, M.

1981-01-01

It is shown that the vacuum expectation values W(C 1 ,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp[igcontour-integral/sub C/iA/sub μ/(x)dx/sup μ/] are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub μ/(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multiplied by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub γ/ is a loop which is smooth and simple except for a single cusp of angle γ, then W/sub R/(C/sub γ/) = Z(γ)W(C/sub γ/) is finite for a suitable renormalization factor Z(γ) which depends on γ but on no other characteristic of C/sub γ/. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub γ/) = 1 for an arbitrary but fixed loop C-bar/sub γ/. Next, if C/sub β/ is a loop which is smooth and simple except for a cross point of angles β, then W(C/sub β/) must be renormalized together with the loop functions of associated sets S/sup i//sub β/ = ]C/sup i/ 1 ,xxx, C/sup i//sub p/i] (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub β/equivalentC 1 1 . Then W/sub R/(S/sup i//sub β/) = Z/sup i/j(β)W(S/sup j//sub β/) is finite for a suitable matrix Z/sup i/j

Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide

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Hinnebusch Alan G

2011-01-01

Full Text Available Abstract Background Eukaryotic translation initiation factor 4G (eIF4G is thought to influence the translational efficiencies of cellular mRNAs by its roles in forming an eIF4F-mRNA-PABP mRNP that is competent for attachment of the 43S preinitiation complex, and in scanning through structured 5' UTR sequences. We have tested this hypothesis by determining the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies (TEs, using gene expression microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes. Results Although depletion of eIF4G is lethal and reduces protein synthesis by ~75%, it had small effects (less than a factor of 1.5 on the relative TE of most genes. Within these limits, however, depleting eIF4G narrowed the range of translational efficiencies genome-wide, with mRNAs of better than average TE being translated relatively worse, and mRNAs with lower than average TE being translated relatively better. Surprisingly, the fraction of mRNAs most dependent on eIF4G display an average 5' UTR length at or below the mean for all yeast genes. Conclusions This finding suggests that eIF4G is more critical for ribosome attachment to mRNAs than for scanning long, structured 5' UTRs. Our results also indicate that eIF4G, and the closed-loop mRNP it assembles with the m7 G cap- and poly(A-binding factors (eIF4E and PABP, is not essential for translation of most (if not all mRNAs but enhances the differentiation of translational efficiencies genome-wide.

Os Retratos de Dorian G(ray – corpo, imagem e subjetividade em um site de relacionamentos

Directory of Open Access Journals (Sweden)

Luiz Felipe Zago

2014-12-01

como utiliza entrevistas realizadas com usuários do site. Foca nas relações entre corpo, imagem e produção de subjetividade no tempo presente, empregando aportes teóricos do pós-estruturalismo. Considera a ligação entre imagem e corpo como legitimação da “verdade” dos corpos, coagidos pelo espectro da velhice e pela exortação à visibilidade.

Analytic results for the one loop NMHV H anti qqgg amplitude

International Nuclear Information System (INIS)

Badger, Simon; Campbell, John M.; Williams, Ciaran

2009-01-01

We compute the one-loop amplitude for a Higgs boson, a quark-antiquark pair and a pair of gluons of negative helicity, i.e. for the next-to-maximally helicity violating (NMHV) case, A(H, 1 - anti q , 2 + q , 3 - g , 4 - g ). The calculation is performed using an effective Lagrangian which is valid in the limit of very large top quark mass. As a result of this paper all amplitudes for the transition of a Higgs boson into 4 partons are now known analytically at one-loop order. (orig.)

Chargino and neutralino production at e{sup +}e{sup -} colliders in the complex MSSM. A full one-loop analysis

Energy Technology Data Exchange (ETDEWEB)

Heinemeyer, S. [Campus of International Excellence UAM+CSIC, Madrid (Spain); Universidad Autonoma de Madrid, Cantoblanco, Instituto de Fisica Teorica (UAM/CSIC), Madrid (Spain); Instituto de Fisica de Cantabria (CSIC-UC), Santander (Spain); Schappacher, C.

2017-09-15

For the search for charginos and neutralinos in the Minimal Supersymmetric Standard Model (MSSM) as well as for future precision analyses of these particles an accurate knowledge of their production and decay properties is mandatory. We evaluate the cross sections for the chargino and neutralino production at e{sup +}e{sup -} colliders in the MSSM with complex parameters (cMSSM). The evaluation is based on a full one-loop calculation of the production mechanisms e{sup +}e{sup -} → χ{sub c}{sup ±}χ{sub c}{sup {sub '}-+} and e{sup +}e{sup -} → χ{sub n}{sup 0}χ{sub n}{sup {sub '}0} including soft and hard photon radiation. We mostly restricted ourselves to a version of our renormalization scheme which is valid for vertical stroke M{sub 1} vertical stroke < vertical stroke M{sub 2} vertical stroke, vertical stroke μ vertical stroke and M{sub 2} ≠ μ to simplify the analysis, even though we are able to switch to other parameter regions and correspondingly different renormalization schemes. The dependence of the chargino/neutralino cross sections on the relevant cMSSM parameters is analyzed numerically. We find sizable contributions to many production cross sections. They amount to roughly ±15% of the tree-level results but can go up to ±40% or higher in extreme cases. Also the complex phase dependence of the one-loop corrections was found non-negligible. The full one-loop contributions are thus crucial for physics analyses at a future linear e{sup +}e{sup -} collider such as the ILC or CLIC. (orig.)

Finding Positive Feedback Loops in Environmental Models: A Mathematical Investigation

Science.gov (United States)

Sheikholeslami, R.; Razavi, S.

2016-12-01

Dynamics of most earth and environmental systems are generally governed by interactions between several hydrological (e.g., soil moisture and precipitation), geological (e.g., and erosion), geochemical (e.g., nutrient loading), and atmospheric (e.g., temperature) processes which operate on a range of spatio-temporal scales. These interactions create numerous feedback mechanisms with complex behaviours, and their understanding and representation can vary depending on the scale in space and/or time at which the system is analyzed. One of the most crucial characteristics of such complex systems is the existence of positive feedback loops. The presence of positive feedbacks may increase complexity, accelerate change, or trigger multiple stable states in the underlying dynamical system. Furthermore, because of the inherent non-linearity, it is often very difficult to obtain a general idea of their complex dynamics. Feedback loops in environmental systems have been well recognized and qualitatively discussed. With a quantitative/mathematical view, in this presentation, we address the question of how the positive feedback loops can be identified/implemented in environmental models. We investigate the nature of different feedback mechanisms and dynamics of simple example case studies that underlie fundamental processes such as vegetation, precipitation and soil moisture. To do this, we apply the concept of "interaction graph" from mathematics which is built from the Jacobian matrix of the dynamical system. The Jacobian matrix contains information on how variations of one state variable depends on variations of other variables, and thus can be used to understand the dynamical possibilities of feedback mechanisms in the underlying system. Moreover, this study highlights that there are some situations where the existence of positive feedback loops can cause multiple stable states, and thereby regime shifts in environmental systems. Systems with multiple stable states are

Characteristics of a foot-and-mouth disease virus with a partial VP1 G-H loop deletion in experimentally infected cattle

DEFF Research Database (Denmark)

Fowler, Veronica; Bashiruddin, John B.; Belsham, Graham

2014-01-01

Previous work in cattle illustrated the protective efficacy and negative marker potential of a A serotype foot-and-mouth disease virus (FMDV) vaccine prepared from a virus lacking a significant portion of the VP1 G-H loop (termed A(−)). Since this deletion also includes the arginine-glycine-aspar......Previous work in cattle illustrated the protective efficacy and negative marker potential of a A serotype foot-and-mouth disease virus (FMDV) vaccine prepared from a virus lacking a significant portion of the VP1 G-H loop (termed A(−)). Since this deletion also includes the arginine...

Chimeric Proton-Pumping Rhodopsins Containing the Cytoplasmic Loop of Bovine Rhodopsin

Science.gov (United States)

Sasaki, Kengo; Yamashita, Takahiro; Yoshida, Kazuho; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2014-01-01

G-protein-coupled receptors (GPCRs) transmit stimuli to intracellular signaling systems. Rhodopsin (Rh), which is a prototypical GPCR, possesses an 11-cis retinal. Photoisomerization of 11-cis to all-trans leads to structural changes in the protein of cytoplasmic loops, activating G-protein. Microbial rhodopsins are similar heptahelical membrane proteins that function as bacterial sensors, light-driven ion-pumps, or light-gated channels. They possess an all-trans retinal, and photoisomerization to 13-cis triggers structural changes in protein. Despite these similarities, there is no sequence homology between visual and microbial rhodopsins, and microbial rhodopsins do not activate G-proteins. In this study, new chimeric proton-pumping rhodopsins, proteorhodopsin (PR) and Gloeobacter rhodopsin (GR) were designed by replacing cytoplasmic loops with bovine Rh loops. Although G-protein was not activated by the PR chimeras, all 12 GR chimeras activated G-protein. The GR chimera containing the second cytoplasmic loop of bovine Rh did not activate G-protein. However, the chimera with a second and third double-loop further enhanced G-protein activation. Introduction of an E132Q mutation slowed the photocycle 30-fold and enhanced activation. The highest catalytic activity of the GR chimera was still 3,200 times lower than bovine Rh but only 64 times lower than amphioxus Go-rhodopsin. This GR chimera showed a strong absorption change of the amide-I band on a light-minus-dark difference FTIR spectrum which could represent a larger helical opening, important for G-protein activation. The light-dependent catalytic activity of this GR chimera makes it a potential optogenetic tool for enzymatic activation by light. PMID:24621599

Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology.

Science.gov (United States)

Hu, Lanying; Lim, Kah Wai; Bouaziz, Serge; Phan, Anh Tuân

2009-11-25

Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic.

Science.gov (United States)

Mahoney, Brendan J; Zhang, Meiling; Zintsmaster, John S; Peng, Jeffrey W

2018-03-02

Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Sequence in the loop domain of hepatitis C virus E2 protein identified in silico as crucial for the selective binding to human CD81.

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Chun-Chun Chang

Full Text Available Hepatitis C virus (HCV is a species-specific pathogenic virus that infects only humans and chimpanzees. Previous studies have indicated that interactions between the HCV E2 protein and CD81 on host cells are required for HCV infection. To determine the crucial factors for species-specific interactions at the molecular level, this study employed in silico molecular docking involving molecular dynamic simulations of the binding of HCV E2 onto human and rat CD81s. In vitro experiments including surface plasmon resonance measurements and cellular binding assays were applied for simple validations of the in silico results. The in silico studies identified two binding regions on the HCV E2 loop domain, namely E2-site1 and E2-site2, as being crucial for the interactions with CD81s, with the E2-site2 as the determinant factor for human-specific binding. Free energy calculations indicated that the E2/CD81 binding process might follow a two-step model involving (i the electrostatic interaction-driven initial binding of human-specific E2-site2, followed by (ii changes in the E2 orientation to facilitate the hydrophobic and van der Waals interaction-driven binding of E2-site1. The sequence of the human-specific, stronger-binding E2-site2 could serve as a candidate template for the future development of HCV-inhibiting peptide drugs.

Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

Directory of Open Access Journals (Sweden)

Zach Hensel

Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

Modern Summation Methods and the Computation of 2- and 3-loop Feynman Diagrams

International Nuclear Information System (INIS)

Ablinger, Jakob; Bluemlein, Johannes; Klein, Sebastian; Schneider, Carsten

2010-01-01

By symbolic summation methods based on difference fields we present a general strategy that transforms definite multi-sums, e.g., in terms of hypergeometric terms and harmonic sums, to indefinite nested sums and products. We succeeded in this task with all our concrete calculations of 2-loop and 3-loop massive single scale Feynman diagrams with local operator insertion.

Facile method for the site-specific, covalent attachment of full-length IgG onto nanoparticles.

Science.gov (United States)

Hui, James Zhe; Al Zaki, Ajlan; Cheng, Zhiliang; Popik, Vladimir; Zhang, Hongtao; Luning Prak, Eline T; Tsourkas, Andrew

2014-08-27

Antibodies, most commonly IgGs, have been widely used as targeting ligands in research and therapeutic applications due to their wide array of targets, high specificity and proven efficacy. Many of these applications require antibodies to be conjugated onto surfaces (e.g. nanoparticles and microplates); however, most conventional bioconjugation techniques exhibit low crosslinking efficiencies, reduced functionality due to non-site-specific labeling and random surface orientation, and/or require protein engineering (e.g. cysteine handles), which can be technically challenging. To overcome these limitations, we have recombinantly expressed Protein Z, which binds the Fc region of IgG, with an UV active non-natural amino acid benzoylphenyalanine (BPA) within its binding domain. Upon exposure to long wavelength UV light, the BPA is activated and forms a covalent link between the Protein Z and the bound Fc region of IgG. This technology was combined with expressed protein ligation (EPL), which allowed for the introduction of a fluorophore and click chemistry-compatible azide group onto the C-terminus of Protein Z during the recombinant protein purification step. This enabled the crosslinked-Protein Z-IgG complexes to be efficiently and site-specifically attached to aza-dibenzocyclooctyne-modified nanoparticles, via copper-free click chemistry. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

„NEW“ – Neue Energien West eG und Bürger-Energiegenossenschaft West eG

OpenAIRE

Amschler, Helmut

2014-01-01

Helmut Amschler, Vorstand der Stadtwerke Grafenwöhr, stellt in seinem Beitrag 2 konkrete Genossenschaften – die Neue Energien West eG und die Bürger-Energiegenossenschaft West eG vor. Dabei diskutiert er u. a. Kriterien wie Bürgerbeteiligung und Transparenz.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

Science.gov (United States)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Analytic results for the one loop NMHV H anti qqgg amplitude

Energy Technology Data Exchange (ETDEWEB)

Badger, Simon [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Campbell, John M. [Glasgow Univ. (United Kingdom). Dept. of Physics and Astronomy; Ellis, R. Keith [Fermilab, Batavia, IL (United States); Williams, Ciaran [Durham Univ. (United Kingdom). Dept. of Physics

2009-10-23

We compute the one-loop amplitude for a Higgs boson, a quark-antiquark pair and a pair of gluons of negative helicity, i.e. for the next-to-maximally helicity violating (NMHV) case, A(H, 1{sup -} {sub anti} {sub q}, 2{sup +}{sub q}, 3{sup -}{sub g}, 4{sup -}{sub g}). The calculation is performed using an effective Lagrangian which is valid in the limit of very large top quark mass. As a result of this paper all amplitudes for the transition of a Higgs boson into 4 partons are now known analytically at one-loop order. (orig.)

Evaluation of a loop-mediated isothermal amplification (LAMP) method for rapid on-site detection of horse meat

NARCIS (Netherlands)

Aartse, Aafke; Scholtens-Toma, Ingrid; A, van der Hans J.G.; Boersma-Greve, Monique M.; Prins, Theo W.; Ginkel, van Leen A.; Kok, Esther J.; Bovee, Toine F.H.

2017-01-01

Detection of horse DNA by loop-mediated isothermal amplification (LAMP) seems one of the most promising methods to meet the criteria of fast, robust, cost efficient, specific, and sensitive on-site detection. In the present study an assessment of the specificity and sensitivity of the LAMP horse

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

Science.gov (United States)

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Epicardial left ventricular lead placement for cardiac resynchronization therapy: optimal pace site selection with pressure-volume loops.

Science.gov (United States)

Dekker, A L A J; Phelps, B; Dijkman, B; van der Nagel, T; van der Veen, F H; Geskes, G G; Maessen, J G

2004-06-01

Patients in heart failure with left bundle branch block benefit from cardiac resynchronization therapy. Usually the left ventricular pacing lead is placed by coronary sinus catheterization; however, this procedure is not always successful, and patients may be referred for surgical epicardial lead placement. The objective of this study was to develop a method to guide epicardial lead placement in cardiac resynchronization therapy. Eleven patients in heart failure who were eligible for cardiac resynchronization therapy were referred for surgery because of failed coronary sinus left ventricular lead implantation. Minithoracotomy or thoracoscopy was performed, and a temporary epicardial electrode was used for biventricular pacing at various sites on the left ventricle. Pressure-volume loops with the conductance catheter were used to select the best site for each individual patient. Relative to the baseline situation, biventricular pacing with an optimal left ventricular lead position significantly increased stroke volume (+39%, P =.01), maximal left ventricular pressure derivative (+20%, P =.02), ejection fraction (+30%, P =.007), and stroke work (+66%, P =.006) and reduced end-systolic volume (-6%, P =.04). In contrast, biventricular pacing at a suboptimal site did not significantly change left ventricular function and even worsened it in some cases. To optimize cardiac resynchronization therapy with epicardial leads, mapping to determine the best pace site is a prerequisite. Pressure-volume loops offer real-time guidance for targeting epicardial lead placement during minimal invasive surgery.

A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

Science.gov (United States)

D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

2018-02-01

The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

Design of a Bioelectronics Hybrid System in Real Time and in Closed Loop

Directory of Open Access Journals (Sweden)

Sylvie Renaud

2012-12-01

Full Text Available Hynets, for Hybrid (living-artificial Networks, are an efficient and adaptable experimental support to explore the dynamics and the adaptation process of biological systems. We present in this paper an innovative platform performing a real-time closed-loop between a cultured network (e.g. neurons and an artificial processing (e.g. software processing or a robotic interface. The system gathers bioware, hardware, and software components and ensures the closed-loop data processing in less than 50 µs. We describe also a methodology that may help to standardize the description of some experiments. This method is associated to a full custom Graphical User Interface. We detail here the system choices, components, and performances.

Identification of cisplatin-binding sites on the large cytoplasmic loop of the Na+/K+-ATPase.

Science.gov (United States)

Šeflová, Jaroslava; Čechová, Petra; Štenclová, Tereza; Šebela, Marek; Kubala, Martin

2018-12-01

Cisplatin is the most widely used chemotherapeutic drug for the treatment of various types of cancer; however, its administration brings also numerous side effects. It was demonstrated that cisplatin can inhibit the Na + /K + -ATPase (NKA), which can explain a large part of the adverse effects. In this study, we have identified five cysteinyl residues (C452, C456, C457, C577, and C656) as the cisplatin binding sites on the cytoplasmic loop connecting transmembrane helices 4 and 5 (C45), using site-directed mutagenesis and mass spectrometry experiments. The identified residues are known to be susceptible to glutathionylation indicating their involvement in a common regulatory mechanism.

Renormalization of vacuum expectation values in spontaneously broken gauge theories: two-loop results

International Nuclear Information System (INIS)

Sperling, Marcus; Stöckinger, Dominik; Voigt, Alexander

2014-01-01

We complete the two-loop calculation of β-functions for vacuum expectation values (VEVs) in gauge theories by the missing O(g 4 )-terms. The full two-loop results are presented for generic and supersymmetric theories up to two-loop level in arbitrary R ξ -gauge. The results are obtained by means of a scalar background field, identical to our previous analysis. As a by-product, the two-loop scalar anomalous dimension for generic supersymmetric theories is presented. As an application we compute the β-functions for VEVs and tan β in the MSSM, NMSSM, and E 6 SSM

Assisted closed-loop optimization of SSVEP-BCI efficiency

Directory of Open Access Journals (Sweden)

Jacobo eFernandez-Vargas

2013-02-01

Full Text Available We designed a novel assisted closed-loop optimization protocol to improve the efficiency of brain computer interfaces (BCI based on steady state visually evoked potentials (SSVEP. In traditional paradigms, the control over the BCI-performance completely depends on the subjects’ ability to learn from the given feedback cues. By contrast, in the proposed protocol both the subject and the machine share information and control over the BCI goal. Generally, the innovative assistance consists in the delivery of online information together with the online adaptation of BCI stimuli properties. In our case, this adaptive optimization process is realized by (i a closed-loop search for the best set of SSVEP flicker frequencies and (ii feedback of actual SSVEP magnitudes to both the subject and the machine. These closed-loop interactions between subject and machine are evaluated in real-time by continuous measurement of their efficiencies, which are used as online criteria to adapt the BCI control parameters. The proposed protocol aims to compensate for variability in possibly unknown subjects’ state and trait dimensions. In a study with N = 18 subjects, we found significant evidence that our protocol outperformed classic SSVEP-BCI control paradigms. Evidence is presented that it takes indeed into account interindividual variabilities: e.g. under the new protocol, baseline resting state EEG measures predict subjects’ BCI performances. This paper illustrates the promising potential of assisted closed-loop protocols in BCI systems. Probably their applicability might be expanded to innovative uses, e.g. as possible new diagnostic/therapeutic tools for clinical contexts and as new paradigms for basic research.

Modern summation methods and the computation of 2- and 3-loop Feynman diagrams

International Nuclear Information System (INIS)

Ablinger, Jakob; Schneider, Carsten; Bluemlein, Johannes; Klein, Sebastian

2010-06-01

By symbolic summation methods based on difference fields we present a general strategy that transforms definite multi-sums, e.g., in terms of hypergeometric terms and harmonic sums, to indefinite nested sums and products. We succeeded in this task with all our concrete calculations of 2-loop and 3-loop massive single scale Feynman diagrams with local operator insertion. (orig.)

Modern summation methods and the computation of 2- and 3-loop Feynman diagrams

Energy Technology Data Exchange (ETDEWEB)

Ablinger, Jakob; Schneider, Carsten [Linz Univ. (AT). Research Inst. for Symbolic Computation (RISC); Bluemlein, Johannes [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Klein, Sebastian [RWTH Aachen (Germany). Inst. fuer Theoretische Teilchenphysik und Kosmologie

2010-06-15

By symbolic summation methods based on difference fields we present a general strategy that transforms definite multi-sums, e.g., in terms of hypergeometric terms and harmonic sums, to indefinite nested sums and products. We succeeded in this task with all our concrete calculations of 2-loop and 3-loop massive single scale Feynman diagrams with local operator insertion. (orig.)

Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

Science.gov (United States)

Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

2014-01-29

We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

Investigations into the molecular mechanism of chromatid breakage in the G2-phase of mammalian cells

International Nuclear Information System (INIS)

Bryant, P.E.; Armstrong, G.N.; Gray, L.; Frankenberg, D.; Mozdarani, H.

2003-01-01

Chromatid breakage following irradiation of cells in the G2-phase of the cell cycle results from the induction of DNA double-strand breaks (dsb). The conversion of dsb into chromatid breaks (cb) has a genetic basis, seemingly different from that of dsb rejoining. The variation in extent of this conversion is exemplified by the stiking variation in frequency of cb in irradiated cycling T-lymphocytes between different normal individuals. Elevated cb frequency in lymphocytes of around 40% of breast cancer patients and their first-degree relatives suggests the presence of mutations in low penetrance cancer predisposing genes that also affect conversion of dsb to cb. Investigation of the mechanism of chromatid radiosensitivity using genetically engineered rodent cell lines containing unique dsb break sites indicate that a single isolated dsb is sufficient to cause a cb. The single-event nature of chromatid breakage is confirmed by the fact that cb are induced as a linear function of radiation dose. Moreover, we have recently shown that ultrasoft carbon-K X-rays also induce chromatid breakage. In this case the energy of the secondary electrons produced by carbon-K X-rays is too low to span more than one DNA double helix, thus further supporting our conclusion that a single dsb is responsible for the formation of a cb. Chromatid breakage is thought to involve a rearrangement between DNA strands at the crossover points of chromatin loop(s) triggered by the presence of a dsb within the loop structure. The occasional observation of 'looped-out' sections of chromatin at cb sites supports this hypothesis. The occurrence of 'colour-switches' between FPG stained chromatids at a proportion of break sites (e.g. about 16% in CHO cells) shows that a significant proportion of cb definitely result from chromatin rearrangements. Measurements of altered colour-switch ratio (csr) in mutant rodent and human cells (irs1 and AT cells respectively) also indicate a genetic basis for the

Dynamical behaviors of Rb-E2F pathway including negative feedback loops involving miR449.

Science.gov (United States)

Yan, Fang; Liu, Haihong; Hao, Junjun; Liu, Zengrong

2012-01-01

MiRNAs, which are a family of small non-coding RNAs, regulate a broad array of physiological and developmental processes. However, their regulatory roles have remained largely mysterious. E2F is a positive regulator of cell cycle progression and also a potent inducer of apoptosis. Positive feedback loops in the regulation of Rb-E2F pathway are predicted and shown experimentally. Recently, it has been discovered that E2F induce a cluster of miRNAs called miR449. In turn, E2F is inhibited by miR449 through regulating different transcripts, thus forming negative feedback loops in the interaction network. Here, based on the integration of experimental evidence and quantitative data, we studied Rb-E2F pathway coupling the positive feedback loops and negative feedback loops mediated by miR449. Therefore, a mathematical model is constructed based in part on the model proposed in Yao-Lee et al. (2008) and nonlinear dynamical behaviors including the stability and bifurcations of the model are discussed. A comparison is given to reveal the implication of the fundamental differences of Rb-E2F pathway between regulation and deregulation of miR449. Coherent with the experiments it predicts that miR449 plays a critical role in regulating the cell cycle progression and provides a twofold safety mechanism to avoid excessive E2F-induced proliferation by cell cycle arrest and apoptosis. Moreover, numerical simulation and bifurcation analysis shows that the mechanisms of the negative regulation of miR449 to three different transcripts are quite distinctive which needs to be verified experimentally. This study may help us to analyze the whole cell cycle process mediated by other miRNAs more easily. A better knowledge of the dynamical behaviors of miRNAs mediated networks is also of interest for bio-engineering and artificial control.

Osmotic mechanism of the loop extrusion process

Science.gov (United States)

Yamamoto, Tetsuya; Schiessel, Helmut

2017-09-01

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

Electroweak one-loop corrections for e+e- annihilation into t anti t including hard bremsstrahlung

International Nuclear Information System (INIS)

Fleischer, J.; Leike, A.; Riemann, T.; Werthenbach, A.

2003-01-01

We present the complete electroweak one-loop corrections to top-pair production at a linear e + e - collider in the continuum region. Besides weak and photonic virtual corrections, real hard bremsstrahlung with simple realistic kinematical cuts is included. For the bremsstrahlung we advocate a semi-analytical approach with a high numerical accuracy. The virtual corrections are parameterized through six independent form factors, suitable for Monte Carlo implementation. Alternatively, our numerical package Topfit, a stand-alone code, can be utilized for the calculation of both differential and integrated cross sections as well as forward-backward asymmetries. (orig.)

PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

International Nuclear Information System (INIS)

Dahlburg, R. B.; Obenschain, K.; Laming, J. M.; Taylor, B. D.

2016-01-01

Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

Energy Technology Data Exchange (ETDEWEB)

Dahlburg, R. B.; Obenschain, K. [LCP and FD, Naval Research Laboratory, Washington, DC 20375 (United States); Laming, J. M. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Taylor, B. D. [AFRL Eglin AFB, Pensacola, FL 32542 (United States)

2016-11-10

Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation

International Nuclear Information System (INIS)

Littler, Dene R.; Walker, John R.; Davis, Tara; Wybenga-Groot, Leanne E.; Finerty, Patrick J. Jr; Newman, Elena; Mackenzie, Farell; Dhe-Paganon, Sirano

2010-01-01

A 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKα2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function

Efficiently computing exact geodesic loops within finite steps.

Science.gov (United States)

Xin, Shi-Qing; He, Ying; Fu, Chi-Wing

2012-06-01

Closed geodesics, or geodesic loops, are crucial to the study of differential topology and differential geometry. Although the existence and properties of closed geodesics on smooth surfaces have been widely studied in mathematics community, relatively little progress has been made on how to compute them on polygonal surfaces. Most existing algorithms simply consider the mesh as a graph and so the resultant loops are restricted only on mesh edges, which are far from the actual geodesics. This paper is the first to prove the existence and uniqueness of geodesic loop restricted on a closed face sequence; it contributes also with an efficient algorithm to iteratively evolve an initial closed path on a given mesh into an exact geodesic loop within finite steps. Our proposed algorithm takes only an O(k) space complexity and an O(mk) time complexity (experimentally), where m is the number of vertices in the region bounded by the initial loop and the resultant geodesic loop, and k is the average number of edges in the edge sequences that the evolving loop passes through. In contrast to the existing geodesic curvature flow methods which compute an approximate geodesic loop within a predefined threshold, our method is exact and can apply directly to triangular meshes without needing to solve any differential equation with a numerical solver; it can run at interactive speed, e.g., in the order of milliseconds, for a mesh with around 50K vertices, and hence, significantly outperforms existing algorithms. Actually, our algorithm could run at interactive speed even for larger meshes. Besides the complexity of the input mesh, the geometric shape could also affect the number of evolving steps, i.e., the performance. We motivate our algorithm with an interactive shape segmentation example shown later in the paper.

[PHAHs levels in soil samples from the E-waste disassembly sites and their sources allocation].

Science.gov (United States)

Zhao, Gao-Feng; Wang, Zi-Jian

2009-06-15

Soil samples (each with 3 replicates of - 1 kg, at the top 0-5 cm layer) were collected from each of the e-waste disassembly sites and the control site. Also obtained from each disassembly site were samples (each weighing - 0.2 kg) of cable coating,stuffing powder, and circuit boards chipping. The contents of 23 PBB congeners, 12 PBDE congeners, and 27 PCB congeners in soil and in their potential sources, including e-waste residues, were measured using the GC-MS5975B technique. The highest level of PBBs was found in the cable coating among the three e-waste residues, with a concentration of 35.25 ng x g(-1). The contents of low-brominated PBBs (including monobromobiphenyls and dibromobiphenyls) accounted for 38% of the total PBBs concentration observed in cable coating sample. The highest levels of PBDEs and PBDE209 were found in the stuffing powder for electronic component among the collected e-waste residues, with a concentration of 29.71 and 4.19 x 10(3) ng x g(-1). PBDE153 and PBDE183 were the most predominant PBDE congeners, with their concentration accounting for 43% and 24% of the total PBDEs concentration observed in the stuffing powder sample, respectively. Levels of PCBs in cable coating were the highest in these e-waste residues, with a concentration of 680.02 ngx g(-1). The observed values of the three PHAHs in soils from the disassembly site were considerably higher than their corresponding values observed in the control site (p < 0.05), which indicates that these PHAHs from e-waste is the pollution source of local environment.

Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

International Nuclear Information System (INIS)

Ramos-Santana, Brenda J.; López-Garriga, Juan

2012-01-01

Highlights: ► H-bonding network loop by PheB10Tyr mutation is proposed. ► The propionate group H-bonding network restricted the flexibility of the heme. ► The hydrogen bonding interaction modulates the electron density of the iron. ► Propionate H-bonding network loop explains the heme-ligand stabilization. -- Abstract: Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. 1 H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00 ppm, GlnE7 N ε1 H/N ε2 H at 10.66 ppm/−3.27 ppm, and PheE11 C δ H at 11.75 ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus, we hypothesize that in hemeproteins with similar electrostatic environment the flexibility of the heme-6-propionate promotes a hydrogen

RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

Science.gov (United States)

NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

2016-12-27

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

Fuel cell hardware-in-loop

Energy Technology Data Exchange (ETDEWEB)

Moore, R.M.; Randolf, G.; Virji, M. [University of Hawaii, Hawaii Natural Energy Institute (United States); Hauer, K.H. [Xcellvision (Germany)

2006-11-08

Hardware-in-loop (HiL) methodology is well established in the automotive industry. One typical application is the development and validation of control algorithms for drive systems by simulating the vehicle plus the vehicle environment in combination with specific control hardware as the HiL component. This paper introduces the use of a fuel cell HiL methodology for fuel cell and fuel cell system design and evaluation-where the fuel cell (or stack) is the unique HiL component that requires evaluation and development within the context of a fuel cell system designed for a specific application (e.g., a fuel cell vehicle) in a typical use pattern (e.g., a standard drive cycle). Initial experimental results are presented for the example of a fuel cell within a fuel cell vehicle simulation under a dynamic drive cycle. (author)

The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

DEFF Research Database (Denmark)

Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

1999-01-01

, and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

Mining protein loops using a structural alphabet and statistical exceptionality

Directory of Open Access Journals (Sweden)

Martin Juliette

2010-02-01

Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

Mining protein loops using a structural alphabet and statistical exceptionality.

Science.gov (United States)

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

Energy Technology Data Exchange (ETDEWEB)

Egli, Martin [Vanderbilt Univ., Nashville, TN (United States); Pattanayek, Rekha [Vanderbilt Univ., Nashville, TN (United States); Sheehan, Jonathan H. [Vanderbilt Univ., Nashville, TN (United States); Xu, Yao [Vanderbilt Univ., Nashville, TN (United States); Mori, Tetsuya [Vanderbilt Univ., Nashville, TN (United States); Smith, Jarrod A. [Vanderbilt Univ., Nashville, TN (United States); Johnson, Carl H. [Vanderbilt Univ., Nashville, TN (United States)

2013-01-25

We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

Multi-parton loop amplitudes and next-to-leading order jet cross-sections

International Nuclear Information System (INIS)

Bern, Z.; Dixon, L.; Kosower, D.A.; Signer, A.

1998-02-01

The authors review recent developments in the calculation of QCD loop amplitudes with several external legs, and their application to next-to-leading order jet production cross-sections. When a number of calculational tools are combined together--helicity, color and supersymmetry decompositions, plus unitarity and factorization properties--it becomes possible to compute multi-parton one-loop QCD amplitudes without ever evaluating analytically standard one-loop Feynman diagrams. One-loop helicity amplitudes are now available for processes with five external partons (ggggg, q anti qggg and q anti qq anti q' g), and for an intermediate vector boson V ≡ γ * , Z, W plus four external partons (V q anti q and V q anti qq'anti q'). Using these amplitudes, numerical programs have been constructed for the next-to-leading order corrections to the processes p anti p → 3 jets (ignoring quark contributions so far) and e + e - → 4 jets

Spatial 't Hooft loop to cubic order in hot QCD

CERN Document Server

Giovannangeli, P.

2002-01-01

Spatial 't Hooft loops of strength k measure the qualitative change in the behaviour of electric colour flux in confined and deconfined phase of SU (N) gauge theory. They show an area law in the deconfined phase, known analytica lly to two loop order with a ``k-scaling'' law k(N-k). In this paper we comput e the O(g^3) correction to the tension. It is due to neutral gluon fields that get their mass through interaction with the wall. The simple k-scaling is lost in cubic order. The generic problem of non-convexity shows up in this order an d the cure is provided. The result for large N is explicitely given. We show tha t nonperturbative effects appear at O(g^5).

Dynamical behaviors of Rb-E2F pathway including negative feedback loops involving miR449.

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Fang Yan

Full Text Available MiRNAs, which are a family of small non-coding RNAs, regulate a broad array of physiological and developmental processes. However, their regulatory roles have remained largely mysterious. E2F is a positive regulator of cell cycle progression and also a potent inducer of apoptosis. Positive feedback loops in the regulation of Rb-E2F pathway are predicted and shown experimentally. Recently, it has been discovered that E2F induce a cluster of miRNAs called miR449. In turn, E2F is inhibited by miR449 through regulating different transcripts, thus forming negative feedback loops in the interaction network. Here, based on the integration of experimental evidence and quantitative data, we studied Rb-E2F pathway coupling the positive feedback loops and negative feedback loops mediated by miR449. Therefore, a mathematical model is constructed based in part on the model proposed in Yao-Lee et al. (2008 and nonlinear dynamical behaviors including the stability and bifurcations of the model are discussed. A comparison is given to reveal the implication of the fundamental differences of Rb-E2F pathway between regulation and deregulation of miR449. Coherent with the experiments it predicts that miR449 plays a critical role in regulating the cell cycle progression and provides a twofold safety mechanism to avoid excessive E2F-induced proliferation by cell cycle arrest and apoptosis. Moreover, numerical simulation and bifurcation analysis shows that the mechanisms of the negative regulation of miR449 to three different transcripts are quite distinctive which needs to be verified experimentally. This study may help us to analyze the whole cell cycle process mediated by other miRNAs more easily. A better knowledge of the dynamical behaviors of miRNAs mediated networks is also of interest for bio-engineering and artificial control.

Dechlorane Plus (DP) in air and plants at an electronic waste (e-waste) site in South China

Energy Technology Data Exchange (ETDEWEB)

Chen Shejun [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Tian Mi; Wang Jing; Shi Tian [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Graduate School, Chinese Academy of Sciences, Beijing 100049 (China); Luo Yong [Guangdong Forestry Survey and Planning Institute, Guangzhou 510520 (China); Luo Xiaojun [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Mai Bixian, E-mail: nancymai@gig.ac.cn [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China)

2011-05-15

Air and foliage samples (Eucalyptus spp. and Pinus massoniana Lamb.) were collected from e-waste and reference sites in South China and analyzed for Dechlorane Plus (DP) and two dechlorinated DPs. DP concentrations in the air were 13.1-1794 pg/m{sup 3} for the e-waste site and 0.47-35.7 pg/m{sup 3} for the reference site, suggesting the recycling of e-waste is an important source of DP to the environment. Plant DP, with concentrations of 0.45-51.9 ng/g dry weight at the e-waste site and 0.09-2.46 ng/g at the reference site, exhibited temporal patterns similar to the air DP except for pine needle at the reference site. The air-plant exchange of DP could be described with the two-compartment model. Anti-Cl{sub 11} DP was measured in most air and plant samples from the e-waste site. The ratios of anti-Cl{sub 11} DP to anti-DP in the air and plants may indicate the preferential uptake of dechlorinated DP by plant compared with DP. - Highlights: > Dechlorane Plus was widely present in the air and plants in South China. > Temporal patterns of the plant DP could be described with the two-compartment model. > Plant uptake can efficiently reduce air DP concentration at the reference site. > Anti-Cl{sub 11} DP was measured in most air and plant samples from the e-waste site. - E-waste recycling in South China results in wide occurrence of DP in the air and plant.

Presenting simulation results in a nested loop plot.

Science.gov (United States)

Rücker, Gerta; Schwarzer, Guido

2014-12-12

Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Choosing bias as criterion of interest, we present a 'nested loop plot', a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots.

Four-loop on-shell integrals. MS-on-shell relation and g-2

Energy Technology Data Exchange (ETDEWEB)

Marquard, P.

2013-12-15

We present first results towards a full four-loop calculation for both the anomalous magnetic moment of the muon and the MS-on-shell relation. The calculation requires the detailed study of an up to now not considered class of diagrams, so-called on-shell diagrams, at four-loop order.

Klebsiella aerogenes UreF: Identification of the UreG Binding Site and Role in Enhancing the Fidelity of Urease Activation†

Science.gov (United States)

Boer, Jodi L.; Hausinger, Robert P.

2012-01-01

The Ni-containing active site of Klebsiella aerogenes urease is assembled through the concerted action of the UreD, UreE, UreF, and UreG accessory proteins. UreE functions as a metallochaperone that delivers Ni to a complex of UreD—UreF—UreG bound to urease apoprotein, with UreG serving as a GTPase during enzyme activation. The present study focuses on the role of UreF, previously proposed to act as a GTPase activating protein (GAP) of UreG. Sixteen conserved UreF surface residues that may play roles in protein:protein interactions were independently changed to Ala. When produced in the context of the entire urease gene cluster, cell-free extracts of nine site-directed mutants had less than 10% of the wild-type urease activity. Enrichment of the variant forms of UreF, as the UreE-F fusion proteins, uniformly resulted in co-purification of UreD and urease apoprotein; whereas UreG bound to only a subset of the species. Notably, reduced interaction with UreG correlated with the low activity mutants. The affected residues in UreF map to a distinct surface on the crystal structure, defining the UreG binding site. In contrast to the hypothesis that UreF is a GAP, the UreD—UreF—UreG—urease apoprotein complex containing K165A UreF exhibited significantly greater levels of GTPase activity than that containing the wild-type protein. Additional studies demonstrated the UreG GTPase activity was largely uncoupled from urease activation for the complex containing this UreF variant. Further experiments with these complexes provided evidence that UreF gates the GTPase activity of UreG to enhance the fidelity of urease metallocenter assembly, especially in the presence of the non-cognate metal Zn. PMID:22369361

Herpes simplex virus immunoglobulin G Fc receptor activity depends on a complex of two viral glycoproteins, gE and gI

International Nuclear Information System (INIS)

Johnson, D.C.; Ligas, M.W.; Frame, M.C.; Cross, A.M.; Stow, N.D.

1988-01-01

Evidence was recently presented that herpes simplex virus type 1 (HSV-1) immunoglobulin G (IgG) Fc receptors are composed of a complex containing a previously described glycoprotein, gE, and a novel virus-induced polypeptide, provisionally named g70. Using a monoclonal antibody designated 3104, which recognizes g70, in conjunction with antipeptide sera and virus mutants unable to express g70 or gE, the authors have mapped the gene encoding g70 to the US7 open reading frame of HSV-1 adjacent to the gE gene. Therefore, g70 appears to be identical to a recently described polypeptide which was named gI. Under mildly denaturing conditions, monoclonal antibody 3104 precipitated both gI and gE from extracts of HSV-1-infected cells. In addition, rabbit IgG precipitated the gE-gI complex from extracts of cells transfected with a fragment of HSV-1 DNA containing the gI, gE, and US9 genes. Cells infected with mutant viruses which were unable to express gE or gI did not bind radiolabeled IgG; however, cells coinfected with two viruses, one unable to express gE and the other unable to express gI, bound levels of IgG approaching those observed with wild-type viruses. These results further support the hypothesis that gE and gI form a complex which binds IgG by the Fc domain and that neither polypeptide alone can bind IgG

Protein Loop Structure Prediction Using Conformational Space Annealing.

Science.gov (United States)

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

Science.gov (United States)

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

Science.gov (United States)

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

2017-05-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Characterization of Site for Installing Open Loop Ground Source Heat Pump System

Science.gov (United States)

Yun, S. W.; Park, Y.; Lee, J. Y.; Yi, M. J.; Cha, J. H.

2014-12-01

This study was conducted to understand hydrogeological properties of site where open loop ground source heat pump system will be installed and operated. Groundwater level and water temperature were hourly measured at the well developed for usage of open loop ground source heat pump system from 11 October 2013 to 8 January 2014. Groundwater was sampled in January and August 2013 and its chemical and isotopic compositions were analyzed. The bedrock of study area is the Jurassic granodiorite that mainly consists of quartz (27.9 to 46.8%), plagioclase (26.0 to 45.5%), and alkali feldspar (9.5 to 18.7%). The groundwater level ranged from 68.30 to 68.94 m (above mean sea level). Recharge rate was estimated using modified watertable fluctuation method and the recharge ratios was 9.1%. The water temperature ranged from 14.8 to 15.0oC. The vertical Increase rates of water temperature were 1.91 to 1.94/100 m. The water temperature showed the significant seasonal variation above 50 m depth, but had constant value below 50 m depth. Therefore, heat energy of the groundwater can be used securely in open loop ground source heat pump system. Electrical conductivity ranged from 120 to 320 µS/cm in dry season and from 133 to 310 µS/cm in wet season. The electrical conductivity gradually decreased with depth. In particular, electrical conductivity in approximately 30 m depth decreased dramatically (287 to 249 µS/cm) in wet season. The groundwater was Ca-HCO3 type. The concentrations of dissolved components did not show the vertically significant variations from 0 to 250 m depth. The δ18O and δD ranged from -9.5 to -9.4‰ and from -69 to -68‰. This work is supported by the New and Renewable Energy of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No.20123040110010).

Protein phosphatase PPM1G regulates protein translation and cell growth by dephosphorylating 4E binding protein 1 (4E-BP1).

Science.gov (United States)

Liu, Jianyu; Stevens, Payton D; Eshleman, Nichole E; Gao, Tianyan

2013-08-09

Protein translation initiation is a tightly controlled process responding to nutrient availability and mitogen stimulation. Serving as one of the most important negative regulators of protein translation, 4E binding protein 1 (4E-BP1) binds to translation initiation factor 4E and inhibits cap-dependent translation in a phosphorylation-dependent manner. Although it has been demonstrated previously that the phosphorylation of 4E-BP1 is controlled by mammalian target of rapamycin in the mammalian target of rapamycin complex 1, the mechanism underlying the dephosphorylation of 4E-BP1 remains elusive. Here, we report the identification of PPM1G as the phosphatase of 4E-BP1. A coimmunoprecipitation experiment reveals that PPM1G binds to 4E-BP1 in cells and that purified PPM1G dephosphorylates 4E-BP1 in vitro. Knockdown of PPM1G in 293E and colon cancer HCT116 cells results in an increase in the phosphorylation of 4E-BP1 at both the Thr-37/46 and Ser-65 sites. Furthermore, the time course of 4E-BP1 dephosphorylation induced by amino acid starvation or mammalian target of rapamycin inhibition is slowed down significantly in PPM1G knockdown cells. Functionally, the amount of 4E-BP1 bound to the cap-dependent translation initiation complex is decreased when the expression of PPM1G is depleted. As a result, the rate of cap-dependent translation, cell size, and protein content are increased in PPM1G knockdown cells. Taken together, our study has identified protein phosphatase PPM1G as a novel regulator of cap-dependent protein translation by negatively controlling the phosphorylation of 4E-BP1.

Concentration and length dependence of DNA looping in transcriptional regulation.

Directory of Open Access Journals (Sweden)

Lin Han

2009-05-01

Full Text Available In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage, to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

MHD modeling of coronal loops: the transition region throat

Science.gov (United States)

Guarrasi, M.; Reale, F.; Orlando, S.; Mignone, A.; Klimchuk, J. A.

2014-04-01

Context. The expansion of coronal loops in the transition region may considerably influence the diagnostics of the plasma emission measure. The cross-sectional area of the loops is expected to depend on the temperature and pressure, and might be sensitive to the heating rate. Aims: The approach here is to study the area response to slow changes in the coronal heating rate, and check the current interpretation in terms of steady heating models. Methods: We study the area response with a time-dependent 2D magnetohydrodynamic (MHD) loop model, including the description of the expanding magnetic field, coronal heating and losses by thermal conduction, and radiation from optically thin plasma. We run a simulation for a loop 50 Mm long and quasi-statically heated to about 4 MK. Results: We find that the area can change substantially with the quasi-steady heating rate, e.g., by ~40% at 0.5 MK as the loop temperature varies between 1 MK and 4 MK, and, therefore, affects the interpretation of the differential emission measure vs. temperature (DEM(T)) curves. The movie associated to Fig. 4 is available in electronic form at http://www.aanda.org

Two-loop massive fermionic operator matrix elements and intial state QED corrections to e{sup +}e{sup -}{yields}{gamma}{sup *}/Z{sup *}

Energy Technology Data Exchange (ETDEWEB)

Bluemlein, J. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Freitas, A. de [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)]|[Universidad Simon Bolivar, Caracas (Venezuela). Dept. de Fisica; Neerven, W. van [Leiden Univ. (Netherlands). Lorentz Institute

2008-12-15

We describe the calculation of the two-loop massive operator matrix elements for massive external fermions. These matrix elements are needed for the calculation of the O({alpha}{sup 2}) initial state radiative corrections to e{sup +}e{sup -} annihilation into a neutral virtual gauge boson, based on the renormalization group technique. (orig.)

Polybrominated diphenyl ethers in e-waste: Level and transfer in a typical e-waste recycling site in Shanghai, Eastern China

Energy Technology Data Exchange (ETDEWEB)

Li, Yue; Duan, Yan-Ping, E-mail: duanyanping@tongji.edu.cn; Huang, Fan; Yang, Jing; Xiang, Nan; Meng, Xiang-Zhou; Chen, Ling

2014-06-01

Highlights: • PBDEs were detected in the majority of e-waste. • PBDEs were found in TVs made in China after 1990. • The levels of ΣPBDEs in e-waste made in Japan far exceed the threshold limit of RoHS. • The inappropriate recycling and disposal of e-waste is an important source of PBDEs. - Abstract: Very few data for polybrominated diphenyl ethers (PBDEs) were available in the electronic waste (e-waste) as one of the most PBDEs emission source. This study reported concentrations of PBDEs in e-waste including printer, rice cooker, computer monitor, TV, electric iron and water dispenser, as well as dust from e-waste, e-waste dismantling workshop and surface soil from inside and outside of an e-waste recycling plant in Shanghai, Eastern China. The results showed that PBDEs were detected in the majority of e-waste, and the concentrations of ΣPBDEs ranged from not detected to 175 g/kg, with a mean value of 10.8 g/kg. PBDEs were found in TVs made in China after 1990. The mean concentrations of ΣPBDEs in e-waste made in Korea, Japan, Singapore and China were 1.84 g/kg, 20.5 g/kg, 0.91 g/kg, 4.48 g/kg, respectively. The levels of ΣPBDEs in e-waste made in Japan far exceed the threshold limit of RoHS (1.00 g/kg). BDE-209 dominated in e-waste, accounting for over 93%. The compositional patterns of PBDEs congeners resembled the profile of Saytex 102E, indicating the source of deca-BDE. Among the samples of dust and surface soil from a typical e-waste recycling site, the highest concentrations of Σ{sub 18}PBDEs and BDE-209 were found in dust in e-waste, ranging from 1960 to 340,710 ng/g and from 910 to 320,400 ng/g, which were 1–2 orders of magnitude higher than other samples. It suggested that PBDEs released from e-waste via dust, and then transferred to surrounding environment.

Vortex spin-torque oscillator stabilized by phase locked loop using integrated circuits

Directory of Open Access Journals (Sweden)

Martin Kreissig

2017-05-01

Full Text Available Spin-torque nano-oscillators (STO are candidates for the next technological implementation of spintronic devices in commercial electronic systems. For use in microwave applications, improving the noise figures by efficient control of their phase dynamics is a mandatory requirement. In order to achieve this, we developed a compact phase locked loop (PLL based on custom integrated circuits (ICs and demonstrate that it represents an efficient way to reduce the phase noise level of a vortex based STO. The advantage of our approach to phase stabilize STOs is that our compact system is highly reconfigurable e.g. in terms of the frequency divider ratio N, RF gain and loop gain. This makes it robust against device to device variations and at the same time compatible with a large range of STOs. Moreover, by taking advantage of the natural highly non-isochronous nature of the STO, the STO frequency can be easily controlled by e.g. changing the divider ratio N.

P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape.

Directory of Open Access Journals (Sweden)

Huiyong Sun

2014-07-01

Full Text Available Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance.

One-loop corrections for e+e- annihilation into μ+μ- in the Weinberg model

NARCIS (Netherlands)

Veltman, M.J.G.; Passarino, G.

1979-01-01

Analytical expressions for the cross section including all the one-loop radiative corrections in the context of the Weinberg model are presented. The systematic calculation of one-loop diagrams has been carried out using a recently proposed scheme. Numerical results are shown in a region from

Exploration of extremely low q_e_d_g_e regime in KSTAR

International Nuclear Information System (INIS)

Kim, Jayhyun; In, Y.; Park, B.H.; Aydemir, A.

2015-01-01

The q_e_d_g_e < 2 regime had long been regarded as an experimentally forbidden regime due to magneto-hydrodynamic instabilities. However, RFX-MOD experiment demonstrated that the control of error field could enable the entrance and sustainment of the discharge even in the forbidden regime. We explored q_e_d_g_e < 2 regime in Korea superconducting tokamak advanced research (KSTAR) without any feedback or feedforward control of error field since the intrinsic level of error field in KSTAR is inherently comparable to the controlled level of other device. The discharge sustained at q_9_5 ∼ 1.9 for 800 ms that is at least one order of magnitude longer than the resistive wall time of the device. Furthermore, simulated error field applied by field error correction coils prevented the passage of q_e_d_g_e = 3 integer rational surface before reaching q_e_d_g_e = 2. The detailed analysis is on-going for revealing the role of error field in the excitation of limiting instability. (author)

Vulnerability Analysis of Urban Drainage Systems: Tree vs. Loop Networks

Directory of Open Access Journals (Sweden)

Chi Zhang

2017-03-01

Full Text Available Vulnerability analysis of urban drainage networks plays an important role in urban flood management. This study analyzes and compares the vulnerability of tree and loop systems under various rainfall events to structural failure represented by pipe blockage. Different pipe blockage scenarios, in which one of the pipes in an urban drainage network is assumed to be blocked individually, are constructed and their impacts on the network are simulated under different storm events. Furthermore, a vulnerability index is defined to measure the vulnerability of the drainage systems before and after the implementation of adaptation measures. The results obtained indicate that the tree systems have a relatively larger proportion of critical hydraulic pipes than the loop systems, thus the vulnerability of tree systems is substantially greater than that of the loop systems. Furthermore, the vulnerability index of tree systems is reduced after they are converted into a loop system with the implementation of adaptation measures. This paper provides an insight into the differences in the vulnerability of tree and loop systems, and provides more evidence for development of adaptation measures (e.g., tanks to reduce urban flooding.

To 80-th anniversary of Shoferistova E.G.

Directory of Open Access Journals (Sweden)

Є. П. Шоферістов

2010-10-01

Full Text Available The life and scientific road of Shoferistova E.G. (E.G. Lysenko scince her childhood and student’s years up to scientistcytogeneticist has been analysed. It is shown that Shoferistova E.G. is a exemplary person and scientist-biologist. It is provided that the biographical information will be necessary for students, post graduate students and for all large family tree of Shoferistov and Lysenko.

Loop groups and Yang-Mills theory in dimension two

DEFF Research Database (Denmark)

Gravesen, Jens

1990-01-01

Given a connection ω in a G-bundle over S2, then a process called radial trivialization from the poles gives a unique clutching function, i.e., an element γ of the loop group ΩG. Up to gauge equivalence, ω is completely determined by γ and a map f:S2 →g into the Lie algebra. Moreover, the Yang......-Mills function of ω is the sum of the energy of γ and the square of a certain norm of f. In particular, the Yang-Mills functional has the same Morse theory as the energy functional on ΩG. There is a similar description of connections in a G-bundle over an arbitrary Riemann surface, but so far not of the Yang...

On the duality-transformed Wilson loop operator

International Nuclear Information System (INIS)

Mizrachi, L.

1981-08-01

Duality transformation of the vacuum expectation value of the Wilson loop operator is performed in the radial gauge (xsub(μ)Asub(μ)sup(a)(x) = 0). It is found to be equal, up to a multiplicative constant, to , where O(c) is a line integral along the loop c (defining the Wilson loop operator) of a function of the dual field variables. In the weak coupling region self duality is recovered in the sense that the Lagrangian is local gauge invariant defined in terms of the dual gauge potentials but with g (the coupling constant) replaced by 1/g, and O(c) is simply the line integral of the dual gauge potentials. For large g, a strong coupling expansion is suggested (but the theory is not local gauge invariant). (author)

Principles of agonist recognition in Cys-loop receptors

Directory of Open Access Journals (Sweden)

Timothy eLynagh

2014-04-01

Full Text Available Cys-loop receptors are ligand-gated ion channels that are activated by a structurally diverse array of neurotransmitters, including acetylcholine, serotonin, glycine and GABA. After the term chemoreceptor emerged over 100 years ago, there was some wait until affinity labeling, molecular cloning, functional studies and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically diverse as glycine and serotonin has been subject to intense research over the last three decades. This review outlines the functional diversity and current structural understanding of agonist-binding sites, including those of invertebrate Cys-loop receptors. Together, this provides a framework to understand the atomic determinants involved in how these valuable therapeutic targets recognize and bind their ligands.

The G_E/G_M-ratio of the proton by recoil polarization measurement in e+parrow e'+p

Science.gov (United States)

Punjabi, Vina; Jones, Mark; Perdrisat, Charles F.; Quemener, Gilles

1998-10-01

The recently commissioned Hall A high resolution spectrometers (HRS) and the focal plane polarimeter (FPP) were used to obtain the ratio of the electric and magnetic form factors of the proton, G_E/G_M. This form factor ratio is proportional to the measured ratio of the transverse, P_t, to longitudinal, P_l, components of the recoiling proton polarization. The method takes advantage of the precession of the proton magnetic moment in the hadron HRS, which rotates the longitudinal polarization component into the plane of the FPP analyzer; this allows simultaneous measurement of both components of the polarization. The ratio P_t/P_l is independent of both the electron beam polarization and the polarimeter analyzing power. Most of the data were obtained with polarized beams of 100 μ A with polarization of ~ 0.39 incident on the 15 cm cell of the high power LH2 target. We will report the results for G_E/GM at several values of Q^2 between 0.5 and 3.5 GeV^2.

Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

DEFF Research Database (Denmark)

Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

2017-01-01

linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

Directory of Open Access Journals (Sweden)

Michal Brylinski

2014-09-01

Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

DIVERSE PROTOSTELLAR EVOLUTIONARY STATES IN THE YOUNG CLUSTER AFGL961

International Nuclear Information System (INIS)

Williams, Jonathan P.; Mann, Rita K.; Beaumont, Christopher N.; Swift, Jonathan J.; Adams, Joseph D.; Hora, Joe; Kassis, Marc; Lada, Elizabeth A.; Roman-Zuniga, Carlos G.

2009-01-01

We present arcsecond resolution mid-infrared and millimeter observations of the center of the young stellar cluster AFGL961 in the Rosette molecular cloud. Within 0.2 pc of each other, we find an early B star embedded in a dense core, a neighboring star of similar luminosity with no millimeter counterpart, a protostar that has cleared out a cavity in the circumcluster envelope, and two massive, dense cores with no infrared counterparts. An outflow emanates from one of these cores, indicating a deeply embedded protostar, but the other is starless, bound, and appears to be collapsing. The diversity of states implies either that protostellar evolution is faster in clusters than in isolation or that clusters form via quasi-static rather than dynamic collapse. The existence of a pre-stellar core at the cluster center shows that some star formation continues after and in close proximity to massive, ionizing stars.

Identification of Bacillus thuringiensis Cry3Aa toxin domain II loop 1 as the binding site of Tenebrio molitor cadherin repeat CR12.

Science.gov (United States)

Zúñiga-Navarrete, Fernando; Gómez, Isabel; Peña, Guadalupe; Amaro, Itzel; Ortíz, Ernesto; Becerril, Baltazar; Ibarra, Jorge E; Bravo, Alejandra; Soberón, Mario

2015-04-01

Bacillus thuringiensis Cry toxins exert their toxic effect by specific recognition of larval midgut proteins leading to oligomerization of the toxin, membrane insertion and pore formation. The exposed domain II loop regions of Cry toxins have been shown to be involved in receptor binding. Insect cadherins have shown to be functionally involved in toxin binding facilitating toxin oligomerization. Here, we isolated a VHH (VHHA5) antibody by phage display that binds Cry3Aa loop 1 and competed with the binding of Cry3Aa to Tenebrio molitor brush border membranes. VHHA5 also competed with the binding of Cry3Aa to a cadherin fragment (CR12) that was previously shown to be involved in binding and toxicity of Cry3Aa, indicating that Cry3Aa binds CR12 through domain II loop 1. Moreover, we show that a loop 1 mutant, previously characterized to have increased toxicity to T. molitor, displayed a correlative enhanced binding affinity to T. molitor CR12 and to VHHA5. These results show that Cry3Aa domain II loop 1 is a binding site of CR12 T. molitor cadherin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inhibition of central insulin-receptor signaling by S961 causes hyperglycemia and glucose intolerance in rats

OpenAIRE

Ajit Vikram; Gopabandhu Jena

2011-01-01

Genetic ablation studies confirmed the role of central insulin-receptor signaling (CIRS) in fuel metabolism. However, the need to examine the role of CIRS in glucose homeostasis under normal physiological condition is indispensable, as insulin affects the neuronal growth, differentiation and synaptic plasticity. Intracerebral administration of S961 induced hyperglycemia and glucose intolerance in normal rats, and provided direct evidence for the involvement of CIRS in the regulation of glucos...

Detection of siRNA Mediated Target mRNA Cleavage Activities in Human Cells by a Novel Stem-Loop Array RT-PCR Analysis

Science.gov (United States)

2016-09-07

sequences of the target mRNA, and a double stranded stem at the 5′ end that forms a stem -loop to function as a forceps to stabilize the secondary...E-mjournal homepage: www.elsevier.com/locate/bbrepDetection of siRNA-mediated target mRNA cleavage activities in human cells by a novel stem -loop...challenges for the accurate and efficient detection and verification of cleavage sites on target mRNAs. Here we used a sensitive stem -loop array reverse

Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G-Proteins, PIP2 and Sodium

Science.gov (United States)

Whorton, Matthew R.; MacKinnon, Roderick

2011-01-01

Summary G-protein-gated K+ channels (Kir3.1–Kir3.4) control electrical excitability in many different cells. Among their functions relevant to human physiology and disease, they regulate the heart rate and govern a wide range of neuronal activities. Here we present the first crystal structures of a G-protein-gated K+ channel. By comparing the wild-type structure to that of a constitutively active mutant, we identify a global conformational change through which G-proteins could open a G-loop gate in the cytoplasmic domain. The structures of both channels in the absence and presence of PIP2 show that G-proteins open only the G-loop gate in the absence of PIP2, but in the presence of PIP2 the G-loop gate and a second inner helix gate become coupled, so that both gates open. We also identify a strategically located Na+ ion-binding site, which would allow intracellular Na+ to modulate GIRK channel activity. These data provide a mechanistic description of multi-ligand regulation of GIRK channel gating. PMID:21962516

Quantitative description of hysteresis loops induced by rf radiation in long Josephson junctions

DEFF Research Database (Denmark)

Olsen, Ole H.; Samuelsen, Mogens Rugholm

1991-01-01

The effect of an applied rf signal on the radiation emitted from a long Josephson junction is examined by means of a model based on the sine-Gordon equation. This system exhibits a variety of interesting phenomena, e.g., chaos and hysteresis. The hysteresis loop is examined in detail. These simple...

Stability assessment on a library scale: a rapid method for the evaluation of the commutability and insertion of residues in C-terminal loops of the CH3 domains of IgG1-Fc.

Science.gov (United States)

Hasenhindl, Christoph; Traxlmayr, Michael W; Wozniak-Knopp, Gordana; Jones, Phil C; Stadlmayr, Gerhard; Rüker, Florian; Obinger, Christian

2013-10-01

Antigen-binding Fc fragments (Fcab) are generated by engineering the C-terminal loop regions in the CH3 domain of human immunoglobulin G class 1-crystallizable fragment (IgG1-Fc). For an optimum library design with high percentage of well-folded clones for efficient binder selection, information about the correlation between primary structure and stability is needed. Here, we present a rapid method that allows determination of the overall stability of whole libraries of IgG1-Fc on the surface of yeast by flow cytometry. Libraries of IgG1-Fc mutants with distinct regions in AB-, CD- and EF-loops of the CH3 domains randomized or carrying therein insertions of five additional residues were constructed, incubated at increasing temperatures and probed for residual binding of generic Fc ligands. Calculated temperatures of half-maximal irreversible denaturation of the libraries gave a clear hierarchy of tolerance to randomization of distinct loop positions. Experimental data were evaluated by a computational approach and are discussed with respect to the structure of IgG1-Fc and variation in sequence and length of these loops in homologous Fc proteins. Generally, the described method allows for quick assessment of the effects of randomization of distinct regions on the foldability and stability of a yeast-displayed protein library.

Dechanneling by dislocation loops

International Nuclear Information System (INIS)

Chalant, Gerard.

1976-09-01

Ion implantation always induces the creation of dislocation loops. When the damage profile is determined by a backscattering technique, the dechanneling by these loops is implicitely at the origin of these measurements. The dechanneling of alpha particles by dislocation loops produced by the coalescence of quenched-in vacancies in aluminium is studied. The dechanneling and the concentration of loops were determined simultaneously. The dechanneling width around dislocation was found equal to lambda=6A, both for perfect and imperfect loops having a mean diameter d=250A. In the latter case, a dechanneling probability chi=0.34 was determined for the stacking fault, in good agreement with previous determination in gold. A general formula is proposed which takes into account the variation of lambda with the curvature (or the diameter d) of the loops. Finally, by a series of isothermal anneals, the self-diffusion energy ΔH of aluminium was measured. The value obtained ΔH=1.32+-0.10eV is in good agreement with the values obtained by other methods [fr

Alternative Splicing of G9a Regulates Neuronal Differentiation

Directory of Open Access Journals (Sweden)

Ana Fiszbein

2016-03-01

Full Text Available Chromatin modifications are critical for the establishment and maintenance of differentiation programs. G9a, the enzyme responsible for histone H3 lysine 9 dimethylation in mammalian euchromatin, exists as two isoforms with differential inclusion of exon 10 (E10 through alternative splicing. We find that the G9a methyltransferase is required for differentiation of the mouse neuronal cell line N2a and that E10 inclusion increases during neuronal differentiation of cultured cells, as well as in the developing mouse brain. Although E10 inclusion greatly stimulates overall H3K9me2 levels, it does not affect G9a catalytic activity. Instead, E10 increases G9a nuclear localization. We show that the G9a E10+ isoform is necessary for neuron differentiation and regulates the alternative splicing pattern of its own pre-mRNA, enhancing E10 inclusion. Overall, our findings indicate that by regulating its own alternative splicing, G9a promotes neuron differentiation and creates a positive feedback loop that reinforces cellular commitment to differentiation.

The 3-loop non-singlet heavy flavor contributions to the structure function g1(x,Q2 at large momentum transfer

Directory of Open Access Journals (Sweden)

A. Behring

2015-08-01

Full Text Available We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the polarized structure function g1(x,Q2 in the asymptotic region Q2≫m2 to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N and the momentum fraction x, and derive heavy flavor corrections to the Bjorken sum-rule. Numerical results are presented for the charm quark contribution. Results on the structure function g2(x,Q2 in the twist-2 approximation are also given.

Effect of closed loop cooling water transit time on containment cooling

International Nuclear Information System (INIS)

Smith, R.P.; Vossahlik, J.E.; Goodwin, E.F.

1996-01-01

Long term containment cooling analyses in nuclear plant systems are usually conducted assuming a quasi steady-state process, that is, a steady state evaluation of the cooling system is completed for each calculational step. In reality, fluid transport in the system, and heat addition to system components may affect the heat removal rate of the system. Transient effects occurring during system startup may affect the maximum temperatures experienced in the system. It is important to ensure that such transient effects do not affect operation of the system (e.g., cause a high temperature trip). To evaluate the effect of fluid transit delays, a closed loop cooling water system model has been developed that incorporates the fluid transport times when determining the closed loop cooling system performance. This paper describes the closed loop cooling system model as implemented in the CONTEMPT-LT/028 code. The evaluation of the transient temperature response of the closed loop cooling system using the model is described. The paper also describes the effect of fluid transit time on the overall containment cooling performance

Description of the Northwest hazardous waste site data base and preliminary analysis of site characteristics

International Nuclear Information System (INIS)

Woodruff, D.L.; Hartz, K.E.; Triplett, M.B.

1988-08-01

The Northwest Hazardous Waste RD and D Center (the Center) conducts research, development, and demonstration (RD and D) activities for hazardous and radioactive mixed-waste technologies applicable to remediating sites in the states of Idaho, Montana, Oregon, and Washington. To properly set priorities for these RD and D activities and to target development efforts it is necessary to understand the nature of the sites requiring remediation. A data base of hazardous waste site characteristics has been constructed to facilitate this analysis. The data base used data from EPA's Region X Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) and from Preliminary Assessment/Site Investigation (PA/SI) forms for sites in Montana. The Center's data base focuses on two sets of sites--those on the National Priorities List (NPL) and other sites that are denoted as ''active'' CERCLIS sites. Active CERCLIS sites are those sites that are undergoing active investigation and analysis. The data base contains information for each site covering site identification and location, type of industry associated with the site, waste categories present (e.g., heavy metals, pesticides, etc.), methods of disposal (e.g., tanks, drums, land, etc.), waste forms (e.g., liquid, solid, etc.), and hazard targets (e.g., surface water, groundwater, etc.). As part of this analysis, the Northwest region was divided into three geographic subregions to identify differences in disposal site characteristics within the Northwest. 2 refs., 18 figs., 5 tabs

Preliminary approach of the MELiSSA loop energy balance

Science.gov (United States)

Poulet, Lucie; Lamaze, Brigitte; Lebrun, Jean

Long duration missions, such as the establishment of permanent bases on the lunar surface or the travel to Mars, require a huge amount of life support consumables (e.g. food, water and oxygen). Current rockets are at the moment unable to launch such a mass from Earth. Consequently Regenerative Life Support Systems are necessary to sustain long-term manned space mission to increase recycling rates and so reduce the launched mass. Thus the European and Canadian research has been concentrating on the MELiSSA (Micro-Ecological Life Support System Alternative) project over the last 20 years. MELiSSA is an Environmental Controlled Life Support System (ECLSS), i.e. a closed regenerative loop inspired of a lake ecosystem. Using light as a source of energy, MELiSSA's goal is the recovery of food, water and oxygen from CO2 and organic wastes, using microorganisms and higher plants. The architecture of a ECLSS depends widely on the mission scenario. To compare several ECLSS architectures and in order to be able to evaluate them, ESA is developing a multi criteria evaluation tool: ALISSE (Advanced LIfe Support System Evaluator). One of these criteria is the energy needed to operate the ECLSS. Unlike other criteria like the physical mass, the energy criterion has not been investigated yet and needs hence a detailed analysis. It will consequently be the focus of this study. The main objective of the work presented here is to develop a dynamic tool able to estimate the energy balance for several configurations of the MELiSSA loop. The first step consists in establishing the energy balance using concrete figures from the MELiSSA Pilot Plant (MPP). This facility located at the Universitat Autonoma de Barcelona (UAB) is aimed at the ground demonstration of the MELiSSA loop. The MELiSSA loop is structured on several subsystems; each of them is characterized by supplies, exhausts and process reactions. For the purpose of this study (i.e. a generic tool) the solver EES (Engineering

Discovery of Specific Inhibitors for Intestinal E. coli  β-Glucuronidase through In Silico Virtual Screening

Directory of Open Access Journals (Sweden)

Ta-Chun Cheng

2015-01-01

Full Text Available Glucuronidation is a major metabolism process of detoxification for carcinogens, 4-(methylnitrosamino-1-(3-pyridy-1-butanone (NNK and 1,2-dimethylhydrazine (DMH, of reactive oxygen species (ROS. However, intestinal E. coli   β-glucuronidase (eβG has been considered pivotal to colorectal carcinogenesis. Specific inhibition of eβG may prevent reactivating the glucuronide-carcinogen and protect the intestine from ROS-mediated carcinogenesis. In order to develop specific eβG inhibitors, we found that 59 candidate compounds obtained from the initial virtual screening had high inhibition specificity against eβG but not human βG. In particular, we found that compounds 7145 and 4041 with naphthalenylidene-benzenesulfonamide (NYBS are highly effective and selective to inhibit eβG activity. Compound 4041  (IC50=2.8 μM shows a higher inhibiting ability than compound 7145  (IC50=31.6 μM against eβG. Furthermore, the molecular docking analysis indicates that compound 4041 has two hydrophobic contacts to residues L361 and I363 in the bacterial loop, but 7145 has one contact to L361. Only compound 4041 can bind to key residue (E413 at active site of eβG via hydrogen-bonding interactions. These novel NYBS-based eβG specific inhibitors may provide as novel candidate compounds, which specifically inhibit eβG to reduce eβG-based carcinogenesis and intestinal injury.

Employing optical code division multiple access technology in the all fiber loop vibration sensor system

Science.gov (United States)

Tseng, Shin-Pin; Yen, Chih-Ta; Syu, Rong-Shun; Cheng, Hsu-Chih

2013-12-01

This study proposes a spectral amplitude coding-optical code division multiple access (SAC-OCDMA) framework to access the vibration frequency of a test object on the all fiber loop vibration sensor (AFLVS). Each user possesses an individual SAC, and fiber Bragg grating (FBG) encoders/decoders using multiple FBG arrays were adopted, providing excellent orthogonal properties in the frequency domain. The system also mitigates multiple access interference (MAI) among users. When an optical fiber is bent to a point exceeding the critical radius, the fiber loop sensor becomes sensitive to external physical parameters (e.g., temperature, strain, and vibration). The AFLVS involves placing a fiber loop with a specific radius on a designed vibration platform.

On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

International Nuclear Information System (INIS)

Meggiolaro, Enrico

2005-01-01

The high-energy elastic scattering amplitude of two colour-singlet qq-bar pairs is governed by the correlation function of two Wilson loops, which follow the classical straight lines for quark (antiquark) trajectories. This quantity is expected to be free of IR divergences, differently from what happens for the parton-parton elastic scattering amplitude, described, in the high-energy limit, by the expectation value of two Wilson lines. We shall explicitly test this IR finiteness by a direct non-perturbative computation of the loop-loop scattering amplitudes in the (pedagogic, but surely physically interesting) case of quenched QED. The results obtained for the Abelian case will be generalized to the case of a non-Abelian gauge theory with Nc colours, but stopping to the order O(g4) in perturbation theory. In connection with the above-mentioned IR finiteness, we shall also discuss some analytic properties of the loop-loop scattering amplitudes in both Abelian and non-Abelian gauge theories, when going from Minkowskian to Euclidean theory, which can be relevant to the still unsolved problem of the s-dependence of hadron-hadron total cross-sections

Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations.

Directory of Open Access Journals (Sweden)

Chih-Chieh Chen

Full Text Available BACKGROUND: The issue of whether patients diagnosed with metastatic colorectal cancer who harbor KRAS codon 13 mutations could benefit from the addition of anti-epidermal growth factor receptor therapy remains under debate. The aim of the current study was to perform computational analysis to investigate the structural implications of the underlying mutations caused by c.38G>A (p.G13D on protein conformation. METHODS: Molecular dynamics (MD simulations were performed to understand the plausible structural and dynamical implications caused by c.35G>A (p.G12D and c.38G>A (p.G13D. The potential of mean force (PMF simulations were carried out to determine the free energy profiles of the binding processes of GTP interacting with wild-type (WT KRAS and its mutants (MT. RESULTS: Using MD simulations, we observed that the root mean square deviation (RMSD increased as a function of time for the MT c.35G>A (p.G12D and MT c.38G>A (p.G13D when compared with the WT. We also observed that the GTP-binding pocket in the c.35G>A (p.G12D mutant is more open than that of the WT and the c.38G>A (p.G13D proteins. Intriguingly, the analysis of atomic fluctuations and free energy profiles revealed that the mutation of c.35G>A (p.G12D may induce additional fluctuations in the sensitive sites (P-loop, switch I and II regions. Such fluctuations may promote instability in these protein regions and hamper GTP binding. CONCLUSIONS: Taken together with the results obtained from MD and PMF simulations, the present findings implicate fluctuations at the sensitive sites (P-loop, switch I and II regions. Our findings revealed that KRAS mutations in codon 13 have similar behavior as KRAS WT. To gain a better insight into why patients with metastatic colorectal cancer (mCRC and the KRAS c.38G>A (p.G13D mutation appear to benefit from anti-EGFR therapy, the role of the KRAS c.38G>A (p.G13D mutation in mCRC needs to be further investigated.

Structure–function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring

Science.gov (United States)

Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

2016-01-01

A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure–function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein–RNA and protein–protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not. PMID:27417296

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter.

Science.gov (United States)

Belotserkovskii, Boris P; Soo Shin, Jane Hae; Hanawalt, Philip C

2017-06-20

Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA-DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA-DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription 'bursting') and may also have practical implications for the design of expression vectors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Experimental infection of calves with a gI, gE, US9 negative bovine herpesvirus type 5

NARCIS (Netherlands)

Hubner, S.O.; Oliveira, A.P.; Franco, A.C.; Rijsewijk, F.A.M.; Roehe, P.M.

2005-01-01

In this work, a role for the genes encoding glycoproteins I (gI) and E (gE) and the US9 protein of bovine herpesvirus type 5 (BHV-5) in neuropathogenicity and reactivation of latent infections was examined. Calves infected intranasally with a gI/gE/US9 deleted recombinant shed up to 102.85 TCID50/ml

Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain.

Science.gov (United States)

Guo, Yahui; Cheng, Junjie; Wang, Jine; Zhou, Xiaodong; Hu, Jiming; Pei, Renjun

2014-09-01

A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade.

Directory of Open Access Journals (Sweden)

Elena Papaleo

Full Text Available The ubiquitin (Ub system controls almost every aspect of eukaryotic cell biology. Protein ubiquitination depends on the sequential action of three classes of enzymes (E1, E2 and E3. E2 Ub-conjugating enzymes have a central role in the ubiquitination pathway, interacting with both E1 and E3, and influencing the ultimate fate of the substrates. Several E2s are characterized by an extended acidic insertion in loop 7 (L7, which if mutated is known to impair the proper E2-related functions. In the present contribution, we show that acidic loop is a conserved ancestral motif in E2s, relying on the presence of alternate hydrophobic and acidic residues. Moreover, the dynamic properties of a subset of family 3 E2s, as well as their binary and ternary complexes with Ub and the cognate E3, have been investigated. Here we provide a model of L7 role in the different steps of the ubiquitination cascade of family 3 E2s. The L7 hydrophobic residues turned out to be the main determinant for the stabilization of the E2 inactive conformations by a tight network of interactions in the catalytic cleft. Moreover, phosphorylation is known from previous studies to promote E2 competent conformations for Ub charging, inducing electrostatic repulsion and acting on the L7 acidic residues. Here we show that these active conformations are stabilized by a network of hydrophobic interactions between L7 and L4, the latter being a conserved interface for E3-recruitment in several E2s. In the successive steps, L7 conserved acidic residues also provide an interaction interface for both Ub and the Rbx1 RING subdomain of the cognate E3. Our data therefore suggest a crucial role for L7 of family 3 E2s in all the E2-mediated steps of the ubiquitination cascade. Its different functions are exploited thank to its conserved hydrophobic and acidic residues in a finely orchestrate mechanism.

Fast loop modeling for protein structures

Science.gov (United States)

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

2015-03-01

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

Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

Science.gov (United States)

Liphardt, J; Napthine, S; Kontos, H; Brierley, I

1999-05-07

RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those

Molecular dynamics analysis reveals structural insights into mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase.

Directory of Open Access Journals (Sweden)

Shan Wang

Full Text Available CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity. A recent site-directed mutagenesis study revealed that a single amino acid substitution, i.e., cysteine to tryptophan at the 330 position in the middle of protein, restores the NND activity of CYP82E3 entirely. However, the same amino acid change caused the loss of the NND activity of CYP82E4. To determine the mechanism of the functional turnover of the two molecules, four 3D structures, i.e., the two molecules and their corresponding cys-trp mutants were modeled. The resulting structures exhibited that the mutation site is far from the active site, which suggests that no direct interaction occurs between the two sites. Simulation studies in different biological scenarios revealed that the mutation introduces a conformation drift with the largest change at the F-G loop. The dynamics trajectories analysis using principal component analysis and covariance analysis suggests that the single amino acid change causes the opening and closing of the transfer channels of the substrates, products, and water by altering the motion of the F-G and B-C loops. The motion of helix I is also correlated with the motion of both the F-G loop and the B-C loop and; the single amino acid mutation resulted in the curvature of helix I. These results suggest that the single amino acid mutation outside the active site region may have indirectly mediated the flexibility of the F-G and B-C loops through helix I, causing a functional turnover of the P450 monooxygenase.

All-loop anomalous dimensions in integrable λ-deformed σ-models

Directory of Open Access Journals (Sweden)

George Georgiou

2015-12-01

Full Text Available We calculate the all-loop anomalous dimensions of current operators in λ-deformed σ-models. For the isotropic integrable deformation and for a semi-simple group G we compute the anomalous dimensions using two different methods. In the first we use the all-loop effective action and in the second we employ perturbation theory along with the Callan–Symanzik equation and in conjunction with a duality-type symmetry shared by these models. Furthermore, using CFT techniques we compute the all-loop anomalous dimension of bilinear currents for the isotropic deformation case and a general G. Finally we work out the anomalous dimension matrix for the cases of anisotropic SU(2 and the two couplings, corresponding to the symmetric coset G/H and a subgroup H, splitting of a group G.

Superbounce and loop quantum ekpyrotic cosmologies from modified gravity: F(R) , F(G) and F(T) theories

Science.gov (United States)

Odintsov, S. D.; Oikonomou, V. K.; Saridakis, Emmanuel N.

2015-12-01

We investigate the realization of two bouncing paradigms, namely of the superbounce and the loop quantum cosmological ekpyrosis, in the framework of various modified gravities. In particular, we focus on the F(R) , F(G) and F(T) gravities, and we reconstruct their specific subclasses which lead to such universe evolutions. These subclasses constitute from power laws, polynomials, or hypergeometric ansatzes, which can be approximated by power laws. The qualitative similarity of the different effective gravities which realize the above two bouncing cosmologies, indicates that a universality might be lying behind the bounce. Finally, performing a linear perturbation analysis, we show that the obtained solutions are conditionally or fully stable.

E-commerce Systems and E-shop Web Sites Security

OpenAIRE

Suchánek, Petr

2009-01-01

Fruitfulnes of contemporary companies rests on new business model development, elimination of communication obstacles, simplification of industrial processes, possibilities of responding in real-time and above all meeting the floating custom needs. Quite a number of company activities and transactions are realized within the framework of e-business. Business transactions are supported by e-commerce systems. One of the e-commerce system part is web interface (web sites). Present trend is putti...

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

Science.gov (United States)

Belotserkovskii, Boris P; Hanawalt, Philip C

2015-11-01

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

Resummed two-loop calculation of the disjoining pressure of a symmetric electrolyte soap film

International Nuclear Information System (INIS)

Dean, D.S.; Horgan, R.R.

2004-01-01

In this paper we consider the calculation of the disjoining pressure of a symmetric electrolytic soap film correct to two loops in perturbation theory. We show that the disjoining pressure is finite when the loop expansion is resummed using a cumulant expansion and requires no short distance cutoff in order to give a finite result. The loop expansion is resummed in terms of an expansion in g=l B /l D where l D is the Debye length and l B is the Bjerrum length. We show that there there is a nonanalytic contribution of order g ln(g). We also show that the two-loop correction is greater than the one-loop term at large film thicknesses suggesting a nonperturbative correction to the one-loop result in this limit

LoopIng: a template-based tool for predicting the structure of protein loops.

KAUST Repository

Messih, Mario Abdel

2015-08-06

Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

Structure-function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring.

Science.gov (United States)

Schwer, Beate; Kruchten, Joshua; Shuman, Stewart

2016-09-01

A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure-function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein-RNA and protein-protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not. © 2016 Schwer et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Nonequilibrium Chromosome Looping via Molecular Slip Links

Science.gov (United States)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Proteins mediating DNA loops effectively block transcription.

Science.gov (United States)

Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

2017-07-01

Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Principles of agonist recognition in Cys-loop receptors

DEFF Research Database (Denmark)

Lynagh, Timothy Peter; Pless, Stephan Alexander

2014-01-01

, functional studies, and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically...

Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic rate of GDP release.

Science.gov (United States)

Guilfoyle, Amy P; Deshpande, Chandrika N; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

2014-12-12

GDP release from GTPases is usually extremely slow and is in general assisted by external factors, such as association with guanine exchange factors or membrane-embedded GPCRs (G protein-coupled receptors), which accelerate the release of GDP by several orders of magnitude. Intrinsic factors can also play a significant role; a single amino acid substitution in one of the guanine nucleotide recognition motifs, G5, results in a drastically altered GDP release rate, indicating that the sequence composition of this motif plays an important role in spontaneous GDP release. In the present study, we used the GTPase domain from EcNFeoB (Escherichia coli FeoB) as a model and applied biochemical and structural approaches to evaluate the role of all the individual residues in the G5 loop. Our study confirms that several of the residues in the G5 motif have an important role in the intrinsic affinity and release of GDP. In particular, a T151A mutant (third residue of the G5 loop) leads to a reduced nucleotide affinity and provokes a drastically accelerated dissociation of GDP.

Results and techniques of multi-loop calculations

International Nuclear Information System (INIS)

Steinhauser, M.

2002-01-01

In this review some recent multi-loop results obtained in the framework of perturbative quantum chromodynamics (QCD) and quantum electrodynamics (QED) are discussed. After reviewing the most advanced techniques used for the computation of renormalization group functions, we consider the decoupling of heavy quarks. In particular, an effective method for the evaluation of the decoupling constants is presented and explicit results are given. Furthermore the connection to observables involving a scalar Higgs boson is worked out in detail. An all-order low energy v theorem is derived which establishes a relation between the coefficient functions in the hadronic Higgs decay and the decoupling constants. We review the radiative corrections of a Higgs boson into gluons and quarks and present explicit results up to order α s 4 and α s 3 , respectively. In this review special emphasis is put on the applications of asymptotic expansions. A method is described which combines expansion terms of different kinematical regions with the help of conformal mapping and Pade approximation. This method allows us to proceed beyond the present scope of exact multi-loop calculations. As far as physical processes are concerned, we review the computation of three-loop current correlators in QCD taking into account the full mass-dependence. In particular, we concentrate on the evaluation of the total cross section for the production of hadrons in e + e - annihilation. The knowledge of the complete mass dependence at order α s 2 has triggered a bunch of theory-driven analyses of the hadronic contribution to the electromagnetic coupling evaluated at high energy scales. The status is summarized in this review. In a further application four-loop diagrams are considered which contribute to the order α 2 QED corrections to the μ decay. Its relevance for the determination of the Fermi constant G F is discussed. Finally the calculation of the three-loop relation between the anti M anti S and on

Regulation of CCL2 expression by an upstream TALE homeodomain protein-binding site that synergizes with the site created by the A-2578G SNP.

Science.gov (United States)

Page, Stephen H; Wright, Edward K; Gama, Lucio; Clements, Janice E

2011-01-01

CC Chemokine Ligand 2 (CCL2) is a potent chemoattractant produced by macrophages and activated astrocytes during periods of inflammation within the central nervous system. Increased CCL2 expression is correlated with disease progression and severity, as observed in pulmonary tuberculosis, HCV-related liver disease, and HIV-associated dementia. The CCL2 distal promoter contains an A/G polymorphism at position -2578 and the homozygous -2578 G/G genotype is associated with increased CCL2 production and inflammation. However, the mechanisms that contribute to the phenotypic differences in CCL2 expression are poorly understood. We previously demonstrated that the -2578 G polymorphism creates a TALE homeodomain protein binding site (TALE binding site) for PREP1/PBX2 transcription factors. In this study, we identified the presence of an additional TALE binding site 22 bp upstream of the site created by the -2578 G polymorphism and demonstrated the synergistic effects of the two sites on the activation of the CCL2 promoter. Using chromatin immunoprecipitation (ChIP) assays, we demonstrated increased binding of the TALE proteins PREP1 and PBX2 to the -2578 G allele, and binding of IRF1 to both the A and G alleles. The presence of TALE binding sites that form inverted repeats within the -2578 G allele results in increased transcriptional activation of the CCL2 distal promoter while the presence of only the upstream TALE binding site within the -2578 A allele exerts repression of promoter activity.

Crystal structure of an eIF4G-like protein from Danio rerio

Energy Technology Data Exchange (ETDEWEB)

Bae, Euiyoung; Bitto, Eduard; Bingman, Craig A.; McCoy, Jason G.; Wesenberg, Gary E.; Phillips, Jr., George N. (UW)

2012-04-18

The gene LOC 91917 Danio rerio (zebrafish) encodes a protein annotated in the UniProt knowledgebase as the middle domain of eukaryotic initiation factor 4G domain containing protein b (MIF4Gdb). Its molecular weight is 25.8 kDa, and it comprises 222 amino acid residues. BLAST searches revealed homologues of D. rerio MIF4Gdb in many eukaryotes including humans. The homologue sand MIF4Gdb were identified as members of the Pfam family, MIF4G (PF2854), which is named after the middle domain of eukaryotic initiation factor 4G (eIF4G). eIF4G is a component of eukaryotic translational initiation complex, and contains binding sites for other initiation factors, suggesting its critical role in translational initiation. The MIF4G domain also occurs in several other proteins involved in RNA metabolism, including the Nonsense-mediated mRNA decay 2 protein (NMD2/UPF2), and the nuclear cap-binding protein 80-kDa subunit (CBP80). Sequence and structure analysis of the MIF4G domains in many proteins indicate that the domain assumes an all helical fold and has tandem repeated motifs. The zebrafish protein described here has homology to domains of other proteins variously referred to as NIC-containing proteins (NMD2, eIF4G, CBP80). The biological function of D. rerio MIF4Gdb has not yet been experimentally characterized, and the annotation is based on amino acid sequence comparison. D. rerio MIF4Gdb did not share more than 25% sequence identity with any protein for which the three-dimensional structure is known and was selected as a target for structure determination by the Center for Eukaryotic Structural Genomics (CESG). Here, they report the crystal structure of D. rerio MIF4Gdb (UniGene code Dr.79360, UniProt code Q5EAQ1, CESG target number GO.79294).

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

Science.gov (United States)

Lee, Hui Sun; Im, Wonpil

2017-01-01

Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

Dark matter, muon g -2 , electric dipole moments, and Z →ℓi+ℓj- in a one-loop induced neutrino model

Science.gov (United States)

Chiang, Cheng-Wei; Okada, Hiroshi; Senaha, Eibun

2017-07-01

We study a simple one-loop induced neutrino mass model that contains both bosonic and fermionic dark matter candidates and has the capacity to explain the muon anomalous magnetic moment anomaly. We perform a comprehensive analysis by taking into account the relevant constraints of charged lepton flavor violation, electric dipole moments, and neutrino oscillation data. We examine the constraints from lepton flavor-changing Z boson decays at the one-loop level, particularly when the involved couplings contribute to the muon g -2 . It is found that BR (Z →μ τ )≃(10-7- 10-6) while BR (τ →μ γ )≲10-11 in the fermionic dark matter scenario. The former can be probed by the precision measurement of the Z boson at future lepton colliders.

VICTORIA Class Submarine Human-in-the-Loop Experimentation Plan

Science.gov (United States)

2014-06-01

1472G. VICTORIA Class Submarine Human-in-the-Loop Experimentation Plan and Preliminary Results © Her Majesty the Queen in Right of...19 th International Command and Control Research and Technology Symposium Title: VICTORIA Class Submarine Human-in-the-Loop...TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE VICTORIA Class Submarine Human-in-the-Loop Experimentation Plan 5a. CONTRACT

As recensões G e W da vida de Esopo

Directory of Open Access Journals (Sweden)

Adriane da Silva Duarte

2014-12-01

Full Text Available A Vida de Esopo é uma obra que apresenta traços de dois gêneros: gênero biográfico e gênero romanesco antigos. Neste trabalho, expomos, em caráter introdutório, algumas características peculiares desse tipo de narrativa e apresentamos uma tradução da parte inicial das duas recensões principais da obra: a recensão G e a recensão W.

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

Science.gov (United States)

Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

ZED-2 experiments on the effect of a Co absorber rod on an NRU loop

International Nuclear Information System (INIS)

Arbique, G.M.; French, P.M.

1983-02-01

A series of experiments has been performed in ZED-2 to measure the perturbing effects of an NRU cobalt absorber rod on a simulated NRU loop site containing graded enrichment U0 2 fuel. The objective of the measurements was to provide data useful in validating NRU reactor physics codes. Using a simulated NRU lattice containing a simulated NRU loop site and an asymmetrically placed Co absorber rod, measurements were made of: (a) reactivity effects, as measured by critical height changes, associated with voiding the loop and stepped insertion of the Co absorber rod, (b) flux perturbations at the simulated loop site and throughout the lattice induced by the Co rod, (c) Westcott r√T/Tsub(o) values throughout the lattice

Site and facility waste transportation services planning documents

International Nuclear Information System (INIS)

Ratledge, J.E.; Schmid, S.; Danese, L.

1991-01-01

The Office of Civilian Radioactive Waste Management (OCRWM) will eventually ship Purchasers' (10 CFR 961.3) spent nuclear fuel from approximately 122 commercial nuclear facilities. The preparation and maintenance of Site- and Facility-Specific Transportation Services Planning Documents (SPDs) and Site-Specific Servicing Plans (SSSPs) provides a focus for advanced planning and the actual shipping of waste, as well as the overall development of transportation requirements for the waste transportation system. SPDs will be prepared for each of the affected nuclear waste facilities, with initial emphasis on facilities likely to be served during the earliest years of the Federal Waste Management System (FWMS) operations

SIMULTANEOUS OBSERVATION OF SOLAR OSCILLATIONS ASSOCIATED WITH CORONAL LOOPS FROM THE PHOTOSPHERE TO THE CORONA

Energy Technology Data Exchange (ETDEWEB)

Su, J. T.; Liu, S.; Zhang, Y. Z.; Zhao, H.; Xu, H. Q.; Xie, W. B. [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Science, Beijing 100012 (China); Liu, Y. [National Astronomical Observatories/Yunnan Observatory, Chinese Academy of Sciences, Kunming 650011 (China)

2013-01-01

The solar oscillations along one coronal loop in AR 11504 are observed simultaneously in white light emission and Doppler velocity by SDO/HMI, and in UV and EUV emissions by SDO/AIA. The technique of the time-distance diagram is used to detect the propagating oscillations of the emission intensities along the loop. We find that although all the oscillation signals were intercorrelated, the low chromospheric oscillation correlated more closely to the oscillations of the transition region and corona than to those of the photosphere. Situated above the sunspot, the oscillation periods were {approx}3 minutes in the UV/EUV emissions; however, moving away from the sunspot and into the quiet Sun, the periods became longer, e.g., up to {approx}5 minutes or more. In addition, along another loop we observe both the high-speed outflows and oscillations, which roughly had a one-to-one corresponding relationship. This indicates that the solar periodic oscillations may modulate the magnetic reconnections between the loops of the high and low altitudes that drive the high-speed outflows along the loop.

Hard-Thermal-Loop QCD thermodynamics and quark number susceptibility

Directory of Open Access Journals (Sweden)

Mogliacci Sylvain

2014-04-01

Full Text Available The weak-coupling expansion of the QCD pressure is known up to the order g6 log g. However, at experimentally relevant temperatures, the corresponding series is poorly convergent. In this proceedings, we discuss at which extent the gauge-invariant resummation scheme, Hard-Thermal-Loop perturbation theory (HTLpt, improves the apparent convergence. We first present HTLpt results for QCD thermodynamic functions up to three-loop order at vanishing chemical potential. Then, we report a preliminary HTLpt result of one-loop quark number susceptibility, probing the finite density equation of state. Our results are consistent with lattice data down to 2 − 3Tc, reinforcing the weakly-coupled quasiparticle picture in the intermediate coupling regime.

Sequencing Analysis of Mutant Allele $cdc$28-$srm$ of Protein Kinase CDC28 and Molecular Dynamics Study of Glycine-Rich Loop in Wild-Type and Mutant Allele G16S of CDK2 as Model

CERN Document Server

Koltovaya, N A; Kholmurodov, Kh T; Kretov, D A

2005-01-01

The central role that cyclin-dependent kinases play in the timing of cell division and the high incidence of genetic alteration of CDKs or deregulation of CDK inhibitors in a number of cancers make CDC28 of the yeast \\textit{Saccharomyces cerevisiae }very attractive model for studies of mechanisms of CDK regulation. Earlier it was found that certain gene mutations including \\textit{cdc28-srm} affect cell cycle progression, maintenance of different genetic structures and increase cell sensitivity to ionizing radiation. A~\\textit{cdc28-srm} mutation is not temperature-sensitive mutation and differs from the known \\textit{cdc28-ts }mutations because it has the evident phenotypic manifestations at 30 $^{\\circ}$C. Sequencing analysis of \\textit{cdc28-srm} revealed a single nucleotide substitution G20S. This is a third glycine in a conserved sequence GxGxxG in the G-rich loop positioned opposite the activation T-loop. Despite its demonstrated importance, the role of the G-loop has remained unclear. The crystal stru...

Closed-Loop and Robust Control of Quantum Systems

Directory of Open Access Journals (Sweden)

Chunlin Chen

2013-01-01

Full Text Available For most practical quantum control systems, it is important and difficult to attain robustness and reliability due to unavoidable uncertainties in the system dynamics or models. Three kinds of typical approaches (e.g., closed-loop learning control, feedback control, and robust control have been proved to be effective to solve these problems. This work presents a self-contained survey on the closed-loop and robust control of quantum systems, as well as a brief introduction to a selection of basic theories and methods in this research area, to provide interested readers with a general idea for further studies. In the area of closed-loop learning control of quantum systems, we survey and introduce such learning control methods as gradient-based methods, genetic algorithms (GA, and reinforcement learning (RL methods from a unified point of view of exploring the quantum control landscapes. For the feedback control approach, the paper surveys three control strategies including Lyapunov control, measurement-based control, and coherent-feedback control. Then such topics in the field of quantum robust control as H∞ control, sliding mode control, quantum risk-sensitive control, and quantum ensemble control are reviewed. The paper concludes with a perspective of future research directions that are likely to attract more attention.

Closed-loop and robust control of quantum systems.

Science.gov (United States)

Chen, Chunlin; Wang, Lin-Cheng; Wang, Yuanlong

2013-01-01

For most practical quantum control systems, it is important and difficult to attain robustness and reliability due to unavoidable uncertainties in the system dynamics or models. Three kinds of typical approaches (e.g., closed-loop learning control, feedback control, and robust control) have been proved to be effective to solve these problems. This work presents a self-contained survey on the closed-loop and robust control of quantum systems, as well as a brief introduction to a selection of basic theories and methods in this research area, to provide interested readers with a general idea for further studies. In the area of closed-loop learning control of quantum systems, we survey and introduce such learning control methods as gradient-based methods, genetic algorithms (GA), and reinforcement learning (RL) methods from a unified point of view of exploring the quantum control landscapes. For the feedback control approach, the paper surveys three control strategies including Lyapunov control, measurement-based control, and coherent-feedback control. Then such topics in the field of quantum robust control as H(∞) control, sliding mode control, quantum risk-sensitive control, and quantum ensemble control are reviewed. The paper concludes with a perspective of future research directions that are likely to attract more attention.

Site and facility transportation services planning documents

Energy Technology Data Exchange (ETDEWEB)

Ratledge, J.E. (Oak Ridge National Lab., TN (USA)); Danese, L.; Schmid, S. (Science Applications International Corp., Oak Ridge, TN (USA))

1990-01-01

The Office of Civilian Radioactive Waste Management (OCRWM) will eventually ship Purchasers' (10 CFR 961.3) spent nuclear fuel from approximately 122 commercial nuclear facilities. The preparation and processing of Site and Facility Specific Transportation Services Planning Documents (SPDs) and Site Specific Servicing Plans (SSSPs) provides a focus for advanced planning and the actual shipping of waste, as well as the overall development of transportation requirements for the waste transportation system. SPDs will be prepared for each of the affected nuclear waste facilities over the next 2 years with initial emphasis on facilities likely to be served during the earliest years of the Federal Waste Management System (FWMS) operations. 3 figs., 1 tab.

Site and facility transportation services planning documents

International Nuclear Information System (INIS)

Ratledge, J.E.; Danese, L.; Schmid, S.

1990-01-01

The Office of Civilian Radioactive Waste Management (OCRWM) will eventually ship Purchasers' (10 CFR 961.3) spent nuclear fuel from approximately 122 commercial nuclear facilities. The preparation and processing of Site and Facility Specific Transportation Services Planning Documents (SPDs) and Site Specific Servicing Plans (SSSPs) provides a focus for advanced planning and the actual shipping of waste, as well as the overall development of transportation requirements for the waste transportation system. SPDs will be prepared for each of the affected nuclear waste facilities over the next 2 years with initial emphasis on facilities likely to be served during the earliest years of the Federal Waste Management System (FWMS) operations. 3 figs., 1 tab

Pour une grille de lecture scientifique des sites web par les géographes

Directory of Open Access Journals (Sweden)

Henry Bakis

2014-02-01

Full Text Available L’utilisation massive et croissante des sites web en recherche pose la question de la nécessité d’établir une grille d’évaluation spécifique permettant d’apprécier la qualité d’un site à travers sa forme et son contenu sémantique. Dans ce contexte, le principal objectif est de déterminer les informations géographiques pertinentes d’un site en vue d’une exploitation pour la recherche en analyse spatiale. Les différentes démarches de l’étude d’un site (pragmatique, documentaire et thématique et ses objectifs (description du fond et de la forme, mise en évidence du potentiel d’interaction géographique sont ainsi présentés. Ce projet de recherche repose sur trois travaux en cours dont l’analyse géographique des sites web est l’élément essentiel. A travers une analyse homogène et rigoureuse des sites web, la grille méthodologique permettra ainsi une meilleure compréhension de la dynamique d’un système d’acteurs, de territoires et de réseaux en recherche.

BWR recirculation loop discharge line break LOCA tests with break areas of 50 and 100% assuming HPCS failure at ROSA-III test facility

International Nuclear Information System (INIS)

Suzuki, Mitsuhiro; Tasaka, Kanji; Yonomoto, Taisuke; Anoda, Yoshinari; Kumamaru, Hiroshige; Nakamura, Hideo; Murata, Hideo; Shiba, Masayoshi; Iriko, Masanori.

1985-03-01

This report presents the experimental results of RUN 962 and RUN 963 in ROSA-III program, which are 50 and 100 % break LOCA tests at the BWR recirculation pump discharge line, respectively. The ROSA-III test facility simulates a volumetrically scaled (1/424) BWR system and has four half-length electrically heated fuel bundles, two active recirculation loops, three types of ECCSs and steam and feedwater systems. The experimental data of RUN 962 and RUN 963 were compared with those of RUN 961, a 200 % discharge line break test to study the break area effects on the transient thermal hydraulic phenomena. The least flow areas at the jet pump drive nozzles and recirculation pump discharge nozzle in the broken recirculation loop limitted the discharge flows from the pressure vessel and the depressurization rate in the 100 and 200 % break tests, whereas the least flow area at break nozzle limitted the depressurization rate in the 50 % break test. The highest PCT was observed in the 50 % break test among the three tests. (author)

The herpes virus Fc receptor gE-gI mediates antibody bipolar bridging to clear viral antigens from the cell surface.

Directory of Open Access Journals (Sweden)

Blaise Ndjamen

2014-03-01

Full Text Available The Herpes Simplex Virus 1 (HSV-1 glycoprotein gE-gI is a transmembrane Fc receptor found on the surface of infected cells and virions that binds human immunoglobulin G (hIgG. gE-gI can also participate in antibody bipolar bridging (ABB, a process by which the antigen-binding fragments (Fabs of the IgG bind a viral antigen while the Fc binds to gE-gI. IgG Fc binds gE-gI at basic, but not acidic, pH, suggesting that IgG bound at extracellular pH by cell surface gE-gI would dissociate and be degraded in acidic endosomes/lysosomes if endocytosed. The fate of viral antigens associated with gE-gI-bound IgG had been unknown: they could remain at the cell surface or be endocytosed with IgG. Here, we developed an in vitro model system for ABB and investigated the trafficking of ABB complexes using 4-D confocal fluorescence imaging of ABB complexes with transferrin or epidermal growth factor, well-characterized intracellular trafficking markers. Our data showed that cells expressing gE-gI and the viral antigen HSV-1 gD endocytosed anti-gD IgG and gD in a gE-gI-dependent process, resulting in lysosomal localization. These results suggest that gE-gI can mediate clearance of infected cell surfaces of anti-viral host IgG and viral antigens to evade IgG-mediated responses, representing a general mechanism for viral Fc receptors in immune evasion and viral pathogenesis.

Dispersion relations in loop calculations

International Nuclear Information System (INIS)

Kniehl, B.A.

1996-01-01

These lecture notes give a pedagogical introduction to the use of dispersion relations in loop calculations. We first derive dispersion relations which allow us to recover the real part of a physical amplitude from the knowledge of its absorptive part along the branch cut. In perturbative calculations, the latter may be constructed by means of Cutkosky's rule, which is briefly discussed. For illustration, we apply this procedure at one loop to the photon vacuum-polarization function induced by leptons as well as to the γf anti-f vertex form factor generated by the exchange of a massive vector boson between the two fermion legs. We also show how the hadronic contribution to the photon vacuum polarization may be extracted from the total cross section of hadron production in e + e - annihilation measured as a function of energy. Finally, we outline the application of dispersive techniques at the two-loop level, considering as an example the bosonic decay width of a high-mass Higgs boson. (author)

Closing the sensorimotor loop: haptic feedback facilitates decoding of motor imagery

Science.gov (United States)

Gomez-Rodriguez, M.; Peters, J.; Hill, J.; Schölkopf, B.; Gharabaghi, A.; Grosse-Wentrup, M.

2011-06-01

The combination of brain-computer interfaces (BCIs) with robot-assisted physical therapy constitutes a promising approach to neurorehabilitation of patients with severe hemiparetic syndromes caused by cerebrovascular brain damage (e.g. stroke) and other neurological conditions. In such a scenario, a key aspect is how to reestablish the disrupted sensorimotor feedback loop. However, to date it is an open question how artificially closing the sensorimotor feedback loop influences the decoding performance of a BCI. In this paper, we answer this issue by studying six healthy subjects and two stroke patients. We present empirical evidence that haptic feedback, provided by a seven degrees of freedom robotic arm, facilitates online decoding of arm movement intention. The results support the feasibility of future rehabilitative treatments based on the combination of robot-assisted physical therapy with BCIs.

New measurement of G_E/GM for the proton

Science.gov (United States)

Segel, Ralph

2003-10-01

Recent polarization transfer measurements of the ratio of the proton electric to magnetic form factor, G E /G_M, find μ_pG E /GM = 1 - 0.13Q ^2 while a long series of L-T separations are fit by μ_pG_E/GM ≈ 1. Jefferson Lab experiment E01-001 used a new technique for making L-T separations that greatly reduces the dominant systematic uncertainties present in previous determinations. Protons from ep scattering were measured over a wide range in ɛ at Q^2 = 2.64, 3.20 and 4.10 GeV^2 and, simultaneously, protons scattered at Q^2 = 0.5 GeV^2 were measured over a small range in ɛ. The Q^2 = 0.5 GeV^2 measurements provided an internal monitor and only kinematic factors and ratios of simultaneously measured cross sections enter into the determinations of G_E/G_M. Measuring the proton cross sections has the advantage that for the same Q^2, count rates change very little with ɛ and also proton momentum is the same at all ɛ thus eliminating the effect of any momentum-dependent inefficiencies. Neither of these is true for L-T separations performed by measuring electron cross sections. Furthermore, the radiative corrections for the proton cross sections are a factor of about 2.5 smaller. All previous L-T separations measured electron cross sections and none had the advantage of an internal monitor. Therefore, the results of E01-001 stringently test whether systematic uncertainties in previous L-T separations may have been sufficient to explain the discrepancy with the recent polarization transfer results.

Interseccionalidade gênero, raça e etnia e a lei Maria da Penha

Directory of Open Access Journals (Sweden)

Raquel da Silva Silveira

2014-01-01

Full Text Available A violência de gênero contra as mulheres é um fenômeno mundial abordado exaustivamente. Este artigo discute como a interseccionalidade gênero, raça e etnia emerge nos discursos jurídicos sobre as mulheres que acessam a justiça. O referencial teórico foi composto pela analítica do poder de Michel Foucault articulada aos conceitos de interseccionalidade, gênero, raça e etnia. A pesquisa de campo foi realizada no Poder Judiciário de Porto Alegre e de Sevilha entre agosto de 2010 e outubro de 2012. Foram construídas três amostras de conveniência: entrevistas com 290 mulheres, análise de 70 processos judiciais e de 55 boletins de ocorrência. Foram realizadas entrevistas com quatro juízes/as de Porto Alegre e dois juízes em Sevilha. Os resultados apontam uma sobrerrepresentação das mulheres negras nos boletins de ocorrência, nas entrevistas, mas não nos processos. Apesar disso, os/as juízes/as entrevistados/as compreendem que a interseccionalidade gênero-raça e etnia não interfere no acesso à justiça.

Use of Hopcalite derived Cu-Mn mixed oxide as Oxygen Carrier for Chemical Looping with Oxygen Uncoupling Process

OpenAIRE

Adánez-Rubio, Iñaki; Abad Secades, Alberto; Gayán Sanz, Pilar; Adánez-Rubio, Imanol; Diego Poza, Luis F. de; Garcia-Labiano, Francisco; Adánez Elorza, Juan

2016-01-01

Chemical-Looping with Oxygen Uncoupling (CLOU) is an alternative Chemical Looping process for the combustion of solid fuels with inherent CO2 capture. The CLOU process needs a material as oxygen carrier with the ability to give gaseous O2 at suitable temperatures for solid fuel combustion, e.g. copper oxide and manganese oxide. In this work, treated commercial Carulite 300® was evaluated as oxygen carrier for CLOU. Carulite 300® is a hopcalite material composed of 29.2 wt.% CuO and 67.4 wt.% ...

Growth kinetics of dislocation loops in irradiated ceramic materials

International Nuclear Information System (INIS)

Ryazanov, A.I.; Kinoshita, C.

2002-01-01

Ceramic materials are expected to be applied in the future fusion reactor as radio frequency (RF) windows, toroidal insulating breaks and diagnostic probes. The radiation resistance of ceramic materials, degradation of the electrical properties and radiation induced conductivity of these materials under neutron irradiation are determined by the kinetics of the accumulation of point defects in the matrix and point defect cluster formation (dislocation loops, voids, etc.). Under irradiation, due to the ionization process, excitation of electronic subsystem and covalent type of interaction between atoms the point defects in ceramic materials are characterized by the charge state (e.g. an F + center, an oxygen vacancy with a single trapped electron) and the effective charge. For the investigation of radiation resistance of ceramic materials for future fusion applications it is very important to understand the physical mechanisms of formation and growth of dislocation loops and voids under irradiation taking into account in this system the effective charge of point defects. In the present paper the physical mechanisms of dislocation loop growth in ceramic material are investigated. For this aim a theoretical model is suggested for the description of the kinetics of point defect accumulation in the matrix taking into account the charge state of the point defects and the effect of an electric field on diffusion migration process of charged point defects. A self-consistent system of kinetic equations describing the generation of electrical fields near dislocation loops and diffusion migration of charged point defects in elastic and electrical fields is formulated. The solution of the kinetic equations allows to find the growth rate of dislocation loops in ceramic materials under irradiation taking into account the charge state of the point defects and the effect of electric and elastic stress fields near dislocation loop on the diffusion processes

A live, attenuated pseudorabies virus strain JS-2012 deleted for gE/gI protects against both classical and emerging strains.

Science.gov (United States)

Tong, Wu; Li, Guoxin; Liang, Chao; Liu, Fei; Tian, Qing; Cao, Yanyun; Li, Lin; Zheng, Xuchen; Zheng, Hao; Tong, Guangzhi

2016-06-01

Emerging pseudorabies virus (PRV) variant have led to pseudorabies outbreaks in Chinese pig farms. The commercially available PRV vaccine provides poor protection against the PRV variant. In this study, a gE/gI deleted PRV strain JS-2012-△gE/gI was generated from a PRV variant strain using homologous DNA recombination. Compared to the parental strain JS-2012, JS-2012-△gE/gI grew slowly and showed small plaque morphology on Vero cells. The safety and immunological efficacy of JS-2012-△gE/gI was evaluated as a vaccine candidate. JS-2012-△gE/gI was avirulent to suckling piglets, but was able to provide full protection for young piglets against challenge with both the classical virulent PRV and the emerging PRV variant. After sows were vaccinated with the gE/gI-deleted strain, their suckling offspring were resistant to an otherwise lethal challenge with the classical and the variant PRVs. Piglets inoculated with JS-2012-△gE/gI did not develop PRV-specific gE-ELISA antibodies. Thus, JS-2012-△gE/gI appears to be a promising marker vaccine candidate to control PRV variant circulating in pig farms in China. Copyright © 2016 Elsevier B.V. All rights reserved.

Full one-loop electroweak corrections to h0(H0,A0)H±W± associated productions at e+e- linear colliders

International Nuclear Information System (INIS)

Liu Jing; Ma Wengan; Zhang Renyu; Guo Lei; Jiang Yi; Han Liang

2007-01-01

We study the complete one-loop electroweak (EW) corrections to the processes of single charged Higgs boson production associated with a neutral Higgs boson (h 0 ,H 0 ,A 0 ) and a gauge boson W ± in the framework of the minimal supersymmetric standard model (MSSM). Numerical results at the SPS1a ' benchmark point as proposed in the SPA project, are presented for demonstration. We find that for the process e + e - →h 0 H ± W ± the EW relative correction can be either positive or negative and in the range of -15%∼20% in our chosen parameter space. While for the processes e + e - →H 0 (A 0 )H ± W ± the corrections generally reduce the Born cross sections and the EW relative corrections are typically of order -10%∼-20%

O gênero negro: apontamentos sobre gênero, feminismo e negritude

Directory of Open Access Journals (Sweden)

Danubia de Andrade Fernandes

2016-09-01

Full Text Available Neste artigo, apresento uma revisão teórica do conceito de gênero à luz dos estudos raciais. Isto significa que os preceitos que estabeleceram importantes teorias feministas são conjugados às perspectivas raciais para entender a dupla alteridade da mulher negra. Este texto busca dar visibilidade às análises históricas e filosóficas construídas por feministas pioneiras no Brasil e nos Estados Unidos

Morfologia e biometria do timo em araras dos gêneros Ara e Anodorhynchus

Directory of Open Access Journals (Sweden)

R.Z. Lima

2013-02-01

Full Text Available Foram utilizados 12 exemplares de Ara ararauna - seis fêmeas e seis machos -, cinco exemplares de Ara chloropterus (uma fêmea e quatro machos e dois exemplares de Anodorhynchus hyacinthinus - uma fêmea e um macho -, todos adultos, doados por criadouro particular, após óbito natural. Os lobos foram dissecados e medidos com paquímetro - comprimento x largura x espessura - e analisados quanto ao peso, à topografia e à morfologia individual. Independentemente do gênero, foram identificados, em 17 casos (89,5%, lobos tímicos nos antímeros cervicais esquerdo e direito, e em oito casos (42,1%, lobos na cavidade celomática. Os lobos apresentaram formatos alongados - 52,6% -, arredondados - 21,1% - ou ovalados - 15,8% -, posicionados preferencialmente ventromedialmente ao longo do plexo vasculoneural do pescoço, com número médio de cinco lobos por antímero, tamanho médio de 0,49cm de comprimento, 0,12cm de largura e 0,05cm de espessura e peso médio de 0,076g.

High-temperature helium-loop facility

International Nuclear Information System (INIS)

Tokarz, R.D.

1981-09-01

The high-temperature helium loop is a facility for materials testing in ultrapure helium gas at high temperatures. The closed loop system is capable of recirculating high-purity helium or helium with controlled impurities. The gas loop maximum operating conditions are as follows: 300 psi pressure, 500 lb/h flow rate, and 2100 0 F temperature. The two test sections can accept samples up to 3.5 in. diameter and 5 ft long. The gas loop is fully instrumented to continuously monitor all parameters of loop operation as well as helium impurities. The loop is fully automated to operate continuously and requires only a daily servicing by a qualified operator to replenish recorder charts and helium makeup gas. Because of its versatility and high degree of parameter control, the helium loop is applicable to many types of materials research. This report describes the test apparatus, operating parameters, peripheral systems, and instrumentation system. The experimental capabilities and test conand presents the results that have been obtained. The study has been conducted using a four-phase approach. The first phase develops the solution to the steady-state radon-diffusion equation in one-dimensieered barriers; disposal charge analysis; analysis of spent fuel policy implementation; spent f water. Field measurements and observations are reported for each site. Analytical data and field measurements are presented in tables and maps. Uranium concentrations in the sediments which were above detection limits ranged from 0.10 t 51.2 ppM. The mean of the logarithms of the uranium concentrations was 0.53. A group of high uranium concentrations occurs near the junctions of quadrangles AB, AC, BB, a 200 mK. In case 2), x-ray studies of isotopic phase separation in 3 He-- 4 He bcc solids were carried out by B. A. Fraass

A Cost-Effective Approach to Hardware-in-the-Loop Simulation

DEFF Research Database (Denmark)

Pedersen, Mikkel Melters; Hansen, M. R.; Ballebye, M.

2012-01-01

This paper presents an approach for developing cost effective hardware-in-the- loop (HIL) simulation platforms for the use in controller software test and development. The approach is aimed at the many smaller manufacturers of e.g. mobile hydraulic machinery, which often do not have very advanced...... testing facilities at their disposal. A case study is presented where a HIL simulation platform is developed for the controller of a truck mounted loader crane. The total expenses in hardware and software is less than 10.000$....

A simple gastropexy for the loop-gastrostomy tube

Directory of Open Access Journals (Sweden)

Pang Ah-San

2012-01-01

Full Text Available The percutaneous endoscopic gastrostomy has been in clinical use for more than three decades. A recent innovation, the loop-gastrostomy, is more suitable for developing countries because the tube cannot be dislodged and is easy to change. Gastropexy and gastrostomy are separate but related moieties. We describe a novel technique to add a gastropexy to the loop-gastrostomy, using it successfully in a man with permanent dysphagia. It involved creating a secondary loop at the mid-portion of the LOOPPEG® 3G tube with absorbable ligatures.

Constricted double loop hysteresis and exchange bias attributed to the surface anisotropy in nanocrystalline La1/3Sr2/3Fe1−xCrxO3

International Nuclear Information System (INIS)

Sabyasachi, Sk.; Patra, M.; Majumdar, S.; Giri, S.

2013-01-01

We investigate magnetic properties of nanocrystalline ferrites with composition La 1/3 Sr 2/3 Fe 1−x Cr x O 3 (LSFCO) for x=0, 0.02, 0.04 and 0.06. Thermal variation of zero field cooled magnetization displays a weak signature close to the charge (T CO ) as well as antiferromagnetic ordering for x=0, 0.02 and 0.04. In addition, another disordered glassy magnetic transition (T g ) is noticed for all the compositions. T g is predominantly observed, although signature of charge ordering almost disappears for x=0.06. Interestingly, a constricted double loop type magnetic hysteresis loop is observed for x=0.02. This structure in the hysteresis loop disappears with further increase in Cr substitution. A systematic shift in the magnetic hysteresis loop is observed for all the compositions, while samples are cooled in a static magnetic field, which is the manifestation of exchange bias (EB) effect. The EB field (H E ) and magnetization (M E ) decrease remarkably due to minor Cr substitution at x=0.02 and then it reveals a sluggish increase with increasing x. For x=0.04 the EB effect emerges below ∼T CO , increases sluggishly with lowering of temperature and below ∼T g , it increases rapidly. The cooling field dependence exhibits significant increase of H E and M E for x=0.04, which is associated with the considerable increase of coercivity. Possible origin of EB correlated with the magnetic phase coexistence has been argued for nanocrystalline LSFCO. - Highlights: • Constricted double loop structure is observed for minor Cr substitution. • Exchange bias decreases significantly due to Cr substitution. • Intricate magnetic phase coexistence leads to the exchange bias effect

Enlarged symmetry algebras of spin chains, loop models, and S-matrices

International Nuclear Information System (INIS)

Read, N.; Saleur, H.

2007-01-01

The symmetry algebras of certain families of quantum spin chains are considered in detail. The simplest examples possess m states per site (m>=2), with nearest-neighbor interactions with U(m) symmetry, under which the sites transform alternately along the chain in the fundamental m and its conjugate representation m-bar. We find that these spin chains, even with arbitrary coefficients of these interactions, have a symmetry algebra A m much larger than U(m), which implies that the energy eigenstates fall into sectors that for open chains (i.e., free boundary conditions) can be labeled by j=0,1,...,L, for the 2L-site chain such that the degeneracies of all eigenvalues in the jth sector are generically the same and increase rapidly with j. For large j, these degeneracies are much larger than those that would be expected from the U(m) symmetry alone. The enlarged symmetry algebra A m (2L) consists of operators that commute in this space of states with the Temperley-Lieb algebra that is generated by the set of nearest-neighbor interaction terms; A m (2L) is not a Yangian. There are similar results for supersymmetric chains with gl(m+n|n) symmetry of nearest-neighbor interactions, and a richer representation structure for closed chains (i.e., periodic boundary conditions). The symmetries also apply to the loop models that can be obtained from the spin chains in a spacetime or transfer matrix picture. In the loop language, the symmetries arise because the loops cannot cross. We further define tensor products of representations (for the open chains) by joining chains end to end. The fusion rules for decomposing the tensor product of representations labeled j 1 and j 2 take the same form as the Clebsch-Gordan series for SU(2). This and other structures turn the symmetry algebra A m into a ribbon Hopf algebra, and we show that this is 'Morita equivalent' to the quantum group U q (sl 2 ) for m=q+q -1 . The open-chain results are extended to the cases vertical bar m vertical

Environmental remediation. Strategies and techniques for cleaning radioactively contaminated sites

International Nuclear Information System (INIS)

Falck, W. Eberhard

2001-01-01

Actions for a cleaner and safety environment have risen on social and political agendas in recent years. They include efforts to remediate contaminated sites posing a radiological risk to humans and the surrounding environment. Radiological risks can result from a variety of nuclear and non-nuclear activities. They include: nuclear or radiological accidents; nuclear weapons production and testing; poor radioactive waste management and disposal practices; industrial manufacturing involving radioactive materials; conventional mining and milling of ores and other production processes, e.g. oil and gas production, resulting in enhanced concentrations of naturally occurring radioactive materials (NORMs). The IAEA has developed a comprehensive programme directed at the remediation of radioactively contaminated sites. The programme collates and distributes knowledge about contaminated sites; appropriate methods for their characterization; assessment of their potential environmental and radiological impact; and applicable methods for their clean-up, following internationally recommended safety criteria. The overall resources, and which are technologically less advanced, to focus their efforts and chose appropriate strategies for the abatement or removal of exposure to radiation. An important aspect is the intention to 'close the loop' in the nuclear fuel cycle in the interests of sustainable energy development including nuclear power

A novel inactivated gE/gI deleted pseudorabies virus (PRV) vaccine completely protects pigs from an emerged variant PRV challenge.

Science.gov (United States)

Gu, Zhenqing; Dong, Jing; Wang, Jichun; Hou, Chengcai; Sun, Haifeng; Yang, Wenping; Bai, Juan; Jiang, Ping

2015-01-02

A highly virulent and antigenic variant of pseudorabies virus (PRV) broke out in China at the end of 2011 and caused great economic loss in the pig industry. In this study, an infectious bacterial artificial chromosome (BAC) clone containing the full-length genome of the emerged variant PRV ZJ01 strain was generated. The BAC-derived viruses, vZJ01-GFPΔgE/gI (gE/gI deleted strain, and exhibiting green autofluorescence), vZJ01ΔgE/gI (gE/gI deleted strain), and vZJ01gE/gI-R (gE/gI revertant strain), showed similar in vitro growth to their parent strain. In pigs, inactivated vZJ01ΔgE/gI vaccine generated significantly high levels of neutralizing antibodies against ZJ01 compared with Bartha-K61 live vaccine (pvaccine group survived without exhibiting any clinical sings, but two of five animals exhibited central nervous signs in the Bartha-K61 group. Meanwhile, all the non-vaccinated control animals died at 7 days post-challenge. This indicates that the inactivated vZJ01ΔgE/gI vaccine is a promising vaccine candidate for controlling the variant strains of PRV now circulating in China. Copyright © 2014 Elsevier B.V. All rights reserved.

Loop Transfer Matrix and Loop Quantum Mechanics

International Nuclear Information System (INIS)

Savvidy, George K.

2000-01-01

The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

Two-loop fermionic corrections to massive Bhabha scattering

Energy Technology Data Exchange (ETDEWEB)

Actis, S.; Riemann, T. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Czakon, M. [Wuerzburg Univ. (Germany). Inst. fuer Theoretische Physik und Astrophysik]|[Institute of Nuclear Physics, NSCR DEMOKRITOS, Athens (Greece); Gluza, J. [Silesia Univ., Katowice (Poland). Inst. of Physics

2007-05-15

We evaluate the two-loop corrections to Bhabha scattering from fermion loops in the context of pure Quantum Electrodynamics. The differential cross section is expressed by a small number of Master Integrals with exact dependence on the fermion masses m{sub e}, m{sub f} and the Mandelstam invariants s, t, u. We determine the limit of fixed scattering angle and high energy, assuming the hierarchy of scales m{sup 2}{sub e}<loop contributions. (orig.)

Consumidoras e heroínas: gênero na telenovela

Directory of Open Access Journals (Sweden)

Heloisa Buarque de Almeida

2007-01-01

Full Text Available http://dx.doi.org/10.1590/S0104-026X2007000100011 Este trabalho explora as correlações entre telenovela, consumo e gênero, buscando compreender como a mídia está articulada à promoção de bens e da cultura do consumo, e como gênero é um eixo importante em tal articulação. A pesquisa foi feita a partir de um estudo etnográfico de recepção de novelas, e se desdobra na análise da relação entre televisão e publicidade, discutindo a feminilização do consumo e a construção de certa imagem feminina hegemônica nas novelas e nos anúncios comerciais.

Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

Directory of Open Access Journals (Sweden)

Jianbin Liu

Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

Direct From Minnesota--E. G. Williamson

Science.gov (United States)

Ewing, Dorlesa Barmettler

1975-01-01

Reminisces about E. G. Williamson, his personality, childhood and philosophy of life which involved striving to achieve excellence. Through an interview format, the author explores Williamson's views about counseling theory and practice, Carl Rogers, educating counselors, the development of counseling in the future, and the history of counseling…

Structure of eEF3 and the mechanism of transfer RNA release from the E-site

DEFF Research Database (Denmark)

Andersen, Christian Brix Folsted; Becker, T.; Blau, M.

2006-01-01

Elongation factor eEF3 is an ATPase, which, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aatRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate...... the clearance of deacyl-tRNA from the E-site. Here, we present the crystal structure of eEF3 showing that it consists of an N-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains with a chromo-domain inserted in ABC2. Moreover, we present the cryo-EM structure of the ATP......-bound form of eEF3 in complex with the post-translocational state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain stabilizing the ribosomal L1 stalk in an open conformation, thus, allowing tRNA release....

Remodeling of the AB site of rat parvalbumin and oncomodulin into a canonical EF-hand

DEFF Research Database (Denmark)

Cox, J A; Durussel, I; Scott, D J

1999-01-01

-residue canonical loop. To create an optical conformational probe we also expressed the homologs with a F102W replacement. Unexpectedly, in none of the proteins did the mutation reactivate the AB site. The AB-remodeled parvalbumins bind two Ca2+ ions with strong positive cooperativity (nH = 2......Parvalbumin (PV) and the homologous protein oncomodulin (OM) contain three EF-hand motifs, but the first site (AB) cannot bind Ca2+. Here we aimed to recreate the putative ancestral proteins [D19-28E]PV and [D19-28E]OM by replacing the 10-residue-long nonfunctional loop in the AB site by a 12...... conformations. The AB-remodeled oncomodulins also bind two Ca2+ with [Ca2+]0.5 = 43 microM and nH = 1.45. Mg2+ does not affect Ca2+ binding. Again the Ca2+ forms display two-thirds of the alpha-helical content in the wild-type, while their core is still strongly hydrophobic as monitored by Trp and Tyr...

CT-guided diagnostic interventions for classification of focal hepatic lesions: A comparison of 14 G- and 18 G-large bore cutting needles; CT-gesteuerte perkutane Biopsien zur Klassifizierung von fokalen Leberlaesionen: Vergleich zwischen 14 G- und 18 G-Stanzbiopsienadeln

Energy Technology Data Exchange (ETDEWEB)

Haage, P.; Piroth, W.; Staatz, G.; Adam, G.; Guenther, R.W. [Klinik fuer Radiologische Diagnostik, Universitaetsklinikum der RWTH Aachen (Germany)

1999-07-01

Purpose: Analysis and comparison of CT-guided 14- and 18-gauge cutting needle biopsies to accurately assess focal liver disease. Methods: The data of 272 CT-guided biopsies in 268 patients were evaluated retrospectively with regard to sensitivity, specificity and complication rate of the chosen needle caliber in differentiating between benign and malignant disease as well as in the ability to determine specific cell types in the various disorders. A 14-gauge (G) needle was used in 101 (37.1%) cases, in 18-g needle biopsy was performed in 171 (62.9%) cases. The Fisher exact test was employed for statistical analysis. Results: Cutting needle biopsy yielded sufficient histologic material in 267 of 272 (98.2%) cases. Correct diagnosis of malignancy was established in 178 of 191 (93.2%) lesions, 73 of 76 (96.1%) disorders were accurately defined as benign, resulting in an overall value of 94.0% (251 of 267). Of these 251 biopsies a definite histological diagnosis could be determined in 90.6% of the cases employing a 14 G needle and in 90.3% using an 18-g needle. The sensitivity, specificity and rate of complications were 94.8%, 92.0%%, 3.0% for the 14-g needle and 92.7%, 97.6%, 0.6% for the 18-g needle, respectively. There were no statistically significant differences with regard to the needle size. Conclusions: CT-guided biopsy of hepatic lesions with the 18-g biopsy needle is of equivalent diagnostic accuracy when compared with the 14-g needle. (orig.) [Deutsch] Ziel: Analyse und Vergleich CT-gesteuerter Fein- und Grobstanzbiopsien zur definitiven Abklaerung unklarer fokaler Leberveraenderungen. Methoden: Die Daten von insgesamt 272 CT-gefuehrten Punktionen an 268 Patienten wurden retrospektiv hinsichtlich Sensitivitaet, Spezifitaet und Komplikationsrate zur Dignitaetsbestimmung und Faehigkeit zur artdiagnostischen Einordnung unter Beruecksichtigung der Groesse der gewaehlten Punktionsnadel ueberprueft und ausgewertet. In 101 (37,1%) Faellen wurde eine 14 Gauge (G

Characterization of the recombinant copper chaperone (CCS) from the plant Glycine (G.) max.

Science.gov (United States)

Sagasti, Sara; Yruela, Inmaculada; Bernal, Maria; Lujan, Maria A; Frago, Susana; Medina, Milagros; Picorel, Rafael

2011-02-01

The goal of the present work was to characterize the recombinant copper chaperone (CCS) from soybean. Very little is known about plant copper chaperones, which makes this study of current interest, and allows for a comparison with the better known homologues from yeast and humans. To obtain sizeable amounts of pure protein suitable for spectroscopic characterization, we cloned and overexpressed the G. max CCS chaperone in E. coli in the presence of 0.5 mM CuSO(4) and 0.5 mM ZnSO(4) in the broth. A pure protein preparation was obtained by using two IMAC steps and pH gradient chromatography. Most of the proteins were obtained as apo-form, devoid of copper atoms. The chaperone showed a high content (i.e., over 40%) of loops, turns and random coil as determined both by circular dichroism and homology modelling. The homology 3-D structural model suggests the protein might fold in three structural protein domains. The 3-D model along with the primary structure and spectroscopic data may suggest that copper atoms occupy the two metal binding sites, MKCEGC and CTC, within the N-terminal domain I and C-terminal domain III, respectively. But only one Zn-binding site was obtained spectroscopically.

Twist operator correlation functions in O(n) loop models

International Nuclear Information System (INIS)

Simmons, Jacob J H; Cardy, John

2009-01-01

Using conformal field theoretic methods we calculate correlation functions of geometric observables in the loop representation of the O(n) model at the critical point. We focus on correlation functions containing twist operators, combining these with anchored loops, boundaries with SLE processes and with double SLE processes. We focus further upon n = 0, representing self-avoiding loops, which corresponds to a logarithmic conformal field theory (LCFT) with c = 0. In this limit the twist operator plays the role of a 0-weight indicator operator, which we verify by comparison with known examples. Using the additional conditions imposed by the twist operator null states, we derive a new explicit result for the probabilities that an SLE 8/3 winds in various ways about two points in the upper half-plane, e.g. that the SLE passes to the left of both points. The collection of c = 0 logarithmic CFT operators that we use deriving the winding probabilities is novel, highlighting a potential incompatibility caused by the presence of two distinct logarithmic partners to the stress tensor within the theory. We argue that both partners do appear in the theory, one in the bulk and one on the boundary and that the incompatibility is resolved by restrictive bulk-boundary fusion rules

HCMV gB shares structural and functional properties with gB proteins from other herpesviruses

Energy Technology Data Exchange (ETDEWEB)

Sharma, Sapna [Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111 (United States); Wisner, Todd W.; Johnson, David C. [Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, OR 97239 (United States); Heldwein, Ekaterina E., E-mail: katya.heldwein@tufts.edu [Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111 (United States)

2013-01-20

Glycoprotein B (gB) facilitates HCMV entry into cells by binding receptors and mediating membrane fusion. The crystal structures of gB ectodomains from HSV-1 and EBV are available, but little is known about the HCMV gB structure. Using multiangle light scattering and electron microscopy, we show here that HCMV gB ectodomain is a trimer with the overall shape similar to HSV-1 and EBV gB ectodomains. HCMV gB ectodomain forms rosettes similar to rosettes formed by EBV gB and the postfusion forms of other viral fusogens. Substitution of several bulky hydrophobic residues within the putative fusion loops with more hydrophilic residues reduced rosette formation and abolished cell fusion. We propose that like gB proteins from HSV-1 and EBV, HCMV gB has two internal hydrophobic fusion loops that likely interact with target membranes. Our work establishes structural and functional similarities between gB proteins from three subfamilies of herpesviruses.

Two-loop electroweak top corrections are they under control?

CERN Document Server

Degrassi, G.; Feruglio, F.; Gambino, P.; Vicini, A.; Degrassi, G; Fanchiotti, S; Feruglio, F; Gambino, P; Vicini, A

1995-01-01

The assumption that two-loop top corrections are well approximated by the O(G_mu^2 mt^4) contribution is investigated. It is shown that in the case of the ratio neutral-to-charged current amplitudes at zero momentum transfer the O(G_mu^2 mt^2 M_Z^2) terms are numerically comparable to the m_t^4 contribution for realistic values of the top mass. An estimate of the theoretical error due to unknown two-loop top effect is presented for a few observables of LEP interest.

How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study.

Science.gov (United States)

Shanker, Sudhanshu; Bandyopadhyay, Pradipta

2017-08-01

The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg 2+ ions through water-mediated interaction. It is important to know the synergic role of Mg 2+ and the water network surrounding Mg 2+ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg 2+ is pulled from RNA, which causes disturbance of the water network. It was found that Mg 2+ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg 2+ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg 2+ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg 2+ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

PCBs and PCDD/Fs in soil from informal e-waste recycling sites and open dumpsites in India: Levels, congener profiles and health risk assessment.

Science.gov (United States)

Chakraborty, Paromita; Selvaraj, Sakthivel; Nakamura, Masafumi; Prithiviraj, Balasubramanian; Cincinelli, Alessandra; Bang, John J

2018-04-15

Growth of informal electronic waste (e-waste) recycling sector is an emerging problem for India. The presence of halogenated compounds in e-wastes may result in the formation of persistent organic pollutants like polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) during recycling processes. We therefore investigated PCBs and PCDD/Fs in surface soils explicitly from the informal e-waste recycling sites and nearby open dumpsites of major metropolitan cities from four corners of India, viz., New Delhi (North), Kolkata (East), Mumbai (West) and Chennai (South). In the informal e-waste recycling sites, the range of Σ 26 PCBs (0.4-488ng/g) and ƩPCDD/Fs (1.0-10.6ng/g) were higher than Ʃ 26 PCBs (0.3-21ng/g) and ƩPCDD/Fs (0.15-7.3ng/g) from open dumpsites. In the e-waste sites, ƩPCDDs were found with increasing trend from ƩTetraCDD to OctaCDD, whereas ƩPCDFs showed a reverse trend. The dominance of PCDF congeners and maximum toxicity equivalents (TEQ) for both PCDDs (17pg TEQ/g) and PCDFs (82pg TEQ/g) at Mandoli in New Delhi has been related to intensive precious metal recovery process using acid bath. Among dumpsites, highest TEQ for PCDD/Fs was observed at Kodangaiyur dumpsite of Chennai (CN DS -02, 45pg TEQ/g). Positive Matrix Factorization (PMF) model identified distinct congener pattern based on the functional activities, such as e-waste dismantling, shredding, precious metal recovery and open burning in dumpsites. E-waste metal recovery factor was loaded with 86-91% of PCB-77, -105, -114, -118 and 30% of PCB-126, possibly associated with the burning of wires during the copper extraction process. Almost 70% of the Ʃ 26 PCB concentrations was comprised of the dioxin-like PCB congeners with a maximum concentration of 437ng/g at New Moore market in Chennai, followed by Wire Lane (102ng/g), in Mumbai. We speculate that PCB-126 might have resulted from combustion of plastic materials in e-waste stream and dumped waste

218-E-8 Borrow Pit Demolition Site closure plan. Revision 1

International Nuclear Information System (INIS)

Ruck, F.R.

1994-01-01

The 218-E-8 Demolition Site was the site of a single demolition event in November of 1984. This demolition event was a form of thermal treatment for discarded explosive chemical products. Because the 218-E-8 Demolition Site will no longer be used for this thermal activity, the site will be closed. Closure will be conducted pursuant to the requirements of the Washington State Department of Ecology (Ecology) ''Dangerous Waste Regulations,'' Washington Administrative Code (WAC) 173-303-610 and 40 Code of Federal Regulations (CFR) 270.1. The 218-E-8 Borrow Pit Demolition Site Closure Plan consists of a Hanford Facility Dangerous Waste Part A Permit Application, Form 3, Revision 4, and a closure plan. An explanation of the Part A Form 3, submitted with this closure plan is provided at the beginning of the Part A Section. The closure plan consists of nine chapters and five appendices. This closure plan presents a description of the 218-E-8 Demolition Site, the history of the waste treated, and the approach that will be followed to close the 218-E-8 Demolition Site. Because there were no radioactively contaminated chemicals involved in t he demolitions at the 218-E-8 Borrow Pit site, the information on radionuclides is provided for ''information only.'' Remediation of any radioactive contamination is not within the scope of this closure plan. Only dangerous constituents derived from 218-E-8 Demolition Site operations will be addressed in this closure plan in accordance with WAC 173-303-610(2)(b)(i)

Assemblée générale

CERN Multimedia

Staff Association

2013-01-01

Mardi 21 mai à 11 h 00 Amphithéâtre Kjell Johnsen, Bât. 30   Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 17 avril 2012. Présentation et approbation du rapport d’activités 2012. Présentation et approbation du rapport financier 2012. Présentation et approbation du rapport des vérificateurs aux comptes pour 2012. Programme 2013. Présentation et approbation du projet de budget et taux de cotisation pour 2014. Modifications aux Statuts de l'Association du personnel. Élections d...

Designing Dialogic E-Learning in Pharmacy Professionalism Using Calibrated Feedback Loops (CFLs

Directory of Open Access Journals (Sweden)

Sue Roff

2013-09-01

Full Text Available The feedback analytics of online software including Articulate and Bristol Online Surveys can be used to facilitate dialogic learning in a community of practice such as Pharmacy and, thereby, promote reflective learning by the creation of formative calibrated feedback loops. Based on work with medical, dental, nursing, osteopathic, and social work students, trainees, and registrants, the paper shows how an online learning community can be created along the continuum from undergraduate to registrant to develop authentic dialogic e-learning around standards of Professionalism. The Dundee PolyProfessionalism inventories and Situational Judgement Scenarios (SJSs can be customised for Pharmacy Professionalism learning to support evidence-based curriculum design along benchmarked learning curves and to profile Professionalism learning in individuals and cohorts.

PERENCANAAN LOKASI SITE BTS LAYANAN 3G-WCDMA DI PEMERINTAH KOTA DENPASAR DENGAN MEMANFAATKAN BALAI BANJAR

Directory of Open Access Journals (Sweden)

I Wayan Aryadi

2015-03-01

Full Text Available Seiring dengan perkembangan kebutuhan bit rate dan kapasitas layanan data yang meningkat di wilayah Kota Denpasar, diperlukan perencanaan lokasi site BTS (Base Transceiver Station yang dapat melayani kebutuhan pelanggan secara kuantitas maupun kualitas. Untuk memperoleh nilai bit rate yang maksimal dibutuhkan jari-jari sel yang kecil. Dengan perbandingan luas wilayah sebesar 130,48 km2 jika dibagi dengan 399 balai banjar di Kota Denpasar maka diperoleh coverage area 0,327 km2 per banjar dengan jari-jari sel sekitar 285 m. Maka pada penelitian ini lokasi site BTS yang digunakan adalah pada Balai Banjar di Kota Denpasar. Tujuan penelitian ini adalah untuk merancang lokasi site BTS layanan 3G-WCDMA (Wideband Code Division Multiple Access untuk wilayah Pemerintah Kota Denpasar sesuai data sebaran penduduk dan mengetahui perbandingan jumlah site BTS secara teoritis untuk layanan 3G-WCDMA memanfaatkan Balai Banjar Pemerintah Kota Denpasar dengan model pemetaan secara geografis. Metode penelitian terdiri dari 3 alur, yaitu perkiraan pertumbuhan pelanggan 3G-WCDMA dan Offered Bit Quantity (OBQ per desa di Kota Denpasar, Perhitungan jumlah dan jari-jari site secara teoritis per desa di Kota Denpasar, dan Pemetaan site di Kota Denpasar memanfaatkan Balai Banjar. Perhitungan secara teoritis menunjukkan bahwa 257 site yang diperlukan untuk melingkupi seluruh wilayah Denpasar. Sementara pemetaan secara geografis dengan memanfaatkan lokasi Balai Banjar adalah sebanyak 311 site. Dari 311 site, 155 site (49,84% terdapat pada kawasan Balai Banjar dan 156 site (50,16% terdapat di luar kawasan Balai Banjar.

Loop residues and catalysis in OMP synthase

DEFF Research Database (Denmark)

Wang, Gary P.; Hansen, Michael Riis; Grubmeyer, Charles

2012-01-01

binding of OMP or PRPP in binary complexes was affected little by loop mutation, suggesting that the energetics of ground-state binding have little contribution from the catalytic loop, or that a favorable binding energy is offset by costs of loop reorganization. Pre-steady-state kinetics for mutants...... values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1?-3H]OMP kinetic isotope effect (KIE) for WT is masked because of high forward and reverse commitment factors. K103A failed to express intrinsic KIEs fully (1.095 ± 0.013). In contrast, H105A, which has a smaller catalytic lesion...... (preceding paper in this issue, DOI 10.1021/bi300083p)]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop. The lower level of expression of the KIE by K103A suggests that in these mutant proteins the major barrier to catalysis is successful closure...

Modulation of translation-initiation in CHO-K1 cells by rapamycin-induced heterodimerization of engineered eIF4G fusion proteins.

Science.gov (United States)

Schlatter, Stefan; Senn, Claudia; Fussenegger, Martin

2003-07-20

Translation-initiation is a predominant checkpoint in mammalian cells which controls protein synthesis and fine-tunes the flow of information from gene to protein. In eukaryotes, translation-initiation is typically initiated at a 7-methyl-guanylic acid cap posttranscriptionally linked to the 5' end of mRNAs. Alternative cap-independent translation-initiation involves 5' untranslated regions (UTR) known as internal ribosome entry sites, which adopt a particular secondary structure. Translation-initiating ribosome assembly at cap or IRES elements is mediated by a multiprotein complex of which the initiation factor 4F (eIF4F) consisting of eIF4A (helicase), eIF4E (cap-binding protein), and eIF4G is a major constituent. eIF4G is a key target of picornaviral protease 2A, which cleaves this initiation factor into eIF4G(Delta) and (Delta)eIF4G to redirect the cellular translation machinery exclusively to its own IRES-containing transcripts. We have designed a novel translation control system (TCS) for conditional as well as adjustable translation of cap- and IRES-dependent transgene mRNAs in mammalian cells. eIF4G(Delta) and (Delta)eIF4G were fused C- and N-terminally to the FK506-binding protein (FKBP) and the FKBP-rapamycin-binding domain (FRB) of the human FKBP-rapamycin-associated protein (FRAP), respectively. Rapamycin-induced heterodimerization of eIF4G(Delta)-FKBP and FRB-(Delta)eIF4G fusion proteins reconstituted a functional chimeric elongation factor 4G in a dose-dependent manner. Rigorous quantitative expression analysis of cap- and IRES-dependent SEAP- (human placental secreted alkaline phosphatase) and luc- (Photinus pyralis luciferase) encoding reporter constructs confirmed adjustable translation control and revealed increased production of desired proteins in response to dimerization-induced heterologous eIF4G in Chinese hamster ovary (CHO-K1) cells. Copyright 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 210-225, 2003.

Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.

Directory of Open Access Journals (Sweden)

Simon Meyer

2009-10-01

Full Text Available MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs. Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlF(x structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 A. With GDP and AlF(x, which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlF(x requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD.

De Marias e Luizes: experiências devocionais e de gênero numa festa mariana

Directory of Open Access Journals (Sweden)

Martín, Eloísa

2003-01-01

Full Text Available O presente artigo parte de uma pesquisa levada a cabo entre 1998 e 2000 na festa da Virgem de Itatí em Corrientes (Argentina. A partir de dois casos, proponho analisar a maneira pela qual as experiências religiosas e de gênero relacionam-se e se constituem mutuamente a través de certas práticas devocionais. Tais práticas, transmitidas e reproduzidas por meio de laços familiares também marcadas por diferenciais de gênero, se processam em termos de um compromisso com a Virgem, mas também com as tradições locais e com os próprios laços de parentesco. Assim, através de certas práticas de devoção, veremos como se aprende a ser, ao mesmo tempo e desde o início, mulher e devota, homem e devoto

Amino-acid composition after loop deletion drives domain swapping.

Science.gov (United States)

Nandwani, Neha; Surana, Parag; Udgaonkar, Jayant B; Das, Ranabir; Gosavi, Shachi

2017-10-01

Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain-swapped oligomer over the monomer. While it is known that the deletion of loops between β-strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop-deletion mutants of the non-domain-swapping protein monellin, frame-shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping. © 2017 The Protein Society.

Elucidation of relaxin-3 binding interactions in the extracellular loops of RXFP3

Directory of Open Access Journals (Sweden)

Ross eBathgate

2013-02-01

Full Text Available Relaxin-3 is a highly conserved neuropeptide in vertebrate species and binds to the Class A G protein-coupled receptor RXFP3. Relaxin-3 is involved in a wide range of behaviours, including feeding, stress responses, arousal and cognitive processes and therefore targeting of RXFP3 may be relevant for a range of neurological diseases. Structural knowledge of RXFP3 and its interaction with relaxin-3 would both increase our understanding of ligand recognition in GPCRs that respond to protein ligands and enable acceleration of the design of drug leads. In this study we have used comparative sequence analysis, molecular modelling and receptor mutagenesis to investigate the binding site of the native ligand human relaxin-3 (H3 relaxin on the human RXFP3 receptor. Previous structure function studies have demonstrated that arginine residues in the H3 relaxin B-chain are critical for binding interactions with the receptor extracellular loops and/or N-terminal domain. Hence we have concentrated on determining the ligand interacting sites in these domains and have focussed on glutamic (E and aspartic acid (D residues in these regions that may form electrostatic interactions with these critical arginine residues. Conserved D/E residues identified from vertebrate species multiple sequence alignments were mutated to Ala in human RXFP3 to test the effect of loss of amino acid side chain on receptor binding using both Eu-labelled relaxin-3 agonist. Finally data from mutagenesis experiments have been used in ligand docking simulations to a homology model of human RXFP3 based on the peptide-bound CXCR4 structure. These studies have resulted in a model of the relaxin-3 interaction with RXFP3 which will inform further interrogation of the agonist binding site.

Sodium characterization during the starting period of a sodium loop

International Nuclear Information System (INIS)

Lievens, F.; Parmentier, C.; Soenen, M.

1976-01-01

A sodium loop for analytical chemistry studies has been built by S.C.K./C.E.N. at Mol Belgium. Its first working period was used to test analytical methods, to characterize the sodium and to define the operating parameters of the loop. This report covers the working parameters of the loop, the characterization of the filling sodium and its purity evolution during the first working period of the loop

Loop kinematics

International Nuclear Information System (INIS)

Migdal, A.A.

1982-01-01

Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

A ideologia da ideologia de gênero e a escola

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Linovaldo Miranda Lemos

2017-12-01

Full Text Available O objetivo do presente texto é o de trazer elementos à compreensão da relação entre ideologia e gênero de forma a contribuir com o debate atual sobre a chamada “ideologia de gênero” e a educação. Embora se trate de argumentos genéricos e sem base científica sólida, os críticos à discussão sobre gênero na escola acabam por criar, eles próprios, uma mistificação da realidade, uma visão de mundo imaginada a ser imposta de forma acrítica. O objetivo do texto foi trazer ao debate a natureza da ideologia e a impossibilidade de se pensar numa neutralidade científica e política em qualquer âmbito de nossas vivências, aí incluída e destacada, a escola.

Four-loop collinear anomalous dimension in N=4 Yang-Mills theory

International Nuclear Information System (INIS)

Cachazo, Freddy; Spradlin, Marcus; Volovich, Anastasia

2007-01-01

We report a calculation in N=4 Yang-Mills of the four-loop term g (4) in the collinear anomalous dimension g(λ) which governs the universal subleading infrared structure of gluon scattering amplitudes. Using the method of obstructions to extract this quantity from the 1/ε singularity in the four-gluon iterative relation at four loops, we find g (4) =-1240.9 with an estimated numerical uncertainty of 0.02%. We also analyze the implication of our result for the strong coupling behavior of g(λ), finding support for the string theory prediction computed recently by Alday and Maldacena using AdS/CFT

Optical and electrochemical detection of a verotoxigenic E. coli gene using DNAzyme-labeled stem-loops

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Gloria Longinotti

2017-12-01

Full Text Available The activity of a peroxidase-mimicking DNAzyme was optimized to be used as a catalytic label in a stem-loop genosensor construction for quantifying the gene sequence Shiga-like toxin I of verotoxigenic E. coli. Experimental conditions such as pH, buffer composition, potassium ion concentration, and hemin-to-oligonucleotides ratio, were analyzed to maximize optical and electrochemical responses using microvolumes. Different stem-loop constructions were evaluated to obtain the optimum response against the target concentration. Linear ranges of 0.05-0.5 µM and limits of detection of 174 nM and 144 nM were estimated for the optical and electrochemical measurements, respectively. Selectivity was proved by assaying other verotoxigenic, enterotoxigenic and enteroinvasive sequences. The results show that, if a combination of small-volume electrochemical cells and low-cost untreated screen-printed electrodes with a relatively high geometric area is used, electrochemical measurements present similar sensitivity and limits of detection to the more usual optical ones, allowing the development of low-cost electrochemical biosensors based on the use of soluble DNAzymes as labels.

Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.

Science.gov (United States)

Zhai, Xiang; Amyes, Tina L; Richard, John P

2015-12-09

The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between k(cat) for isomerization of GAP and K(d)(⧧) for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.

In situ closed-loop bioremediation: Rapid closure in a northern climate

International Nuclear Information System (INIS)

Weymann, D.F.; Hammerbeck, L.M.

1995-01-01

In situ closed-loop bioremediation was employed to achieve site closure at a former railyard in Minneapolis, Minnesota. Soil and groundwater were contaminated with gasoline. The closed-loop remediation system design incorporated three downgradient groundwater recovery wells and a low-pressure pipe infiltration gallery. Aboveground treatment of recovered groundwater was provided by a fixed-film bioreactor. The total reported benzene, toluene, ethylbenzene, and xylenes (BTEX)-removal efficiency of the bioreactor ranged from 98.8% to 100%. Concentrations of BTEX components in groundwater wells were reduced by 45% to 98%. The cleanup goals set by the Minnesota Pollution Control Agency were met within the first 6 months of treatment, and the remediation system was shut down after 20 months of operation. This project further demonstrates the effectiveness of reactor-based, closed-loop in situ bioremediation at sites with favorable conditions

Phonological loop affects children's interpretations of explicit but not ambiguous questions: Research on links between working memory and referent assignment.

Science.gov (United States)

Meng, Xianwei; Murakami, Taro; Hashiya, Kazuhide

2017-01-01

Understanding the referent of other's utterance by referring the contextual information helps in smooth communication. Although this pragmatic referential process can be observed even in infants, its underlying mechanism and relative abilities remain unclear. This study aimed to comprehend the background of the referential process by investigating whether the phonological loop affected the referent assignment. A total of 76 children (43 girls) aged 3-5 years participated in a reference assignment task in which an experimenter asked them to answer explicit (e.g., "What color is this?") and ambiguous (e.g., "What about this?") questions about colorful objects. The phonological loop capacity was measured by using the forward digit span task in which children were required to repeat the numbers as an experimenter uttered them. The results showed that the scores of the forward digit span task positively predicted correct response to explicit questions and part of the ambiguous questions. That is, the phonological loop capacity did not have effects on referent assignment in response to ambiguous questions that were asked after a topic shift of the explicit questions and thus required a backward reference to the preceding explicit questions to detect the intent of the current ambiguous questions. These results suggest that although the phonological loop capacity could overtly enhance the storage of verbal information, it does not seem to directly contribute to the pragmatic referential process, which might require further social cognitive processes.

Phonological loop affects children's interpretations of explicit but not ambiguous questions: Research on links between working memory and referent assignment.

Directory of Open Access Journals (Sweden)

Xianwei Meng

Full Text Available Understanding the referent of other's utterance by referring the contextual information helps in smooth communication. Although this pragmatic referential process can be observed even in infants, its underlying mechanism and relative abilities remain unclear. This study aimed to comprehend the background of the referential process by investigating whether the phonological loop affected the referent assignment. A total of 76 children (43 girls aged 3-5 years participated in a reference assignment task in which an experimenter asked them to answer explicit (e.g., "What color is this?" and ambiguous (e.g., "What about this?" questions about colorful objects. The phonological loop capacity was measured by using the forward digit span task in which children were required to repeat the numbers as an experimenter uttered them. The results showed that the scores of the forward digit span task positively predicted correct response to explicit questions and part of the ambiguous questions. That is, the phonological loop capacity did not have effects on referent assignment in response to ambiguous questions that were asked after a topic shift of the explicit questions and thus required a backward reference to the preceding explicit questions to detect the intent of the current ambiguous questions. These results suggest that although the phonological loop capacity could overtly enhance the storage of verbal information, it does not seem to directly contribute to the pragmatic referential process, which might require further social cognitive processes.

Aborto, direitos humanos e desigualdade de gênero no Brasil

OpenAIRE

Lucena, Rosana Batista de

2008-01-01

Este estudo analisa o impacto da criminalização do aborto para os direitos humanos das mulheres, sua relação com a desigualdade de gênero, a morbimortalidade materna e práticas punitivas e discriminatórias de violência institucional, particularmente para as mulheres negras, pobres e excluídas economicamente. Estas práticas de violência institucional no âmbito da saúde pública e do judiciário estão fundamentadas em estereótipos de gênero e de maternidade. A legalização do abo...

Surface representations of Wilson loop expectations in lattice gauge theory

International Nuclear Information System (INIS)

Brydges, D.C.; Giffen, C.; Durhuus, B.; Froehlich, J.

1986-01-01

Expectations of Wilson loops in lattice gauge theory with gauge group G=Z 2 , U(1) or SU(2) are expressed as weighted sums over surfaces with boundary equal to the loops labelling the observables. For G=Z 2 and U(1), the weights are all positive. For G=SU(2), the weights can have either sign depending on the Euler characteristic of the surface. Our surface (or flux sheet-) representations are partial resummations of the strong coupling expansion and provide some qualitative understanding of confinement. The significance of flux sheets with nontrivial topology for permanent confinement in the SU(2)-theory is elucidated. (orig.)

Effect of T- and C-loop mutations on the Herbaspirillum seropedicae GlnB protein in nitrogen signalling.

Science.gov (United States)

Bonatto, Ana C; Souza, Emanuel M; Pedrosa, Fábio O; Yates, M Geoffrey; Benelli, Elaine M

2005-01-01

Proteins of the PII family are found in species of all kingdoms. Although these proteins usually share high identity, their functions are specific to the different organisms. Comparison of structural data from Escherichia coli GlnB and GlnK and Herbaspirillum seropedicae GlnB showed that the T-loop and C-terminus were variable regions. To evaluate the role of these regions in signal transduction by the H. seropedicae GlnB protein, four mutants were constructed: Y51F, G108A/P109a, G108W and Q3R/T5A. The activities of the native and mutated proteins were assayed in an E. coli background constitutively expressing the Klebsiella pneumoniae nifLA operon. The results suggested that the T-loop and C-terminus regions of H. seropedicae GlnB are involved in nitrogen signal transduction.

Brain network dynamics in the human articulatory loop.

Science.gov (United States)

Nishida, Masaaki; Korzeniewska, Anna; Crone, Nathan E; Toyoda, Goichiro; Nakai, Yasuo; Ofen, Noa; Brown, Erik C; Asano, Eishi

2017-08-01

The articulatory loop is a fundamental component of language function, involved in the short-term buffer of auditory information followed by its vocal reproduction. We characterized the network dynamics of the human articulatory loop, using invasive recording and stimulation. We measured high-gamma activity 70-110 Hz recorded intracranially when patients with epilepsy either only listened to, or listened to and then reproduced two successive tones by humming. We also conducted network analyses, and analyzed behavioral responses to cortical stimulation. Presentation of the initial tone elicited high-gamma augmentation bilaterally in the superior-temporal gyrus (STG) within 40ms, and in the precentral and inferior-frontal gyri (PCG and IFG) within 160ms after sound onset. During presentation of the second tone, high-gamma augmentation was reduced in STG but enhanced in IFG. The task requiring tone reproduction further enhanced high-gamma augmentation in PCG during and after sound presentation. Event-related causality (ERC) analysis revealed dominant flows within STG immediately after sound onset, followed by reciprocal interactions involving PCG and IFG. Measurement of cortico-cortical evoked-potentials (CCEPs) confirmed connectivity between distant high-gamma sites in the articulatory loop. High-frequency stimulation of precentral high-gamma sites in either hemisphere induced speech arrest, inability to control vocalization, or forced vocalization. Vocalization of tones was accompanied by high-gamma augmentation over larger extents of PCG. Bilateral PCG rapidly and directly receives feed-forward signals from STG, and may promptly initiate motor planning including sub-vocal rehearsal for short-term buffering of auditory stimuli. Enhanced high-gamma augmentation in IFG during presentation of the second tone may reflect high-order processing of the tone sequence. The articulatory loop employs sustained reciprocal propagation of neural activity across a network of

Plant Biomass Leaching for Nutrient Recovery in Closed Loop Systems Project

Science.gov (United States)

Zeitlin, Nancy P.; Wheeler, Raymond (Compiler); Lunn, Griffin

2015-01-01

Plants will be important for food and O2 production during long term human habitation in space. Recycling of nutrients (e.g., from waste materials) could reduce the resupply costs of fertilizers for growing these plants. Work at NASA's Kennedy Space Center has shown that ion exchange resins can extract fertilizer (plant essential nutrients) from human waste water, after which the residual brine could be treated with electrodialysis to recover more water and produce high value chemicals (e.g., acids and bases). In habitats with significant plant production, inedible biomass becomes a major source of solid waste. To "close the loop" we also need to recover useful nutrients and fertilizer from inedible biomass. We are investigating different approaches to retrieve nutrients from inedible plant biomass, including physical leaching with water, processing the biomass in bioreactors, changing the pH of leaching processing, and/or conducting multiple leaches of biomass residues.

Two-loop renormalization in the standard model, part II. Renormalization procedures and computational techniques

Energy Technology Data Exchange (ETDEWEB)

Actis, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Passarino, G. [Torino Univ. (Italy). Dipt. di Fisica Teorica; INFN, Sezione di Torino (Italy)

2006-12-15

In part I general aspects of the renormalization of a spontaneously broken gauge theory have been introduced. Here, in part II, two-loop renormalization is introduced and discussed within the context of the minimal Standard Model. Therefore, this paper deals with the transition between bare parameters and fields to renormalized ones. The full list of one- and two-loop counterterms is shown and it is proven that, by a suitable extension of the formalism already introduced at the one-loop level, two-point functions suffice in renormalizing the model. The problem of overlapping ultraviolet divergencies is analyzed and it is shown that all counterterms are local and of polynomial nature. The original program of 't Hooft and Veltman is at work. Finite parts are written in a way that allows for a fast and reliable numerical integration with all collinear logarithms extracted analytically. Finite renormalization, the transition between renormalized parameters and physical (pseudo-)observables, are discussed in part III where numerical results, e.g. for the complex poles of the unstable gauge bosons, are shown. An attempt is made to define the running of the electromagnetic coupling constant at the two-loop level. (orig.)

Scoping erosion flow loop test results in support of Hanford WTP

International Nuclear Information System (INIS)

Duignan, M.; Imrich, K.; Fowley, M.; Restivo, M.; Reigel, M.

2015-01-01

The Waste Treatment and Immobilization Plant (WTP) will process Hanford Site tank waste by converting the waste into a stable glass form. Before the tank waste can be vitrified, the baseline plan is to process the waste through the Pretreatment (PT) Facility where it will be mixed in various process vessels using Pulse Jet Mixers (PJM) and transferred to the High Level Waste (HLW) or Low Activity Waste (LAW) vitrification facilities. The Department of Energy (DOE) and Defense Nuclear Facility Safety Board (DNFSB), as well as independent review groups, have raised concerns regarding the design basis for piping erosion in the PT Facility. Due to the complex nature of slurry erosion/corrosion wear and the unique conditions that exist within the PT Facility, additional testing has been recommended by these entities. Pipe loop testing is necessary to analyze the potential for localized wear at elbows and bends, close the outstanding PT and HLW erosion/corrosion technical issues, and underpin BNI's design basis for a 40-year operational life for black cell piping and vessels. SRNL is consulting with the DOE Office of River Protection (ORP) to resolve technical concerns related to piping erosion/corrosion (wear) design basis for PT. SRNL was tasked by ORP to start designing, building, and testing a flow loop to obtain long-term total-wear rate data using bounding simulant chemistry, operating conditions, and prototypical materials. The initial test involved a scoping paint loop to locate experimentally the potential high-wear locations. This information will provide a basis for the placement of the many sensitive wear measurement instruments in the appropriate locations so that the principal flow-loop test has the best chance to estimate long-term erosion and corrosion. It is important to note that the scoping paint loop test only utilized a bounding erosion simulant for this test. A full chemical simulant needs to be added for the complete test flow loop. The

QED contributions to electron g-2

Science.gov (United States)

Laporta, Stefano

2018-05-01

In this paper I briefly describe the results of the numerical evaluation of the mass-independent 4-loop contribution to the electron g-2 in QED with 1100 digits of precision. In particular I also show the semi-analytical fit to the numerical value, which contains harmonic polylogarithms of eiπ/3, e2iπ/3 and eiπ/2 one-dimensional integrals of products of complete elliptic integrals and six finite parts of master integrals, evaluated up to 4800 digits. I give also some information about the methods and the program used.

218 E-8 Borrow Pit Demolition Site clean closure soil evaluation report

International Nuclear Information System (INIS)

Korematsu-Olund, D.M.

1995-01-01

This report summarizes the sampling activities undertaken and the analytical results obtained in a soil sampling and analyses study performed for the 218 E-8 Borrow Pit Demolition Site (218 E-8 Demolition Site). The 218 E-8 Demolition Site is identified as a Resource Conservation and Recovery Act (RCRA) treatment unit that will be closed in accordance with the applicable laws and regulations. The site was used for the thermal treatment of discarded explosive chemical products. No constituents of concern were found in concentrations indicating contamination of the soil by 218 E-8 Demolition Site activities

Interaction between the cellular protein eEF1A and the 3'-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis.

Science.gov (United States)

Davis, William G; Blackwell, Jerry L; Shi, Pei-Yong; Brinton, Margo A

2007-09-01

RNase footprinting and nitrocellulose filter binding assays were previously used to map one major and two minor binding sites for the cell protein eEF1A on the 3'(+) stem-loop (SL) RNA of West Nile virus (WNV) (3). Base substitutions in the major eEF1A binding site or adjacent areas of the 3'(+) SL were engineered into a WNV infectious clone. Mutations that decreased, as well as ones that increased, eEF1A binding in in vitro assays had a negative effect on viral growth. None of these mutations affected the efficiency of translation of the viral polyprotein from the genomic RNA, but all of the mutations that decreased in vitro eEF1A binding to the 3' SL RNA also decreased viral minus-strand RNA synthesis in transfected cells. Also, a mutation that increased the efficiency of eEF1A binding to the 3' SL RNA increased minus-strand RNA synthesis in transfected cells, which resulted in decreased synthesis of genomic RNA. These results strongly suggest that the interaction between eEF1A and the WNV 3' SL facilitates viral minus-strand synthesis. eEF1A colocalized with viral replication complexes (RC) in infected cells and antibody to eEF1A coimmunoprecipitated viral RC proteins, suggesting that eEF1A facilitates an interaction between the 3' end of the genome and the RC. eEF1A bound with similar efficiencies to the 3'-terminal SL RNAs of four divergent flaviviruses, including a tick-borne flavivirus, and colocalized with dengue virus RC in infected cells. These results suggest that eEF1A plays a similar role in RNA replication for all flaviviruses.

Structure of AscE and Induced Burial Regions in AscE and AscG upon Formation of the Chaperone Needle-subunit Complex of Type III Secretion System in Aeromonas Hydrophila

Energy Technology Data Exchange (ETDEWEB)

Tan, Y.; Yu, H; Leung, K; Sivaraman, J; Mok, Y

2008-01-01

In the type III secretion system (T3SS) of Aeromonas hydrophila, the putative needle complex subunit AscF requires both putative chaperones AscE and AscG for formation of a ternary complex to avoid premature assembly. Here we report the crystal structure of AscE at 2.7 A resolution and the mapping of buried regions of AscE, AscG, and AscF in the AscEG and AscEFG complexes using limited protease digestion. The dimeric AscE is comprised of two helix-turn-helix monomers packed in an antiparallel fashion. The N-terminal 13 residues of AscE are buried only upon binding with AscG, but this region is found to be nonessential for the interaction. AscE functions as a monomer and can be coexpressed with AscG or with both AscG and AscF to form soluble complexes. The AscE binding region of AscG in the AscEG complex is identified to be within the N-terminal 61 residues of AscG. The exposed C-terminal substrate-binding region of AscG in the AscEG complex is induced to be buried only upon binding to AscF. However, the N-terminal 52 residues of AscF remain exposed even in the ternary AscEFG complex. On the other hand, the 35-residue C-terminal region of AscF in the complex is resistant to protease digestion in the AscEFG complex. Site-directed mutagenesis showed that two C-terminal hydrophobic residues, Ile83 and Leu84, of AscF are essential for chaperone binding.

Feedback Loop Gains and Feedback Behavior (1996)

DEFF Research Database (Denmark)

Kampmann, Christian Erik

2012-01-01

Linking feedback loops and system behavior is part of the foundation of system dynamics, yet the lack of formal tools has so far prevented a systematic application of the concept, except for very simple systems. Having such tools at their disposal would be a great help to analysts in understanding...... large, complicated simulation models. The paper applies tools from graph theory formally linking individual feedback loop strengths to the system eigenvalues. The significance of a link or a loop gain and an eigenvalue can be expressed in the eigenvalue elasticity, i.e., the relative change...... of an eigenvalue resulting from a relative change in the gain. The elasticities of individual links and loops may be found through simple matrix operations on the linearized system. Even though the number of feedback loops can grow rapidly with system size, reaching astronomical proportions even for modest systems...

Contamination by trace elements at e-waste recycling sites in Bangalore, India.

Science.gov (United States)

Ha, Nguyen Ngoc; Agusa, Tetsuro; Ramu, Karri; Tu, Nguyen Phuc Cam; Murata, Satoko; Bulbule, Keshav A; Parthasaraty, Peethmbaram; Takahashi, Shin; Subramanian, Annamalai; Tanabe, Shinsuke

2009-06-01

The recycling and disposal of electronic waste (e-waste) in developing countries is causing an increasing concern due to its effects on the environment and associated human health risks. To understand the contamination status, we measured trace elements (TEs) in soil, air dust, and human hair collected from e-waste recycling sites (a recycling facility and backyard recycling units) and the reference sites in Bangalore and Chennai in India. Concentrations of Cu, Zn, Ag, Cd, In, Sn, Sb, Hg, Pb, and Bi were higher in soil from e-waste recycling sites compared to reference sites. For Cu, Sb, Hg, and Pb in some soils from e-waste sites, the levels exceeded screening values proposed by US Environmental Protection Agency (EPA). Concentrations of Cr, Mn, Co, Cu, In, Sn, Sb, Tl, Pb and Bi in air from the e-waste recycling facility were relatively higher than the levels in Chennai city. High levels of Cu, Mo, Ag, Cd, In, Sb, Tl, and Pb were observed in hair of male workers from e-waste recycling sites. Our results suggest that e-waste recycling and its disposal may lead to the environmental and human contamination by some TEs. To our knowledge, this is the first study on TE contamination at e-waste recycling sites in Bangalore, India.

Polyakov loop and the hadron resonance gas model.

Science.gov (United States)

Megías, E; Arriola, E Ruiz; Salcedo, L L

2012-10-12

The Polyakov loop has been used repeatedly as an order parameter in the deconfinement phase transition in QCD. We argue that, in the confined phase, its expectation value can be represented in terms of hadronic states, similarly to the hadron resonance gas model for the pressure. Specifically, L(T)≈1/2[∑(α)g(α)e(-Δ(α)/T), where g(α) are the degeneracies and Δ(α) are the masses of hadrons with exactly one heavy quark (the mass of the heavy quark itself being subtracted). We show that this approximate sum rule gives a fair description of available lattice data with N(f)=2+1 for temperatures in the range 150 MeVmodels. For temperatures below 150 MeV different lattice results disagree. One set of data can be described if exotic hadrons are present in the QCD spectrum while other sets do not require such states.

Near BPS Wilson loop in β-deformed theories

International Nuclear Information System (INIS)

Chu, C-S; Giataganas, Dimitrios

2007-01-01

We propose a definition of the Wilson loop operator in the N = 1 β-deformed supersymmetric Yang-Mills theory. Although the operator is not BPS, it has a finite expectation value at least up to order (g 2 N) 2 . This does not happen generally for a generic non-BPS Wilson loop whose expectation value is UV divergent. For this reason we call this a near-BPS Wilson loop. We derive the general form of the boundary condition satisfied by the dual string worldsheet and find that it is deformed. Finiteness of the expectation value of the Wilson loop fixes the boundary condition to be one which is characterized by the vielbein of the deformed supergravity metric. The Wilson loop operators provide natural candidates as dual descriptions to some of the existing D-brane configurations in the Lunin-Maldacena background. We also construct the string dual configuration for a near-1/4 BPS circular Wilson loop operator. The string lies on a deformed three-sphere instead of a two-sphere as in the undeformed case. The expectation value of the Wilson loop operator is computed using the AdS/CFT correspondence and is found to be independent of the deformation. We conjecture that the exact expectation value of the Wilson loop is given by the same matrix model as in the undeformed case

SLSF loop handling system. Volume I. Structural analysis

International Nuclear Information System (INIS)

Ahmed, H.; Cowie, A.; Ma, D.

1978-10-01

SLSF loop handling system was analyzed for deadweight and postulated dynamic loading conditions, identified in Chapters II and III in Volume I of this report, using a linear elastic static equivalent method of stress analysis. Stress analysis of the loop handling machine is presented in Volume I of this report. Chapter VII in Volume I of this report is a contribution by EG and G Co., who performed the work under ANL supervision

A kinematic view of loop closure.

Science.gov (United States)

Coutsias, Evangelos A; Seok, Chaok; Jacobson, Matthew P; Dill, Ken A

2004-03-01

We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 510-528, 2004

Effect of closed-loop order processing on the time to initial antimicrobial therapy.

Science.gov (United States)

Panosh, Nicole; Rew, Richardd; Sharpe, Michelle

2012-08-15

The results of a study comparing the average time to initiation of i.v. antimicrobial therapy with closed-versus open-loop order entry and processing are reported. A retrospective cohort study was performed to compare order-to-administration times for initial doses of i.v. antimicrobials before and after a closed-loop order-processing system including computerized prescriber order entry (CPOE) was implemented at a large medical center. A total of 741 i.v. antimicrobial administrations to adult patients during designated five-month preimplementation and postimplementation study periods were assessed. Drug-use reports generated by the pharmacy database were used to identify order-entry times, and medication administration records were reviewed to determine times of i.v. antimicrobial administration. The mean ± S.D. order-to-administration times before and after the implementation of the CPOE system and closed-loop order processing were 3.18 ± 2.60 and 2.00 ± 1.89 hours, respectively, a reduction of 1.18 hours (p Closed-loop order processing was associated with significant reductions in the average time to initiation of i.v. therapy in all patient care areas evaluated (cardiology, general medicine, and oncology). The study results suggest that CPOE-based closed-loop order processing can play an important role in achieving compliance with current practice guidelines calling for increased efforts to ensure the prompt initiation of i.v. antimicrobials for severe infections (e.g., sepsis, meningitis). Implementation of a closed-loop order-processing system resulted in a significant decrease in order-to-administration times for i.v. antimicrobial therapy.

Two-loop polygon Wilson loops in N = 4 SYM

International Nuclear Information System (INIS)

Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

2009-01-01

We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

Active sites of two orthologous cytochromes P450 2E1: Differences revealed by spectroscopic methods

International Nuclear Information System (INIS)

Anzenbacherova, Eva; Hudecek, Jiri; Murgida, Daniel; Hildebrandt, Peter; Marchal, Stephane; Lange, Reinhard; Anzenbacher, Pavel

2005-01-01

Cytochromes P450 2E1 of human and minipig origin were examined by absorption spectroscopy under high hydrostatic pressure and by resonance Raman spectroscopy. Human enzyme tends to denature to the P420 form more easily than the minipig form; moreover, the apparent compressibility of the heme active site (as judged from a redshift of the absorption maximum with pressure) is greater than that of the minipig counterpart. Relative compactness of the minipig enzyme is also seen in the Raman spectra, where the presence of planar heme conformation was inferred from band positions characteristic of the low-spin heme with high degree of symmetry. In this respect, the CYP2E1 seems to be another example of P450 conformational heterogeneity as shown, e.g., by Davydov et al. for CYP3A4 [Biochem. Biophys. Res. Commun. 312 (2003) 121-130]. The results indicate that the flexibility of the CYP active site is likely one of its basic structural characteristics

Constructing QCD one-loop amplitudes

International Nuclear Information System (INIS)

Forde, D

2008-01-01

In the context of constructing one-loop amplitudes using a unitarity bootstrap approach we discuss a general systematic procedure for obtaining the coefficients of the scalar bubble and triangle integral functions of one-loop amplitudes. Coefficients are extracted after examining the behavior of the cut integrand as the unconstrained parameters of a specifically chosen parameterization of the cut loop momentum approach infinity. Measurements of new physics at the forthcoming experimental program at CERN's Large Hadron Collider (LHC) will require a precise understanding of processes at next-to-leading order (NLO). This places increased demands for the computation of new one-loop amplitudes. This in turn has spurred recent developments towards improved calculational techniques. Direct calculations using Feynman diagrams are in general inefficient. Developments of more efficient techniques have usually centered around unitarity techniques [1], where tree amplitudes are effectively 'glued' together to form loops. The most straightforward application of this method, in which the cut loop momentum is in D = 4, allows for the computation of 'cut-constructible' terms only, i.e. (poly)logarithmic containing terms and any related constants. QCD amplitudes contain, in addition to such terms, rational pieces which cannot be derived using such cuts. These 'missing' rational parts can be extracted using cut loop momenta in D = 4-2 (var e psilon). The greater difficulty of such calculations has restricted the application of this approach, although recent developments [3, 4] have provided new promise for this technique. Recently the application of on-shell recursion relations [5] to obtaining the 'missing' rational parts of one-loop processes [6] has provided an alternative very promising solution to this problem. In combination with unitarity methods an 'on-shell bootstrap' approach provides an efficient technique for computing complete one-loop QCD amplitudes [7]. Additionally

Afferent loop syndrome: Role of sonography and CT

Energy Technology Data Exchange (ETDEWEB)

Lee, Dong Ho; Lim, Jae Hoon; Ko, Young Tae [Kyung Hee University Hospital, Seoul (Korea, Republic of)

1992-03-15

Afferent loop syndrome(ALS) is caused by obstruction of the afferent loop after subtotal gastrectomy with Billroth II gastrojejunostomy. Prompt diagnosis of ALS is important as perforation of the loop occurs. The aim of study is to ascertain the sonography and CT to diagnose ALS. We describe the radiologic findings in ten patients with ALS. The cause of ALS, established at surgery, included cancer recurrence (n=4), internal hernia (n=4), marginal ulcer (n=1), and development of cancer at the anastomosis site (n=1). Abdominal X-ray and sonography were performed in all cases, upper GI series in five cases and computed tomography in two cases. The dilated afferent loop was detected in only two cases out often patients in retrospective review of abdominal X-ray. ALS with recurrence of cancer was diagnosed in three cases by upper GI series. Of the cases that had sonography, the afferent loop was seen in the upper abdomen crossing transversely over the midline in all ten patients. The cause of ALS were predicated on the basis of the sonograms in three of the five patients. In two cases of computed tomography, the dilated afferent loop and recurrent cancer at the remnant stomach were seen.Our experience suggests that the diagnosis of afferent syndrome can be made on the basis of the typical anatomic location and shape of the dilated bowel loop in both sonography and computed tomography.

GPR Imaging of Clastic Dikes at the Hanford Site, Hanford, Washington

International Nuclear Information System (INIS)

Clement, William P.; Murray, Christopher J.

2007-01-01

We use ground penetrating radar (GPR) data to help determine the spatial distribution and the subsurface geometry of clastic injection dikes at the Hanford site. This information will help to improve the understanding of the hydrological role of these ubiquitous clastic dikes at the Hanford Site. We collected 100 MHz ground penetrating radar (GPR) 3D surface reflection data at two sites, the S-16 Pond and the Army Loop Road sites, and 2D reflection data along a 6.9 km linear transect near the Army Loop Road site. The dikes are distinguished in the GPR data by a strongly attenuated zone, disruptions in the continuity of reflections, and diffractions where reflections are disrupted. In general, the data quality is better at the Army Loop Road and Traverse sites than at the S-16 Pond site, probably due to the presence of cobbles at the S-16 Pond site. A high-moisture, fine-grained unit probably causes the strong reflections at the Army Loop Road site and the Traverse survey site. The signal penetration varies between 5 to 12 m below the land surface

Building eCommerce sites with Drupal commerce cookbook

CERN Document Server

Carter, Richard

2013-01-01

Building eCommerce Sites with Drupal Commerce Cookbook is written in a helpful, practical style with numerous hands-on recipes to help you build attractive eCommerce sites.This book is primarily for store owners and web designers with little or no experience of Drupal and Drupal Commerce who want to build and customise a store in Drupal Commerce. You will have a basic knowledge of websites, but you don't need to be familiar with Drupal or PHP. However, this book would also suit experienced Drupal and Ubercart users who want to migrate to or build a Drupal Commerce store

Alternative loop rings

CERN Document Server

Goodaire, EG; Polcino Milies, C

1996-01-01

For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

Astroclimatic characterization of Vallecitos: a candidate site for the Cherenkov Telescope Array at San Pedro Mártir

Czech Academy of Sciences Publication Activity Database

Tovmassian, G.; Hernandez, M.-S.; Ochoa, J.L.; Ernenwein, J.-P.; Mandát, D.; Pech, M.; Frayn, I.P.; Colorado, E.; Murillo, J.M.; Ceseña, U.; Garcia, B.; Lee, W.H.; Bulik, T.; Garczarczyk, M.; Fruck, C.; Costantini, H.; Cieslar, M.; Aune, T.; Vincent, S.; Carr, J.; Serre, N.; Janeček, Petr; Haefner, D.

2016-01-01

Roč. 128, č. 961 (2016), 1-13, č. článku 035004. ISSN 0004-6280 R&D Projects: GA MŠk LG14019; GA MŠk LE13012; GA MŠk LM2015046 Institutional support: RVO:68378271 Keywords : high energy gama rays * Cherencov telescopes * site characterization Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 4.446, year: 2016

Evaluation of cysticercus-specific IgG (total and subclasses and IgE antibody responses in cerebrospinal fluid samples from patients with neurocysticercosis showing intrathecal production of specific IgG antibodies Avaliação das respostas de anticorpos anti-cisticercos IgG (total e subclasses e IgE em amostras de líquido cefalorraquidiano de pacientes com neurocisticercose apresentando produção intratecal de anticorpos específicos IgG

Directory of Open Access Journals (Sweden)

Lisandra Akemi Suzuki

2013-01-01

Full Text Available In the present study, an enzyme-linked immunosorbent assay (ELISA standardized with vesicular fluid of Taenia solium cysticerci was used to screen for IgG (total and subclasses and IgE antibodies in cerebrospinal fluid (CSF samples from patients with neurocysticercosis showing intrathecal production of specific IgG antibodies and patients with other neurological disorders. The following results were obtained: IgG-ELISA: 100% sensitivity (median of the ELISA absorbances (MEA=1.17 and 100% specificity; IgG1-ELISA: 72.7% sensitivity (MEA=0.49 and 100% specificity; IgG2-ELISA: 81.8% sensitivity (MEA=0.46 and 100% specificity; IgG3-ELISA: 63.6% sensitivity (MEA=0.12 and 100% specificity; IgG4-ELISA: 90.9% sensitivity (MEA=0.85 and 100% specificity; IgE-ELISA 93.8% sensitivity (MEA=0.60 and 100% specificity. There were no significant differences between the sensitivities and specificities in the detection of IgG-ELISA and IgE-ELISA, although in CSF samples from patients with neurocysticercosis the MEA of the IgG-ELISA was significantly higher than that of the IgE-ELISA. The sensitivity and MEA values of the IgG4-ELISA were higher than the corresponding values for the other IgG subclasses. Future studies should address the contribution of IgG4 and IgE antibodies to the physiopathology of neurocysticercosis.No presente estudo, uma reação imunoenzimática (ELISA padronizada com o fluido vesicular de cisticercos de Taenia solium foi utilizada para avaliar as respostas de anticorpos anti-cisticercos IgG (total e subclasses e IgE em amostras de líquido cefalorraquidiano (LCR de pacientes com neurocisticercose apresentando produção intratecal de anticorpos específicos IgG e pacientes com outras desordens neurológicas. Os seguintes resultados foram obtidos: ELISA-IgG: 100% de sensibilidade (mediana das absorbâncias das reações ELISA (MAE=1,17 e especificidade 100%; ELISA-IgG1: sensibilidade 72,7% (MAE=0,49 e especificidade 100%; ELISA-IgG2

Classe social e gênero: ativos de herança e ativos de escolha

Directory of Open Access Journals (Sweden)

Elizabeth B. Silva

2014-12-01

Full Text Available Este artigo discute até que ponto as posições de classe na Grã-Bretanha contemporânea foram herdadas dos pais e que tipo de escolhas em termos conjugais (e seus efeitos homens e mulheres fazem em posições sociais diferentes. De modo inovador, o artigo investiga os diferentes ativos herdados de pais e mães por filhos e filhas, visando a um exame refinado dos efeitos de gênero, ainda não presente na literatura. Discriminam-se também as escolhas conjugais de homens e mulheres. Essas explorações se apoiam no material empírico desenvolvido para o estudo britânico Capital Cultural e Exclusão Social (CCSE, na sigla em inglês, inspirado pelo trabalho de Pierre Bourdieu sobre capitais e habitus na definição das posições dos indivíduos nas classes sociais. O artigo indica que o gênero, uma ativo mal compreendido por Bourdieu, afeta a posição de classe de formas sutis e complexas, sendo muito significativo em certos aspectos.

Virtual unit delay for digital frequency adaptive T/4 delay phase-locked loop system

DEFF Research Database (Denmark)

Yang, Yongheng; Zhou, Keliang; Blaabjerg, Frede

2016-01-01

/processor with a fixed sampling rate considering the cost and complexity, where the number of unit delays that have been adopted should be an integer. For instance, in conventional digital control systems, a single-phase T/4 Delay Phase-Locked Loop (PLL) system takes 50 unit delays (i.e., in a 50-Hz system...... Delay PLL system should be done in its implementation. This process will result in performance degradation in the digital control system, as the exactly required number of delays is not realized. Hence, in this paper, a Virtual Unit Delay (VUD) has been proposed to address such challenges to the digital......Digital micro-controllers/processors enable the cost-effective control of grid-connected power converter systems in terms of system monitoring, signal processing (e.g., grid synchronization), control (e.g., grid current and voltage control), etc. Normally, the control is implemented in a micro-controller...

Targeting the autolysis loop of urokinase-type plasminogen activator with conformation-specific monoclonal antibodies.

Science.gov (United States)

Botkjaer, Kenneth A; Fogh, Sarah; Bekes, Erin C; Chen, Zhuo; Blouse, Grant E; Jensen, Janni M; Mortensen, Kim K; Huang, Mingdong; Deryugina, Elena; Quigley, James P; Declerck, Paul J; Andreasen, Peter A

2011-08-15

Tight regulation of serine proteases is essential for their physiological function, and unbalanced states of protease activity have been implicated in a variety of human diseases. One key example is the presence of uPA (urokinase-type plasminogen activator) in different human cancer types, with high levels correlating with a poor prognosis. This observation has stimulated efforts into finding new principles for intervening with uPA's activity. In the present study we characterize the so-called autolysis loop in the catalytic domain of uPA as a potential inhibitory target. This loop was found to harbour the epitopes for three conformation-specific monoclonal antibodies, two with a preference for the zymogen form pro-uPA, and one with a preference for active uPA. All three antibodies were shown to have overlapping epitopes, with three common residues being crucial for all three antibodies, demonstrating a direct link between conformational changes of the autolysis loop and the creation of a catalytically mature active site. All three antibodies are potent inhibitors of uPA activity, the two pro-uPA-specific ones by inhibiting conversion of pro-uPA to active uPA and the active uPA-specific antibody by shielding the access of plasminogen to the active site. Furthermore, using immunofluorescence, the conformation-specific antibodies mAb-112 and mAb-12E6B10 enabled us to selectively stain pro-uPA or active uPA on the surface of cultured cells. Moreover, in various independent model systems, the antibodies inhibited tumour cell invasion and dissemination, providing evidence for the feasibility of pharmaceutical intervention with serine protease activity by targeting surface loops that undergo conformational changes during zymogen activation. © The Authors Journal compilation © 2011 Biochemical Society

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.

Science.gov (United States)

Saraiya, Ashesh A; Lamichhane, Tek N; Chow, Christine S; SantaLucia, John; Cunningham, Philip R

2008-02-22

The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m(2)G966 and m(5)C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this ribosomal RNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Nonrandom nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m(2)G966 or m(5)C967 produce more protein in vivo than do wild-type ribosomes. Overexpression of initiation factor 3 specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for initiation factor 3 binding and for the proper initiation of protein synthesis.

IgA, IgE e subclasses de IgG anti-Candida albicans no soro e lavado vaginal de pacientes com candidíase vulvovaginal IgA, IgE and IgG subclasses to Candida albicans in serum and vaginal fluid from patients with vulvovaginal candidiasis

Directory of Open Access Journals (Sweden)

Ricardo José Victal de Carvalho

2003-01-01

Full Text Available OBJETIVO: Determinar níveis de anticorpos IgA, IgE, IgG e subclasses (IgG1, IgG4 específicos a C. albicans no soro e lavado vaginal de mulheres com ou sem candidíase vulvovaginal para avaliar o papel destes anticorpos na imunopatogênese desta doença. MÉTODOS: Foram selecionadas 30 mulheres com sintomas clínicos de candidíase vulvovaginal (15 com cultura de secreção vaginal positiva para C. albicans, 11 com cultura negativa e quatro com cultura positiva para Candida não-albicans e 12 mulheres controles assintomáticas (nove com cultura negativa. Amostras de soro e lavado vaginal foram obtidas para a detecção de anticorpos anti-C. albicans por ELISA. RESULTADOS: Pacientes sintomáticas com cultura positiva apresentaram níveis de IgA específicas significativamente maiores no lavado vaginal e menores no soro do que aquelas com cultura negativa. Níveis séricos de IgE específica foram extremamente baixos em relação ao lavado vaginal. Altos níveis de IgG total específica foram encontrados no soro e lavado vaginal em ambos os grupos, independente da presença do fungo. Níveis de IgG1 e IgG4 específicas foram significativamente maiores somente no lavado vaginal de mulheres sintomáticas e cultura positiva, com relação IgG1/IgG4 ligeiramente maior, indicando que a resposta de anticorpos IgG1 possa estar predominantemente envolvida na resolução da infecção fúngica. CONCLUSÕES: Nossos resultados indicam resposta acentuada de IgA, IgG1 e IgG4 anti-C. albicans no lavado vaginal de mulheres sintomáticas com cultura positiva, sugerindo importante papel destes anticorpos na resposta imune local estimulada pela presença do fungo.PURPOSE: To determine the levels of IgA, IgE, IgG and subclasses (IgG1, IgG4 antibodies specific to C. albicans in serum and vaginal washes from women with or without vulvovaginal candidiasis in order to evaluate the role of these antibodies in the immunopathogenesis of the disease. METHODS: Thirty women

Interaction of hydrogen and helium with nanometric dislocation loops in tungsten assessed by atomistic calculations

Energy Technology Data Exchange (ETDEWEB)

Grigorev, Petr [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Ghent University, Applied Physics EA17 FUSION-DC, St. Pietersnieuwstraat, 41 B4, B-9000 Gent (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation); Bakaev, Alexander; Terentyev, Dmitry [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Van Oost, Guido; Noterdaeme, Jean-Marie [Ghent University, Applied Physics EA17 FUSION-DC, St. Pietersnieuwstraat, 41 B4, B-9000 Gent (Belgium); Zhurkin, Evgeny E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation)

2017-02-15

The interaction of H and He interstitial atoms with ½〈1 1 1〉 and 〈1 0 0〉 loops in tungsten (W) was studied by means of Molecular Static and Molecular Dynamics simulations. A recently developed interatomic potential was benchmarked using data for dislocation loops obtained earlier with two other W potentials available in literature. Molecular Static calculations demonstrated that ½〈1 1 1〉 loops feature a wide spectrum of the binding energy with a maximum value of 1.1 eV for H and 1.93 eV for He as compared to 0.89 eV and 1.56 eV for a straight ½〈1 1 1〉{1 1 0} edge dislocation. For 〈1 0 0〉 loops, the values of the binding energy were found to be 1.63 eV and 2.87 eV for H and He, respectively. These results help to better understand the role played by dislocation loops in H/He retention in tungsten. Based on the obtained results, a contribution of the considered dislocation loops to the trapping and retention under plasma exposure is discussed.

The structures of colour string for e+e- → qq-barg and υ → 3g

International Nuclear Information System (INIS)

Tian Lili; Xie Qubing; Si Zongguo

1993-01-01

In Lund model, the explanation of e + e - → qq-barg → 3 jets and υ → 3g → h's is based on applying Lund string fragmentation model to their assumed structures of colour string for qq-barg and 3g systems. In this paper, starting from the colour wave functions of qq-barg and 3 g systems, we study these colour string structures by QCD directly. The results reveal the reasonableness and accuracy of Lund string pictures

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

Science.gov (United States)

Chen, Liang; Chen, Jia-Yu; Zhang, Xuan; Gu, Ying; Xiao, Rui; Shao, Changwei; Tang, Peng; Qian, Hao; Luo, Daji; Li, Hairi; Zhou, Yu; Zhang, Dong-Er; Fu, Xiang-Dong

2017-11-16

R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed. Copyright © 2017 Elsevier Inc. All rights reserved.

Closed-loop 15N measurement of N2O and its isotopomers for real-time greenhouse gas tracing

Science.gov (United States)

Slaets, Johanna; Mayr, Leopold; Heiling, Maria; Zaman, Mohammad; Resch, Christian; Weltin, Georg; Gruber, Roman; Dercon, Gerd

2016-04-01

Quantifying sources of nitrous oxide is essential to improve understanding of the global N cycle and to develop climate-smart agriculture, as N2O has a global warming potential 300 times higher than CO2. The isotopic signature and the intramolecular distribution (site preference) of 15N are powerful tools to trace N2O, but the application of these methods is limited as conventional methods cannot provide continuous and in situ data. Here we present a method for closed-loop, real time monitoring of the N2O flux, the isotopic signature and the intramolecular distribution of 15N by using off-axis integrated cavity output spectroscopy (ICOS, Los Gatos Research). The developed method was applied to a fertilizer inhibitor experiment, in which N2O emissions were measured on undisturbed soil cores for three weeks. The treatments consisted of enriched urea-N (100 kg urea-N/ha), the same fertilizer combined with the nitrification inhibitor nitrapyrin (375 g/100 kg urea), and control cores. Monitoring the isotopic signature makes it possible to distinguish emissions from soil and fertilizer. Characterization of site preference could additionally provide a tool to identify different microbial processes leading to N2O emissions. Furthermore, the closed-loop approach enables direct measurement on site and does not require removal of CO2 and H2O. Results showed that 75% of total N2O emissions (total=11 346 μg N2O-N/m2) in the fertilized cores originated from fertilizer, while only 55% of total emissions (total=2 450 μg N2ON/m2) stemmed from fertilizer for the cores treated with nitrapyrin. In the controls, N2O derived from soil was only 40% of the size of the corresponding pool from the fertilized cores, pointing towards a priming effect on the microbial community from the fertilizer and demonstrating the bias that could be introduced by relying on non-treated cores to estimate soil emission rates, rather than using the isotopic signature. The site preference increased linearly

The mechanism of reduced IgG/IgE-binding of β-lactoglobulin by pulsed electric field pretreatment combined with glycation revealed by ECD/FTICR-MS.

Science.gov (United States)

Yang, Wenhua; Tu, Zongcai; Wang, Hui; Zhang, Lu; Kaltashov, Igor A; Zhao, Yunlong; Niu, Chendi; Yao, Honglin; Ye, Wenfeng

2018-01-24

Bovine β-lactoglobulin (β-Lg) is a major allergen existing in milk and causes about 90% of IgE-mediated cow's milk allergies. Previous studies showed that pulsed electric field (PEF) treatment could partially unfold the protein, which may contribute to the improvement of protein glycation. In this study, the effect of PEF pretreatment combined with glycation on the IgG/IgE-binding ability and the structure of β-Lg was investigated. The result showed that PEF pretreatment combined with glycation significantly reduced the IgG and IgE binding abilities, which was attributed to the changes of secondary and tertiary structure and the increase in glycation sites and degree of substitution per peptide (DSP) value determined by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry (ECD/FTICR-MS). Unexpectedly, glycation sites (K47, K91 and K135) added by two mannose molecules were identified in glycated β-Lg with PEF pretreatment. Moreover, the results indicated that PEF pretreatment at 25 kV cm -1 for 60 μs promoted the reduction of IgG/IgE-binding capacity by increasing the glycation degree of β-Lg, whereas single PEF treatment under the same conditions markedly enhanced the IgG/IgE-binding ability by partially unfolding the structure of β-Lg. The results suggested that ECD/FTICR-MS could help us to understand the mechanism of reduction in the IgG/IgE-binding of β-Lg by structural characterization at the molecular level. Therefore, PEF pretreatment combined with glycation may provide an alternative method for β-Lg desensitization.

Flux sensitivity of a piecewise normal and superconducting metal loop

International Nuclear Information System (INIS)

Buettiker, M.; Klapwijk, T.M.

1986-01-01

We consider a loop composed of a superconducting segment and a normal segment with an Aharonov-Bohm flux through the hole of the loop. The normal segment is assumed to be long compared to the superconducting coherence length xi but short compared to a mean inelastic diffusion length. The elementary excitation spectrum of the ground state of this loop is periodic with period hc/2e as long as the superconducting segment is larger than xi. If the superconducting segment length becomes of the order of xi, quasiparticles can tunnel through the superconducting gap and give rise to an excitation spectrum which is periodic with period hc/e. .AE

Redoable Tie-Over Dressing Using Multiple Loop Silk Threads

Directory of Open Access Journals (Sweden)

Hyeon Jong Jo

2013-05-01

Full Text Available After skin grafting, to prevent hematoma or seroma collection at the graft site, a tie-over dressing has been commonly used. However, although the conventional tie-over dressing by suture is a useful method for securing a graft site, refixation is difficult when repeated tie-over dressing is needed. Therefore, we recommend a redoable tie-over dressing technique with multiple loops threads and connecting silk threads. After the raw surface of each of our cases was covered with a skin graft, multiple loop silk thread attached with nylon at the skin graft margin. We applied the ointment gauze and wet cotton/fluffy gauze over the skin graft, then fixed the dressing by connecting cross-counter multiple loop thread with connecting silk threads. When we opened the tie-over dressing by cutting the connecting silk threads, we repeated the tie-over dressing with the same method. The skin graft was taken successfully without hematoma or seroma collection or any other complications. In conclusion, we report a novel tie-over dressing enabling simple fixation of the dressing to maintain proper tension for wounds that require repetitive fixation. Further, with this reliable method, the skin grafts were well taken.

Redoable Tie-Over Dressing Using Multiple Loop Silk Threads

Directory of Open Access Journals (Sweden)

Hyeon Jong Jo

2013-05-01

Full Text Available After skin grafting, to prevent hematoma or seroma collection at the graft site, a tie-over dressing has been commonly used. However, although the conventional tie-over dressing by suture is a useful method for securing a graft site, refixation is difficult when repeated tieover dressing is needed. Therefore, we recommend a redoable tie-over dressing technique with multiple loops threads and connecting silk threads. After the raw surface of each of our cases was covered with a skin graft, multiple loop silk thread attached with nylon at the skin graft margin. We applied the ointment gauze and wet cotton/fluffy gauze over the skin graft, then fixed the dressing by connecting cross-counter multiple loop thread with connecting silk threads. When we opened the tie-over dressing by cutting the connecting silk threads, we repeated the tie-over dressing with the same method. The skin graft was taken successfully without hematoma or seroma collection or any other complications. In conclusion, we report a novel tie-over dressing enabling simple fixation of the dressing to maintain proper tension for wounds that require repetitive fixation. Further, with this reliable method, the skin grafts were well taken.

Random walk loop soups and conformal loop ensembles

NARCIS (Netherlands)

van de Brug, T.; Camia, F.; Lis, M.

2016-01-01

The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

Expression of Aleutian mink disease parvovirus capsid proteins in defined segments: localization of immunoreactive sites and neutralizing epitopes to specific regions.

Science.gov (United States)

Bloom, M E; Martin, D A; Oie, K L; Huhtanen, M E; Costello, F; Wolfinbarger, J B; Hayes, S F; Agbandje-McKenna, M

1997-01-01

The capsid proteins of the ADV-G isolate of Aleutian mink disease parvovirus (ADV) were expressed in 10 nonoverlapping segments as fusions with maltose-binding protein in pMAL-C2 (pVP1, pVP2a through pVP2i). The constructs were designed to capture the VP1 unique sequence and the portions analogous to the four variable surface loops of canine parvovirus (CPV) in individual fragments (pVP2b, pVP2d, pVP2e, and pVP2g, respectively). The panel of fusion proteins was immunoblotted with sera from mink infected with ADV. Seropositive mink infected with either ADV-TR, ADV-Utah, or ADV-Pullman reacted preferentially against certain segments, regardless of mink genotype or virus inoculum. The most consistently immunoreactive regions were pVP2g, pVP2e, and pVP2f, the segments that encompassed the analogs of CPV surface loops 3 and 4. The VP1 unique region was also consistently immunoreactive. These findings indicated that infected mink recognize linear epitopes that localized to certain regions of the capsid protein sequence. The segment containing the hypervariable region (pVP2d), corresponding to CPV loop 2, was also expressed from ADV-Utah. An anti-ADV-G monoclonal antibody and a rabbit anti-ADV-G capsid antibody reacted exclusively with the ADV-G pVP2d segment but not with the corresponding segment from ADV-Utah. Mink infected with ADV-TR or ADV-Utah also preferentially reacted with the pVP2d sequence characteristic of that virus. These results suggested that the loop 2 region may contain a type-specific linear epitope and that the epitope may also be specifically recognized by infected mink. Heterologous antisera were prepared against the VP1 unique region and the four segments capturing the variable surface loops of CPV. The antisera against the proteins containing loop 3 or loop 4, as well as the anticapsid antibody, neutralized ADV-G infectivity in vitro and bound to capsids in immune electron microscopy. These results suggested that regions of the ADV capsid proteins

G. Nuclear power plant siting

International Nuclear Information System (INIS)

1976-01-01

The selection of a site for a nuclear power site is a complex process involving considerations of public health and safety, engineering design, economics, and environmental impact. Although policies adopted in various countries differ in some details, a common philosophy usually underlies the criteria employed. The author discusses the basic requirements, as they relate to New Zealand, under the headings: engineering and economics; health and safety; environmental factors

Loop Quantum Cosmology

Directory of Open Access Journals (Sweden)

Bojowald Martin

2008-07-01

Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

Loop Quantum Cosmology

Directory of Open Access Journals (Sweden)

Bojowald Martin

2005-12-01

Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

Transition probability spaces in loop quantum gravity

Science.gov (United States)

Guo, Xiao-Kan

2018-03-01

We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.

Temporary loop ileostomy: prospective study of indications and complication

International Nuclear Information System (INIS)

Rajput, A.; Samad, A.; Khanzada, T.W.

2007-01-01

To asses the indications and complications of temporary loop ileostomy. This was a prospective cohort study conducted at Isra University Hospital, Hyderabad, Pakistan between February 2003 and August 2006. All patients who had temporary loop ileostomy during that period were included in this study. The indications and various postoperative complications were noted during postoperative hospital stay and subsequently during follow up till stoma were closed. Fifty six patients fulfilled the selection criteria during the study period. Typhoid (enteric) perforation was the most common indication of loop ileostomy accounting for about two thirds of all cases. Other indications were iatrogenic, covering ileostomy for rectal cancers, following resection anastomosis, tuberculosis, blunt abdominal trauma, anastomosis leak and rectovaginal fistula. Post operative skin excoriation was the most common complication while poor siting, transient edema, retraction and high output were other less common complications. Temporary loop ileostomy is the stoma of choice for temporary faecal diversion as most of its complications are manageable conservatively. (author)

In-111-oxine red cells for imaging of intermittent G.I. bleeding sites

International Nuclear Information System (INIS)

Marcus, C.S.; Angulo, M.C.; Salk, R.D.; Essex, C.E.

1985-01-01

Sequential daily abdominal imaging was performed for up to 7 days in 11 patients with intermittent G.I. bleeding after the intravenous administration of lmCi autologous In-111-oxine labeled RBC's. The bleeding sites were identified in 3 patients. The causes were colon carcinoma, diverticulitis, and eroding distal aortic aneutysm. In addition to the imaging information, the authors have obtained preliminary biodistribution and kinetic data on the In-RBC's. Distribution to liver, spleen, and bone marrow was approximately 40%, 40%, and 20%, respectively. (This does not include the quantity of In-111 in the blood pool, which is very high initially and declines with time.) The survival of circulating In-RBC's is described by the equation: Surviving fraction=0.26e/sup -0.0021t/+0.74e/sup -0.00083t/ The halflives of the fast and slow components (x-bar+-x-bar) are 33.4 +- 1.6 hours and 35.0 +- 1.25 days, respectively. The In-oxine label is less stable than Cr-51 but more stable than Tc-99m. At 24 hours, Cr-RBC/In-RBC survival is 1.11 and Cr-RBC/Tc-RBC survival is 1.23. This imaging procedure is quite useful in selected patients

Identidade de gênero/sexo de atletas e sedentários

Directory of Open Access Journals (Sweden)

Fernando Luiz Cardoso

2012-12-01

Full Text Available Existem diferenças no processo de estruturação da identidade de gênero/sexo de atletas e não-atletas? Este estudo teve como objetivo comparar a identidade de gênero/sexo autopercebida e autoquantificada de atletas de diferentes modalidades (180 homens e 180 mulheres em relação a sedentários (22 homens e 22 mulheres, no tocante a personalidade e preferências lúdicas da infância. Os homens se perceberam mais masculinos e as mulheres mais femininas. Encontraram-se mais mulheres não heterossexuais do que homens, entre as atletas. Os homens assumiram-se mais propensos a gostar de quebrar as regras e sonhavam em ser campeão esportivo quando crianças. As atletas mulheres que brincaram mais com meninos na infância se avaliaram como mais masculinas, ousando em transgredir as fronteiras dos papéis de gênero, o que pode ter facilitado o interesse delas pelo treinamento esportivo.

Dynamic modelling and hardware-in-the-loop testing of PEMFC

Energy Technology Data Exchange (ETDEWEB)

Vath, Andreas; Soehn, Matthias; Nicoloso, Norbert; Hartkopf, Thomas [Technische Universitaet Darmstadt/Institut fuer Elektrische Energie wand lung, Landgraf-Georg-Str. 4, D-64283 Darmstadt (Germany); Lemes, Zijad; Maencher, Hubert [MAGNUM Automatisierungstechnik GmbH, Bunsenstr. 22, D-64293 Darmstadt (Germany)

2006-07-03

Modelling and hardware-in-the-loop (HIL) testing of fuel cell components and entire systems open new ways for the design and advance development of FCs. In this work proton exchange membrane fuel cells (PEMFC) are dynamically modelled within MATLAB-Simulink at various operation conditions in order to establish a comprehensive description of their dynamic behaviour as well as to explore the modelling facility as a diagnostic tool. Set-up of a hardware-in-the-loop (HIL) system enables real time interaction between the selected hardware and the model. The transport of hydrogen, nitrogen, oxygen, water vapour and liquid water in the gas diffusion and catalyst layers of the stack are incorporated into the model according to their physical and electrochemical characteristics. Other processes investigated include, e.g., the membrane resistance as a function of the water content during fast load changes. Cells are modelled three-dimensionally and dynamically. In case of system simulations a one-dimensional model is preferred to reduce computation time. The model has been verified by experiments with a water-cooled stack. (author)

K0-anti K0 mixing at three loops

International Nuclear Information System (INIS)

Eeg, J.O.

1987-01-01

We consider diagrams of order α s 2 G F 2 for the K 0 -anti K 0 mixing, topologically different from the gluon-corrected standard box. The treatment of three-loop diagrams is simplified by factorizing them in terms of momentum-dependent effective vertices for s → dG and s → dGG transitions. An enhancement from the remaining loop-momentum integration compensates for the extra powers of the strong coupling. This gives a significant contribution to the CP-violating part (-15% to -40% of the standard-box value). The dependence of the results on the involved mass parameters is illustrated by LEGO plots for both the CP-conserving and CP-violating parts. (orig.)

Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.

Science.gov (United States)

Guilfoyle, Amy P; Deshpande, Chandrika N; Vincent, Kimberley; Pedroso, Marcelo M; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

2014-05-01

GTPases (G proteins) hydrolyze the conversion of GTP to GDP and free phosphate, comprising an integral part of prokaryotic and eukaryotic signaling, protein biosynthesis and cell division, as well as membrane transport processes. The G protein cycle is brought to a halt after GTP hydrolysis, and requires the release of GDP before a new cycle can be initiated. For eukaryotic heterotrimeric Gαβγ proteins, the interaction with a membrane-bound G protein-coupled receptor catalyzes the release of GDP from the Gα subunit. Structural and functional studies have implicated one of the nucleotide binding sequence motifs, the G5 motif, as playing an integral part in this release mechanism. Indeed, a Gαs G5 mutant (A366S) was shown to have an accelerated GDP release rate, mimicking a G protein-coupled receptor catalyzed release state. In the present study, we investigate the role of the equivalent residue in the G5 motif (residue A143) in the prokaryotic membrane protein FeoB from Streptococcus thermophilus, which includes an N-terminal soluble G protein domain. The structure of this domain has previously been determined in the apo and GDP-bound states and in the presence of a transition state analogue, revealing conformational changes in the G5 motif. The A143 residue was mutated to a serine and analyzed with respect to changes in GTPase activity, nucleotide release rate, GDP affinity and structural alterations. We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base. © 2014 FEBS.

DNA loop domain organization in nucleoids from cells of different types.

Science.gov (United States)

Afanasieva, Katerina; Chopei, Marianna; Lozovik, Alexandra; Semenova, Anastasia; Lukash, Lyubov; Sivolob, Andrei

2017-01-29

The loop domain organization of chromatin plays an important role in transcription regulation and thus may be assumed to vary in cells of different types. We investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay) for nucleoids obtained from human lymphocytes, lymphoblasts and glioblastoma T98G cells. The results confirm our previous observation that there are three parts of DNA in nucleoids: DNA on the nucleoid surface, loops up to ∼150 kb inside the nucleoid, and larger loops that cannot migrate. However, the relative amounts of the three parts were found to be very different for different cell types. The distributions of the loop length up to 150 kb were shown to be exponential, with the distribution parameter, the loop density, to be dependent on the cell type. Copyright © 2016 Elsevier Inc. All rights reserved.

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E

Czech Academy of Sciences Publication Activity Database

Réblová, K.; Špačková, Naďa; Štefl, R.; Csaszar, K.; Koča, J.; Leontis, N. B.; Šponer, Jiří

2003-01-01

Roč. 84, č. 6 (2003), s. 3564-3582 ISSN 0006-3495 R&D Projects: GA MŠk LN00A016 Grant - others:National Institutes of Health(US) 2R15 GM55898; National Science Foundation(US) CHE-9732563 Institutional research plan: CEZ:AV0Z5004920 Keywords : non-Watson-Crick base pairs * ribosomal RNA * Loop E Subject RIV: BO - Biophysics Impact factor: 4.463, year: 2003

Closing the loop.

Science.gov (United States)

Dassau, E; Atlas, E; Phillip, M

2010-02-01

The dream of closing the loop is actually the dream of creating an artificial pancreas and freeing the patients from being involved with the care of their own diabetes. Insulin-dependent diabetes (type 1) is a chronic incurable disease which requires constant therapy without the possibility of any 'holidays' or insulin-free days. It means that patients have to inject insulin every day of their life, several times per day, and in order to do it safely they also have to measure their blood glucose levels several times per day. Patients need to plan their meals, their physical activities and their insulin regime - there is only very small room for spontaneous activities. This is why the desire for an artificial pancreas is so strong despite the fact that it will not cure the diabetic patients. Attempts to develop a closed-loop system started in the 1960s but never got to a clinical practical stage of development. In recent years the availability of continuous glucose sensors revived those efforts and stimulated the clinician and researchers to believe that closing the loop might be possible nowadays. Many papers have been published over the years describing several different ideas on how to close the loop. Most of the suggested systems have a sensing arm that measures the blood glucose repeatedly or continuously, an insulin delivery arm that injects insulin upon command and a computer that makes the decisions of when and how much insulin to deliver. The differences between the various published systems in the literature are mainly in their control algorithms. However, there are also differences related to the method and site of glucose measurement and insulin delivery. SC glucose measurements and insulin delivery are the most studied option but other combinations of insulin measurements and glucose delivery including intravascular and intraperitoneal (IP) are explored. We tried to select recent publications that we believe had influenced and inspired people interested

Site-specific proteolytic degradation of IgG monoclonal antibodies expressed in tobacco plants.

Science.gov (United States)

Hehle, Verena K; Lombardi, Raffaele; van Dolleweerd, Craig J; Paul, Mathew J; Di Micco, Patrizio; Morea, Veronica; Benvenuto, Eugenio; Donini, Marcello; Ma, Julian K-C

2015-02-01

Plants are promising hosts for the production of monoclonal antibodies (mAbs). However, proteolytic degradation of antibodies produced both in stable transgenic plants and using transient expression systems is still a major issue for efficient high-yield recombinant protein accumulation. In this work, we have performed a detailed study of the degradation profiles of two human IgG1 mAbs produced in plants: an anti-HIV mAb 2G12 and a tumour-targeting mAb H10. Even though they use different light chains (κ and λ, respectively), the fragmentation pattern of both antibodies was similar. The majority of Ig fragments result from proteolytic degradation, but there are only a limited number of plant proteolytic cleavage events in the immunoglobulin light and heavy chains. All of the cleavage sites identified were in the proximity of interdomain regions and occurred at each interdomain site, with the exception of the VL /CL interface in mAb H10 λ light chain. Cleavage site sequences were analysed, and residue patterns characteristic of proteolytic enzymes substrates were identified. The results of this work help to define common degradation events in plant-produced mAbs and raise the possibility of predicting antibody degradation patterns 'a priori' and designing novel stabilization strategies by site-specific mutagenesis. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

A Two-Stage Algorithm for the Closed-Loop Location-Inventory Problem Model Considering Returns in E-Commerce

Directory of Open Access Journals (Sweden)

Yanhui Li

2014-01-01

Full Text Available Facility location and inventory control are critical and highly related problems in the design of logistics system for e-commerce. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Focusing on the existing problem in e-commerce logistics system, we formulate a closed-loop location-inventory problem model considering returned merchandise to minimize the total cost which is produced in both forward and reverse logistics networks. To solve this nonlinear mixed programming model, an effective two-stage heuristic algorithm named LRCAC is designed by combining Lagrangian relaxation with ant colony algorithm (AC. Results of numerical examples show that LRCAC outperforms ant colony algorithm (AC on optimal solution and computing stability. The proposed model is able to help managers make the right decisions under e-commerce environment.

Two-loop operator matrix elements for massive fermionic local twist-2 operators in QED

International Nuclear Information System (INIS)

Bluemlein, J.; Freitas, A. de; Universidad Simon Bolivar, Caracas; Neerven, W.L. van

2011-11-01

We describe the calculation of the two--loop massive operator matrix elements with massive external fermions in QED. We investigate the factorization of the O(α 2 ) initial state corrections to e + e - annihilation into a virtual boson for large cms energies s >>m 2 e into massive operator matrix elements and the massless Wilson coefficients of the Drell-Yan process adapting the color coefficients to the case of QED, as proposed by F. A. Berends et. al. (Nucl. Phys. B 297 (1988)429). Our calculations show explicitly that the representation proposed there works at one-loop order and up to terms linear in ln (s/m 2 e ) at two-loop order. However, the two-loop constant part contains a few structural terms, which have not been obtained in previous direct calculations. (orig.)

Demonstration of In-Situ Stabilization of Buried Waste at Pit G-11 at the Brookhaven National laboratory Glass Pits Disposal Site

International Nuclear Information System (INIS)

Dwyer, B.P.; Gilbert, J.; Heiser, J.

1999-01-01

In 1989 BNL was added to the EPAs National Priorities List. The site is divided into seven operable units (OU). OU-I includes the former landfill area. The field task site is noted as the AOC 2C Glass Holes location. Beginning in the 1960s and continuing into the 1980s, BNL disposed of laboratory waste (glassware, chemicals and animal carcasses) in numerous shallow pits. The drivers for remediating the pits are; historical records that indicate hazardous materials may have been disposed of in the pits; ground water contamination down gradient of the pits; a test excavation of one of the glass holes that unearthed laboratory glass bottles with unidentified liquids still contained; and the fact that BNL rests atop an EPA designated sole-source aquifer. The specific site chosen for this demonstration was pit G-11. The requirements that lead to choosing this pit were; a well characterized pit and a relatively isolated pit where our construction operations would not impact on adjacent pits. The glass holes area, including pit G-11, was comprehensively surveyed using a suite of geophysical techniques (e.g., EM-31, EM-61, GPR). Prior to stabilizing the waste form a subsurface barrier was constructed to contain the entire waste pit. The pit contents were then stabilized using a cement grout applied via jet grouting. The stabilization was performed to make removal of the waste from the pit easier and safer in terms of worker exposure. The grouting process would mix and masticate the waste and grout and form a single monolithic waste form. This large monolith would then be subdivided into smaller 4 foot by 4 foot by 10-12 foot block using a demolition grout. The smaller blocks would then be easily removed from the site and disposed of in a CERCLA waste site

Incidência de fumonisina B1, aflatoxinas B1, B2, G1 e G2, ocratoxina A e zearalenona em produtos de milho Occurrence of fumonisin B1, aflatoxins B1, B2, G1, and G2, ochratoxin A and zearalenone in corn products

Directory of Open Access Journals (Sweden)

Luciane Mie Kawashima

2006-09-01

Full Text Available Levantamentos de ocorrência de micotoxinas em alimentos foram realizados nas últimas duas décadas nas regiões Sudeste e Sul do Brasil. Levantamentos em alimentos comercializados em outras regiões têm-se limitado a aflatoxinas em amendoim e castanhas do Brasil. O presente trabalho pesquisou a presença de fumonisina B1, aflatoxinas B1, B2, G1 e G2, ocratoxina A e zearalenona em 74 amostras de produtos a base de milho adquiridas no comércio da cidade de Recife, PE, durante o período de 1999 a 2001. Fumonisina B1 foi determinada por cromatografia líquida de alta eficiência com detecção por fluorescência e as demais toxinas foram determinadas por cromatografia em camada delgada. Fumonisina B1 foi encontrada em 94,6% das amostras em concentrações variando de 20 a 8600 µg/kg. Apenas 5 amostras continham aflatoxina B1 e o teor máximo encontrado foi 20 µg/kg. Duas amostras ultrapassaram o limite de 20 µg/kg para a somatória das aflatoxinas B1, B2, G1 e G2 (farinha de milho pré-cozida com 21,5 µg/kg e quirera (xerém com 23,3 µg/kg. As aflatoxinas G1 e G2, ocratoxina A e zearalenona não foram detectadas em nenhuma das amostras. Todas as amostras contaminadas com aflatoxinas também apresentaram fumonisina B1.Research concerning the presence of mycotoxin in food has been conducted in the Southwest and South regions of Brazil over the last two decades. Research in other regions has been limited to aflatoxin in peanuts and Brazil nuts. The aim of this work is to study the presence of fumonisin B1, aflatoxins B1, B2, G1, and G2, ochratoxin A and zearalenone in 74 samples of corn products acquired in shops and food markets in the city of Recife (PE from 1999 to 2001. Fumonisin B1 was determined by high performance liquid chromatography and fluorescence was detected. The other toxins were determined by thin layer chromatography. Fumonisin B1 was found in 94.6% of the samples in levels from 20 to 8600 µg/kg. Only 5 samples contained

The Fusion Loops of the Initial Prefusion Conformation of Herpes Simplex Virus 1 Fusion Protein Point Toward the Membrane

Directory of Open Access Journals (Sweden)

Juan Fontana

2017-08-01

Full Text Available All enveloped viruses, including herpesviruses, must fuse their envelope with the host membrane to deliver their genomes into target cells, making this essential step subject to interference by antibodies and drugs. Viral fusion is mediated by a viral surface protein that transits from an initial prefusion conformation to a final postfusion conformation. Strikingly, the prefusion conformation of the herpesvirus fusion protein, gB, is poorly understood. Herpes simplex virus (HSV, a model system for herpesviruses, causes diseases ranging from mild skin lesions to serious encephalitis and neonatal infections. Using cryo-electron tomography and subtomogram averaging, we have characterized the structure of the prefusion conformation and fusion intermediates of HSV-1 gB. To this end, we have set up a system that generates microvesicles displaying full-length gB on their envelope. We confirmed proper folding of gB by nondenaturing electrophoresis-Western blotting with a panel of monoclonal antibodies (MAbs covering all gB domains. To elucidate the arrangement of gB domains, we labeled them by using (i mutagenesis to insert fluorescent proteins at specific positions, (ii coexpression of gB with Fabs for a neutralizing MAb with known binding sites, and (iii incubation of gB with an antibody directed against the fusion loops. Our results show that gB starts in a compact prefusion conformation with the fusion loops pointing toward the viral membrane and suggest, for the first time, a model for gB’s conformational rearrangements during fusion. These experiments further illustrate how neutralizing antibodies can interfere with the essential gB structural transitions that mediate viral entry and therefore infectivity.

A systems analysis approach to nuclear facility siting

International Nuclear Information System (INIS)

Gros, J.G.; Avenhaus, R.; Linnerooth, J.; Pahner, P.D.; Otway, H.J.

1975-01-01

An attempt is made to demonstrate an application of the techniques of systems analysis, which have been successful in solving a variety of problems, to nuclear facility siting. Within the framework of an overall regional land-use plan, a methodology for establishing the acceptability of a combination of site and facility is discussed. The consequences (e.g. the energy produced, thermal and chemical discharges, radioactive releases, aeshetic values, etc.) of the site-facility combination are identified and compared with formalized criteria in order to ensure 'legal acceptability'. Failure of any consequences to satisfy standard requirements results in a feedback channel which works to effect design changes in the facility. When 'legal acceptability' has been assured, the project enters the public sector for consideration. The responses of individuals and of various interested groups to the external attributes of the nuclear facility gradually emerge. The criteria by which interest groups judge technological advances reflect both their rational assessment and unconscious motivations. This process operates on individual, group, societal and international levels and may result in two basic feedback loops: one which might act to change regulatory criteria; the other which might influence facility design or site selection. Such reactions and responses on these levels result in a continuing process of confrontation, collaborative interchange and possible resolution in the direction of an acceptable solution. Finally, a Paretian approach to optimizing the site-facility combination is presented for the case where there are several possible combinations of site and facility. A hypothetical example of the latter is given, based upon typical preference functions determined for four interest groups. The research effort of the IIASA Energy Systems Project and the Joint IAEA/IIASA Research Project in the area of nuclear siting is summarized. (author)

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

Science.gov (United States)

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Active fault diagnosis in closed-loop uncertain systems

DEFF Research Database (Denmark)

Niemann, Hans Henrik

2006-01-01

Fault diagnosis of parametric faults in closed-loop uncertain systems by using an auxiliary input vector is considered in this paper, i.e. active fault diagnosis (AFD). The active fault diagnosis is based directly on the socalled fault signature matrix, related to the YJBK (Youla, Jabr, Bongiorno...... and Kucera) parameterization. Conditions are given for exact detection and isolation of parametric faults in closed-loop uncertain systems....

Digital Discernment: An E-Commerce Web Site Evaluation Tool

Science.gov (United States)

Sigman, Betsy Page; Boston, Brian J.

2013-01-01

Students entering the business workforce today may well share some responsibility for developing, revising, or evaluating their company's Web site. They may lack the experience, however, to critique their employer's Web presence effectively. The purpose of developing Digital Discernment, an e-commerce Web site evaluation tool, was to prepare…

Three classes of ligands each bind to distinct sites on the orphan G protein-coupled receptor GPR84.

Science.gov (United States)

Mahmud, Zobaer Al; Jenkins, Laura; Ulven, Trond; Labéguère, Frédéric; Gosmini, Romain; De Vos, Steve; Hudson, Brian D; Tikhonova, Irina G; Milligan, Graeme

2017-12-20

Medium chain fatty acids can activate the pro-inflammatory receptor GPR84 but so also can molecules related to 3,3'-diindolylmethane. 3,3'-Diindolylmethane and decanoic acid acted as strong positive allosteric modulators of the function of each other and analysis showed the affinity of 3,3'-diindolylmethane to be at least 100 fold higher. Methyl decanoate was not an agonist at GPR84. This implies a key role in binding for the carboxylic acid of the fatty acid. Via homology modelling we predicted and confirmed an integral role of arginine 172 , located in the 2nd extracellular loop, in the action of decanoic acid but not of 3,3'-diindolylmethane. Exemplars from a patented series of GPR84 antagonists were able to block agonist actions of both decanoic acid and 3,3'-diindolylmethane at GPR84. However, although a radiolabelled form of a related antagonist, [ 3 H]G9543, was able to bind with high affinity to GPR84, this was not competed for by increasing concentrations of either decanoic acid or 3,3'-diindolylmethane and was not affected adversely by mutation of arginine 172 . These studies identify three separable ligand binding sites within GPR84 and suggest that if medium chain fatty acids are true endogenous regulators then co-binding with a positive allosteric modulator would greatly enhance their function in physiological settings.

Loop Quantum Cosmology.

Science.gov (United States)

Bojowald, Martin

2008-01-01

Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

Closed-Loop Control Without Meal Announcement in Type 1 Diabetes.

Science.gov (United States)

Cameron, Faye M; Ly, Trang T; Buckingham, Bruce A; Maahs, David M; Forlenza, Gregory P; Levy, Carol J; Lam, David; Clinton, Paula; Messer, Laurel H; Westfall, Emily; Levister, Camilla; Xie, Yan Yan; Baysal, Nihat; Howsmon, Daniel; Patek, Stephen D; Bequette, B Wayne

2017-09-01

A fully closed-loop insulin-only system was developed to provide glucose control in patients with type 1 diabetes without requiring announcement of meals or activity. Our goal was to assess initial safety and efficacy of this system. The multiple model probabilistic controller (MMPPC) anticipates meals when the patient is awake. The controller used the subject's basal rates and total daily insulin dose for initialization. The system was tested at two sites on 10 patients in a 30-h inpatient study, followed by 15 subjects at three sites in a 54-h supervised hotel study, where the controller was challenged by exercise and unannounced meals. The system was implemented on the UVA DiAs system using a Roche Spirit Combo Insulin Pump and a Dexcom G4 Continuous Glucose Monitor. The mean overall (24-h basis) and nighttime (11 PM-7 AM) continuous glucose monitoring (CGM) values were 142 and 125 mg/dL during the inpatient study. The hotel study used a different daytime tuning and manual announcement, instead of automatic detection, of sleep and wake periods. This resulted in mean overall (24-h basis) and nighttime CGM values of 152 and 139 mg/dL for the hotel study and there was also a reduction in hypoglycemia events from 1.6 to 0.91 events/patient/day. The MMPPC system achieved a mean glucose that would be particularly helpful for people with an elevated A1c as a result of frequent missed meal boluses. Current full closed loop has a higher risk for hypoglycemia when compared with algorithms using meal announcement.

Revisão dos gêneros Sitalces, Eusitalces e Parasitalces (Orthoptera, Acrididae, Abracrini e descrição de três novos gêneros

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Maria Kátia Matiotti da Costa

2006-06-01

Full Text Available Revisão dos gêneros Sitalces, Eusitalces e Parasitalces (Orthoptera, Acrididae, Abracrini e descrição de três novos gêneros. Os gêneros sulamericanos de Abracrini Sitalces Stål, 1878, Eusitalces Bruner, 1911, Parasitalces Bruner, 1911, Liebermannacris gen. nov., Robustusacris gen. nov., e Arimacris gen. nov. são revisados, descritos, redescritos e redefinidos. Quatro espécies são novas combinações: Liebermannacris dorsualis (Giglio-Tos, 1898 comb. nov., Liebermannacris punctifrons (Stål,1878 comb. nov., Robustusacris balzapambae (Rehn, 1913 comb. nov., e Arimacris trinitatis (Bruner, 1906 comb. nov., todas removidas de Sitalces Stål, 1878. Nove espécies são novos sinônimos: Sitalces robustus Bruner, 1908 (de S. volxemi Stål, 1878; S. infuscatus Bruner, 1908, S. nudus Bruner, 1908, S. ovatipennis Bruner, 1908, S. madeirensis Rehn, 1916 (de Liebermannacris dorsualis (Giglio-Tos, 1898; S. rubripes Hebard, 1924 (de Robustusacris balzapambae (Rehn, 1913; E. amazonicus Günther, 1940 e S. apolinari Hebard, 1923 (de Eusitalces vittatus Bruner, 1911; E. rubripes Günther, 1940 (de P. vulneratus (Bruner,1919. Lectótipos e paralectótipos são designados. São fornecidas chaves para identificação, medidas, mapa de distribuição geográfica e ilustrações dos gêneros e espécies.Revision of the genera Sitalces, Eusitalces and Parasitalces (Orthoptera, Acrididae, Abracrini and description of three new genera. The South American Abracrini genera Sitalces Stål, 1878, Eusitalces Bruner, 1911, Parasitalces Bruner, 1911, Liebermannacris gen. nov., Robustusacris gen. nov., and Arimacris gen. nov. are reviewed, described, redescribed and redefined. Four species are new combinations: Liebermannacris dorsualis (Giglio-Tos, 1898 comb. nov., Liebermannacris punctifrons (Stål,1878 comb. nov., Arimacris trinitatis (Bruner, 1906 comb. nov., and Robustusacris balzapambae (Rehn, 1913 comb. nov., all removed of Sitalces Stål, 1878. Nine species

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Science.gov (United States)

Sanborn, Adrian; Rao, Suhas; Huang, Su-Chen; Durand, Neva; Huntley, Miriam; Jewett, Andrew; Bochkov, Ivan; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher; McKenna, Doug; Stamenova, Elena; Gnirke, Andreas; Melnikov, Alexandre; Lander, Eric; Aiden, Erez

Our recent kilobase-resolution genome-wide maps of DNA self-contacts demonstrated that mammalian genomes are organized into domains and loops demarcated by the DNA-binding protein CTCF. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that domains are inconsistent with equilibrium and fractal models. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during condensation leads to formation of an anisotropic ``tension globule.'' In the other, CTCF and cohesin act together to extrude unknotted loops. Both models are consistent with the observed domains and loops. However, the extrusion model explains a far wider array of observations, such as why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The extrusion model predicts in silico the experimental maps using only CTCF-binding sites. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

Mouse allergen exposure and immunologic responses: IgE-mediated mouse sensitization and mouse specific IgG and IgG4 levels

NARCIS (Netherlands)

Matsui, Elizabeth C.; Krop, Esmeralda J. M.; Diette, Gregory B.; Aalberse, Rob C.; Smith, Abigail L.; Eggleston, Peyton A.

2004-01-01

Although there is evidence that contact with mice is associated with IgE-mediated mouse sensitization and mouse specific antibody responses, the exposure-response relationships remain unclear. To determine whether IgE-mediated mouse sensitization and mouse specific IgG (mIgG) and mIgG4 levels

Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor.

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Cyril F Reboul

Full Text Available BACKGROUND: The C-terminal domain of MotB (MotB-C shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. METHODOLOGY/PRINCIPAL FINDINGS: We determined the structure of a new crystalline form (Form B of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. CONCLUSION/SIGNIFICANCE: Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall.

Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.

Science.gov (United States)

Guédin, Aurore; Lin, Linda Yingqi; Armane, Samir; Lacroix, Laurent; Mergny, Jean-Louis; Thore, Stéphane; Yatsunyk, Liliya A

2018-06-01

Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

The one-loop Green's functions of dimensionally reduced gauge theories

International Nuclear Information System (INIS)

Ketov, S.V.; Prager, Y.S.

1988-01-01

The dimensional regularization technique as well as that by dimensional reduction is applied to the calculation of the regularized one-loop Green's functions in dsub(o)-dimensional Yang-Mills theory with real massless scalars and spinors in arbitrary (real) representations of a gauge group G. As a particular example, the super-symmetrically regularized one-loop Green's functions of the N=4 supersymmetric Yang-Mills model are derived. (author). 17 refs

The pressure of hot QCD up to $g^{6}$ ln(1/g)

CERN Document Server

Kajantie, Keijou; Rummukainen, K; Schröder, Y

2003-01-01

The free energy density, or pressure, of QCD has at high temperatures an expansion in the coupling constant g, known so far up to order g^5. We compute here the last contribution which can be determined perturbatively, g^6 ln(1/g), by summing together results for the 4-loop vacuum energy densities of two different three-dimensional effective field theories. We also demonstrate that the inclusion of the new perturbative g^6 ln(1/g) terms, together with the so far unknown perturbative and non-perturbative g^6 terms, could potentially extend the applicability of the resummed coupling constant series down to surprisingly low temperatures.

G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch.

Science.gov (United States)

Yan, Yi-Yong; Tan, Jia-Heng; Lu, Yu-Jing; Yan, Siu-Cheong; Wong, Kwok-Yin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

2013-10-01

G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates. © 2013.

Two-loop hard-thermal-loop thermodynamics with quarks

International Nuclear Information System (INIS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-01-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

Physical stability comparisons of IgG1-Fc variants: effects of N-glycosylation site occupancy and Asp/Gln residues at site Asn 297.

Science.gov (United States)

Alsenaidy, Mohammad A; Okbazghi, Solomon Z; Kim, Jae Hyun; Joshi, Sangeeta B; Middaugh, C Russell; Tolbert, Thomas J; Volkin, David B

2014-06-01

The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and nonglycosylated) were determined. In addition, the physical stability profiles of three different forms of nonglycosylated Fc molecules (varying amino-acid residues at site 297 in the CH 2 domain due to the point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high-throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0-6.0, the di- and monoglycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability, respectively, with the nonglycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

LoopIng: a template-based tool for predicting the structure of protein loops.

KAUST Repository

Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

2015-01-01

) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

Renoprotective effects of thiazides combined with loop diuretics in patients with type 2 diabetic kidney disease.

Science.gov (United States)

Hoshino, Taro; Ookawara, Susumu; Miyazawa, Haruhisa; Ito, Kiyonori; Ueda, Yuichiro; Kaku, Yoshio; Hirai, Keiji; Mori, Honami; Yoshida, Izumi; Tabei, Kaoru

2015-04-01

Type 2 diabetic kidney disease (DKD) is frequently accompanied by uncontrollable hypertension due to the sodium sensitivity inherent in DKD and to diuretic-resistant edema. In general, diuretics are effective in treating this condition, but thiazide diuretics are thought to be innocuous in advanced chronic kidney disease (CKD). We examined the renoprotective effects of combination therapy with thiazides and loop diuretics in type 2 DKD patients with CKD stage G4 or G5. This study included 11 patients with type 2 DKD and an estimated glomerular filtration rate (eGFR) diuretics. Each patient received additional hydrochlorothiazide (HCTZ) therapy, which was continued for more than 12 months. We examined clinical parameters including blood pressure (BP), proteinuria, and eGFR before and after the addition of HCTZ. Patients received a 13.6 ± 3.8 mg/day dose of HCTZ in addition to loop diuretics (azosemide: 120 mg/day in 6 cases, 60 mg/day in 3 cases and furosemide: 80 mg/day in 1 case, 120 mg/day in 1 case). Side effects of HCTZ were not observed in all patients. After the addition of HCTZ therapy, systolic and diastolic blood pressures (S-BP, D-BP) as well as proteinuria significantly decreased (S-BP: at 6 months, p diuretics improves BP levels, and decreases proteinuria even in advanced stage type 2 DKD patients with severe edema. The addition of HCTZ therapy was not found to negatively affect the change in eGFR in the present study.

Fundamental Fermions (e.g. Neutrinos) as Topological Objects

Science.gov (United States)

Fitzpatrick, Gerald L.

1999-05-01

A new internal ``macroscopic'' description of fundamental fermions based on a matrix-generalization (F) of the scalar fermion-number f, predicts that only three families of quarks and leptons, and their associated neutrinos (ν_e, ν_μ and ν_τ), exist [1]. Moreover, this description places important phtopological constraints on neutrino mixtures [2]. With respect to F, the topology of the νe (ν_μ or ν_τ) is that of a cylinder (Möbius strip). Assuming that topology-changing neutrino-neutrino transitions are suppressed (e.g., one cannot continuously deform a donut into a sphere), while topology-maintaining transitions are relatively enhanced, one may have an explanation for short-distance observations of (nearly) maximal ν_μ-ν_τ mixing [3]. To test this idea, simple topological arguments were used to deduce a matrix describing long-distance neutrino mixtures, which is phidentical to that proposed by Georgi and Glashow on different grounds [4]. Experimental confirmation of this prediction would support the new description, which requires the νe and (ν_μ or ν_τ) to start ``life'' as topologically-distinct quantum objects.l [1] http://www.amazon.com/exec/obidos/ISBN=0965569500, [2] G. L. Fitzpatrick, aps1999feb12\\underbar001 at http://publish.aps.org/eprint/, [3] hep-ex/981001, [4] hep-ph/9808293, p. 5, Eq. 20.

Por uma outra classificação:gêneros discursivos jornalísticos e gêneros discursivos jornálicos.

Directory of Open Access Journals (Sweden)

Lia Seixas

2010-02-01

Full Text Available Este artigo representa nossa tese de doutorado, para a qual o gênero jornalístico é uma enunciação relativamente estável, ao invés de enunciado relativamente estável, no dizer de Bakhtin. O gênero do jornalismo de atualidade se constitui nas combinações regulares de quatro elementos principais: 1 a lógica enunciativa; 2 a força argumentativa; 3 a identidade discursiva e 4 o mídium. Segundo as competências empregadas pelos sujeitos comunicantes, sugerimos repensar a divisão entre gêneros discursivos jornalísticos e gêneros discursivos jornálicos. Fundamentada na formação discursiva de Foucault, na análise do discurso (Charaudeau e Maingueneau e na pragmática da comunicação (Austin, Searle, a pesquisa partiu das ocorrências (acontecimentos jornalísticos e das condições extralinguísticas (condições de produção com entrevistas em direção à compreensão da relação entre discurso e realidade. A tese analisou sistematicamente composições discursivas de seis veículos impressos e digitais de uma empresa brasileira (Grupo Folha da Manhã S.A., uma espanhola (RCS MediaGroup, maior acionista do El Mundo e uma francesa (Le Monde S.A..

Predictive value of IgE/IgG4 antibody ratio in children with egg allergy

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Okamoto Shindou

2012-06-01

Full Text Available Abstract Background The aim of this study was to investigate the role of specific IgG4 antibodies to hen’s egg white and determine their utility as a marker for the outcome of oral challenge test in children sensitized to hen’s egg Methods The hen’s egg oral food challenge test was performed in 105 sensitized children without atopic dermatitis, and the titers of egg white-specific immunoglobulin G4 (IgG4 and immunoglobulin E (IgE antibodies were measured. To set the cut-off values of IgG4, IgE, and the IgE/IgG4 ratio for predicting positive results in oral challenges, receiver operating characteristic curves were plotted and the area under the curves (AUC were calculated. Results Sixty-four of 105 oral challenges with whole eggs were assessed as positive. The AUC for IgE, IgG4, and IgE/IgG4 for the prediction of positive results were 0.609, 0.724, and 0.847, respectively. Thus, the IgE/IgG4 ratio generated significantly higher specificity, sensitivity, positive predictive value (%, and negative predictive value (% than the individual IgE and IgG4. The negative predictive value of the IgE/IgG4 ratio was 90% at a value of 1. Conclusions We have demonstrated that the egg white-specific serum IgE/IgG4 ratio is important for predicting reactivity to egg during food challenges.

Biophysical characterization and membrane interaction of the two fusion loops of glycoprotein B from herpes simplex type I virus.

Directory of Open Access Journals (Sweden)

Annarita Falanga

Full Text Available The molecular mechanism of entry of herpesviruses requires a multicomponent fusion system. Cell invasion by Herpes simplex virus (HSV requires four virally encoded glycoproteins: namely gD, gB and gH/gL. The role of gB has remained elusive until recently when the crystal structure of HSV-1 gB became available and the fusion potential of gB was clearly demonstrated. Although much information on gB structure/function relationship has been gathered in recent years, the elucidation of the nature of the fine interactions between gB fusion loops and the membrane bilayer may help to understand the precise molecular mechanism behind herpesvirus-host cell membrane fusion. Here, we report the first biophysical study on the two fusion peptides of gB, with a particular focus on the effects determined by both peptides on lipid bilayers of various compositions. The two fusion loops constitute a structural subdomain wherein key hydrophobic amino acids form a ridge that is supported on both sides by charged residues. When used together the two fusion loops have the ability to significantly destabilize the target membrane bilayer, notwithstanding their low bilayer penetration when used separately. These data support the model of gB fusion loops insertion into cholesterol enriched membranes.

Fluctuation current in superconducting loops

International Nuclear Information System (INIS)

Berger, Jorge

2012-01-01

A superconducting loop that encloses noninteger flux holds a permanent current. On the average, this current is also present above T c , and has been measured in recent years. We are able to evaluate the permanent current within the TDGL or the Kramer-Watts-Tobin models for loops of general configuration, i.e., we don't require uniform cross section, material or temperature. We can also consider situations in which the width is not negligible in comparison to the radius. Our results agree with experiments. The situations with which we deal at present include fluctuation superconductivity in two-band superconductors, equilibrium thermal fluctuations of supercurrent along a weak link, and ratchet effects.

Instrument calibration optimization at Bruce Power: ECI loops

International Nuclear Information System (INIS)

Chugh, V.; Angelova, M.; Ghias, S.; Parmar, R.; Wang, V.; Xie, H.; Higgs, J.; Schut, J.; Cruchley, I.

2011-01-01

Most instruments in a nuclear power plant are calibrated at regular intervals to ensure consistency with the assumptions in the plant Technical Specifications and/or Safe Operating Envelope (SOE) compliance limits (e.g., As-Found Tolerance). In the Instrument Uncertainty Calculations (IUC), As-Found Tolerance for instrument drift is estimated based on statistical analysis of As-Found and As-Left calibration data such as that carried out for Bruce NGS by EPRI (Electric Power Research Institute) in 1998. Bruce specific drift values were found to compare favorably with industry benchmarks. Recently a significant amount of work has been done by EPRI and IAEA (International Atomic Energy Agency) on extending calibration intervals of safety related instruments. Reduction in calibration frequency reduces time commitments on the part of Authorized Nuclear Operators and safety system qualified Control Maintenance Technicians, and allows more schedule flexibility. To establish the proof of concept, As-Left/As-Found tolerances and available margins have been evaluated for the Bruce B Emergency Coolant Injection (ECI) system instrument loops to determine whether an extension of the calibration period from one or two year to three years is justifiable on the basis that these loops will still be in compliance with SOE. The analysis showed that 60% of instruments in the ECI system are qualified for calibration interval extension up to three years. Sensitivity assessment of the effect of proposed changes in calibration intervals for 60% of the instruments on the ECI system unavailability has also been performed using the current Bruce Power ECI unavailability model. The results show that, the largest ECI Predicted Future Unavailability (PFU) is 9.2E-4 year/year for in-core LOCA accident. This value is still below the target unavailability of 1.0E-3 year/year. (author)

Instrument calibration optimization at Bruce Power: ECI loops

Energy Technology Data Exchange (ETDEWEB)

Chugh, V.; Angelova, M.; Ghias, S.; Parmar, R.; Wang, V.; Xie, H. [AMEC NSS, Toronto, Ontario (Canada); Higgs, J.; Schut, J.; Cruchley, I. [Bruce Power, Tiverton, Ontario (Canada)

2011-07-01

Most instruments in a nuclear power plant are calibrated at regular intervals to ensure consistency with the assumptions in the plant Technical Specifications and/or Safe Operating Envelope (SOE) compliance limits (e.g., As-Found Tolerance). In the Instrument Uncertainty Calculations (IUC), As-Found Tolerance for instrument drift is estimated based on statistical analysis of As-Found and As-Left calibration data such as that carried out for Bruce NGS by EPRI (Electric Power Research Institute) in 1998. Bruce specific drift values were found to compare favorably with industry benchmarks. Recently a significant amount of work has been done by EPRI and IAEA (International Atomic Energy Agency) on extending calibration intervals of safety related instruments. Reduction in calibration frequency reduces time commitments on the part of Authorized Nuclear Operators and safety system qualified Control Maintenance Technicians, and allows more schedule flexibility. To establish the proof of concept, As-Left/As-Found tolerances and available margins have been evaluated for the Bruce B Emergency Coolant Injection (ECI) system instrument loops to determine whether an extension of the calibration period from one or two year to three years is justifiable on the basis that these loops will still be in compliance with SOE. The analysis showed that 60% of instruments in the ECI system are qualified for calibration interval extension up to three years. Sensitivity assessment of the effect of proposed changes in calibration intervals for 60% of the instruments on the ECI system unavailability has also been performed using the current Bruce Power ECI unavailability model. The results show that, the largest ECI Predicted Future Unavailability (PFU) is 9.2E-4 year/year for in-core LOCA accident. This value is still below the target unavailability of 1.0E-3 year/year. (author)

Loop corrections and other many-body effects in relativistic field theories

International Nuclear Information System (INIS)

Ainsworth, T.L.; Brown, G.E.; Prakash, M.; Weise, W.

1988-01-01

Incorporation of effective masses into negative energy states (nucleon loop corrections) gives rise to repulsive many-body forces, as has been known for some time. Rather than renormalizing away the three- and four-body terms, we introduce medium corrections into the effective σ-exchange, which roughly cancel the nucleon loop terms for densities ρ ≅ ρ nm , where ρ nm is nuclear matter density. Going to higher densities, the repulsive contributions tend to saturate whereas the attractive ones keep on growing in magnitude. The latter is achieved through use of a density-dependent effective mass for the σ-particle, m σ = m σ (ρ), such that m σ (ρ) decreases with increasing density. Such a behavior is seen e.g. in the Nambu-Jona-Lasinio model. It is argued that a smooth transition to chiral restoration implies a similar behavior. The resulting nuclear equation of state is, because of the self-consistency in the problem, immensely insensitive to changes in the mass or coupling constant of the σ-particle. (orig.)

QED loop effects in the spacetime background of a Schwarzschild black hole

Science.gov (United States)

Emelyanov, Viacheslav A.

2017-12-01

The black-hole evaporation implies that the quantum-field propagators in a local Minkowski frame acquire a correction, which gives rise to this process. The modification of the propagators causes, in turn, non-trivial local effects due to the radiative/loop diagrams in non-linear QFTs. In particular, there should be imprints of the evaporation in QED, if one goes beyond the tree-level approximation. Of special interest in this respect is the region near the black-hole horizon, which, already at tree level, appears to show highly non-classical features, e.g., negative energy density and energy flux into the black hole.

Gravity duals of half-BPS Wilson loops

International Nuclear Information System (INIS)

D'Hoker, Eric; Estes, John; Gutperle, Michael

2007-01-01

We explicitly construct the fully back-reacted half-BPS solutions in Type IIB supergravity which are dual to Wilson loops with 16 supersymmetries in N = 4 super Yang-Mills. In a first part, we use the methods of a companion paper to derive the exact general solution of the half-BPS equations on the space AdS 2 x S 2 x S 4 x Σ, with isometry group SO(2, 1) x SO(3) x SO(5) in terms of two locally harmonic functions on a Riemann surface Σ with boundary. These solutions, generally, have varying dilaton and axion, and non-vanishing 3-form fluxes. In a second part, we impose regularity and topology conditions. These non-singular solutions may be parametrized by a genus g ≥ 0 hyperelliptic surface Σ, all of whose branch points lie on the real line. Each genus g solution has only a single asymptotic AdS 5 x S 5 region, but exhibits g homology 3-spheres, and an extra g homology 5-spheres, carrying respectively RR 3-form and RR 5-form charges. For genus 0, we recover AdS 5 x S 5 with 3 free parameters, while for genus g ≥ 1, the solution has 2g+5 free parameters. The genus 1 case is studied in detail. Numerical analysis is used to show that the solutions are regular throughout the g = 1 parameter space. Collapse of a branch cut on Σ subtending either a homology 3-sphere or a homology 5-sphere is non-singular and yields the genus g-1 solution. This behavior is precisely expected of a proper dual to a Wilson loop in gauge theory

Organohalogen pollutants in surface particulates from workshop floors of four major e-waste recycling sites in China and implications for emission lists

Energy Technology Data Exchange (ETDEWEB)

Zeng, Yan-Hong [State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Tang, Bin [State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Graduate University of Chinese Academy of Sciences, Beijing 100049 (China); Luo, Xiao-Jun [State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Zheng, Xiao-Bo [College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642 (China); Peng, Ping-An [State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Mai, Bi-Xian, E-mail: nancymai@gig.ac.cn [State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China)

2016-11-01

To examine the environmental pollution associated with e-waste recycling activities, the concentrations of organohologenated pollutants (OHPs), i.e., short- and medium-chain chlorinated paraffins (SCCPs and MCCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and several other halogenated flame retardants (OHFRs), were investigated in surface particulates from the workshop floors of four major e-waste recycling sites (Taizhou, Guiyu, Dali and Qingyuan) in China. The mean levels of SCCPs, MCCPs, PCBs, PBDEs and OHFRs in surface particulates ranged from 30,000–61,000, 170,000–890,000, 2700–27,000, 52,000–240,000, and 62,000–140,000 ng/g dry weight (dw), respectively. OHFRs, including decabromodiphenyl ethane, dechlorane plus, 1,2-bis(2,4,6-tribromophenoxy)ethane, tetrabromobisphenol A, hexabromocyclododecanes, polybrominated biphenyls, hexabromobenzene, pentabromotoluene, and pentabromoethylbenzene, were frequently (> 50% detection frequency) detected in surface particulates with mean concentration ranges of 39,000–63,000, 310–2700, 98–16,000, 21,000–56,000, 55–5700, 1700–27,000, 42–1600, 3.2–220, and 5.8–12 ng/g dw, respectively. The composition of OHPs varied depend on the e-waste items processing in different regions. Guiyu and Dali were typical sites contaminated by halogenated flame retardants (HFRs) and CPs, respectively, while Qingyuan, and Taizhou were representative PCB-polluted regions. The evidence produced by this preliminary study indicated that electronic devices and plastics may account for the high content of HFRs and the metal products are likely the major source of CPs in these e-waste sites. - Highlights: • Report of characterizing the types and possible sources of OHPs in e-waste sites • Guiyu was a typical site contaminated by HFRs, while Dali was dominated by CPs. • Qingyuan and Taizhou were representative PCB-polluted regions. • Electronic devices and plastics may account for the

Organohalogen pollutants in surface particulates from workshop floors of four major e-waste recycling sites in China and implications for emission lists

International Nuclear Information System (INIS)

Zeng, Yan-Hong; Tang, Bin; Luo, Xiao-Jun; Zheng, Xiao-Bo; Peng, Ping-An; Mai, Bi-Xian

2016-01-01

To examine the environmental pollution associated with e-waste recycling activities, the concentrations of organohologenated pollutants (OHPs), i.e., short- and medium-chain chlorinated paraffins (SCCPs and MCCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and several other halogenated flame retardants (OHFRs), were investigated in surface particulates from the workshop floors of four major e-waste recycling sites (Taizhou, Guiyu, Dali and Qingyuan) in China. The mean levels of SCCPs, MCCPs, PCBs, PBDEs and OHFRs in surface particulates ranged from 30,000–61,000, 170,000–890,000, 2700–27,000, 52,000–240,000, and 62,000–140,000 ng/g dry weight (dw), respectively. OHFRs, including decabromodiphenyl ethane, dechlorane plus, 1,2-bis(2,4,6-tribromophenoxy)ethane, tetrabromobisphenol A, hexabromocyclododecanes, polybrominated biphenyls, hexabromobenzene, pentabromotoluene, and pentabromoethylbenzene, were frequently (> 50% detection frequency) detected in surface particulates with mean concentration ranges of 39,000–63,000, 310–2700, 98–16,000, 21,000–56,000, 55–5700, 1700–27,000, 42–1600, 3.2–220, and 5.8–12 ng/g dw, respectively. The composition of OHPs varied depend on the e-waste items processing in different regions. Guiyu and Dali were typical sites contaminated by halogenated flame retardants (HFRs) and CPs, respectively, while Qingyuan, and Taizhou were representative PCB-polluted regions. The evidence produced by this preliminary study indicated that electronic devices and plastics may account for the high content of HFRs and the metal products are likely the major source of CPs in these e-waste sites. - Highlights: • Report of characterizing the types and possible sources of OHPs in e-waste sites • Guiyu was a typical site contaminated by HFRs, while Dali was dominated by CPs. • Qingyuan and Taizhou were representative PCB-polluted regions. • Electronic devices and plastics may account for the

The activation energy for loop growth in Cu and Cu-Ni alloys

International Nuclear Information System (INIS)

Barlow, P.; Leffers, T.; Singh, B.N.

1978-08-01

The apparent activation energy for the growth of interstitial dislocation loops in copper, Cu-1%Ni, Cu-2%Ni, and Cu-5%Ni during high voltage electron microscope irradiation was determined. The apparent activation energy for loop growth in all these materials can be taken to be 0.34eV+-0.02eV. This value together with the corresponding value of 0.44eV+-0.02eV determined earlier for Cu-10%Ni is discussed with reference to the void growth rates observed in these materials. The apparent activation energy for loop growth in copper (and in Cu-1%Ni that has a void growth rate similar to that in pure copper) is interpreted as twice the vacancy migration energy (indicating that divacancies do not play any significant role). For the materials with higher Ni content (in which the void growth rate is much lower than that in Cu and Cu-1%Ni) the measured apparent activation energy is interpreted to be characteristic of loops positioned fairly close to the foil surface and not of loops in ''bulk material''. From the present results in combination with the earlier results for Cu-10%Ni it is concluded that interstitial trapping is the most likely explanation of the reduced void growth rate in Cu-Ni alloys. (author)

One-loop calculations with massive particles

International Nuclear Information System (INIS)

Oldenborgh, G.J. van.

1990-01-01

In this thesis some techniques for performing one-loop calculations with massive particles are presented. Numerical techniques are presented necessary for evaluating one-loop integrals which occur in one-loop calculations of photon-photon scattering. The algorithms have been coded in FORTRAN (to evaluate the scalar integrals) and the algebraic language FORM (to reduce the tensor integrals to scalar integrals). Applications are made in the theory of the strong interaction, QCD, i.e. in handling one-loop integrals with massive particles, in order to regulate the infinities by mass parameters encountered in this theory. However this simplifies the computation considerably, the description of the proton structure functions have to be renormalized in order to obtain physical results. This renormalization is different from the published results for the gluon and thus has to be redone. The first physics results that have been obtained with these new methods are presented. These concern heavy quark production in semi-leptonic interactions, for instance neutrino charm production and top production at the electron-proton (ep) collider HERA and the proposed LEP/LHC combination. Total and differential cross-sections for one-loop corrections to top production at the HERA and proposed LEP/HLC ep colliders are given and structure functions for charmed quark production are compared with previously published results. (author). 58 refs.; 18 figs.; 5 tabs

Fluorescent IgG fusion proteins made in E. coli

Science.gov (United States)

Luria, Yael; Raichlin, Dina; Benhar, Itai

2012-01-01

Antibodies are among the most powerful tools in biological and biomedical research and are presently the fastest growing category of new bio-pharmaceutics. The most common format of antibody applied for therapeutic, diagnostic and analytical purposes is the IgG format. For medical applications, recombinant IgGs are made in cultured mammalian cells in a process that is too expensive to be considered for producing antibodies for diagnostic and analytical purposes. Therefore, for such purposes, mouse monoclonal antibodies or polyclonal sera from immunized animals are used. While looking for an easier and more rapid way to prepare full-length IgGs for therapeutic purposes, we recently developed and reported an expression and purification protocol for full-length IgGs, and IgG-based fusion proteins in E. coli, called “Inclonals.” By applying the Inclonals technology, we could generate full-length IgGs that are genetically fused to toxins. The aim of the study described herein was to evaluate the possibility of applying the “Inclonals” technology for preparing IgG-fluorophore fusion proteins. We found that IgG fused to the green fluorescent proteins enhanced GFP (EGFP) while maintaining functionality in binding, lost most of its fluorescence during the refolding process. In contrast, we found that green fluorescent Superfolder GFP (SFGFP)-fused IgG and red fluorescent mCherry-fused IgG were functional in antigen binding and maintained fluorescence intensity. In addition, we found that we can link several SFGFPs in tandem to each IgG, with fluorescence intensity increasing accordingly. Fluorescent IgGs made in E. coli may become attractive alternatives to monoclonal or polyclonal fluorescent antibodies derived from animals. PMID:22531449

End-user perspectives on e-commerce and health care web site quality.

Science.gov (United States)

Le Rouge, Cynthia; De Leo, Gianluca

2008-11-06

We explore and compare the importance of various quality dimensions for health care and e-commerce web sites. The results show that the importance of various quality attributes for all except four of ten quality dimensions studied differ between health care and e-commerce web sites. These results can help health care managers to improve and/or to guide the design of their web sites.

Muon g-2 theory. The hadronic part

International Nuclear Information System (INIS)

Jegerlehner, Fred

2017-04-01

I present a status report of the hadronic vacuum polarization effects for the muon g-2, to be considered as an update of an earlier paper (F. Jegerlehner, 2016). The update concerns recent new inclusive R measurements from KEDR in the energy range 1.84 to 3.72 GeV. For the leading order contributions I find a had(1) μ =(688.07±4.14)[688.77±3.38] x 10 -10 based on e + e - data [incl. τ data], a had(2) μ =(-9.93±0.07) x 10 -10 (NLO) and a had(3) μ =(1.22±0.01) x 10 -10 (NNLO). Collecting recent progress in the hadronic light-by-light scattering I adopt π 0 ,η,η ' [95±12]+axial-vector[8± 3]+scalar [-6 ±1]+π,K loops[-20±5]+quark loops[22±4]+tensor [1±0]+NLO[3±2] which yields a (6) μ (lbl,had)=(103±29) x 10 -11 . With these updates I find a exp μ -a the μ =(31.3±7.7) x 10 -10 a 4.1σ deviation. Recent lattice QCD results and future prospects to improve hadronic contributions are discussed.

Construindo Vera Cruz e desconstruindo gênero: aproximações entre Pedro Almodóvar e Judith Butler

Directory of Open Access Journals (Sweden)

Carla Rodrigues

Full Text Available Este artigo aproxima as proposições de desconstrução da distinção sexo/gênero tal qual proposta por Judith Butler com as questões apresentadas no filme A pele que habito, do cineasta Pedro Almodóvar. Neste diálogo, o trabalho debate questões como o diagnóstico de disforia de gênero e o problema da essencialização das categorias feminino/masculino e sua binaridade, a partir dos quais tematiza a normatividade de gênero e a autonomia do sujeito diante das normas.

Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation

DEFF Research Database (Denmark)

Rannversson, Hafsteinn; Wilson, Pamela; Kristensen, Kristina Birch

2015-01-01

) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced...... to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4...

Pump integrated closed loop control. The intelligent actuator pump - state of the art and perspectives; Pumpenintegrierte Prozessregelung. Der intelligente Aktor Pumpe - Stand und Moeglichkeiten

Energy Technology Data Exchange (ETDEWEB)

Paulus, Thomas; Schullerer, Joachim; Oesterle, Manfred [KSB AG, Frankenthal (Germany)

2009-07-01

In many areas of industrial automation, centrifugal pumps and systems of centrifugal pumps are important actuators of a process und therefore a fundamental part of the entire plant. In contrary to the controlled valves, located behind the pump in the pipework system, the functions of the intelligent actuator pump or system of pumps are rarely used and noticed. With regard to the reduction of life cycle costs of the asset pump, pump integrated closed loop control of the fluid transport task has advantages over central closed loop control e.g. in a process control system. This article contains a survey of the intelligent actuator pump, its structure and functions with regard to the solution of the fluid transport task and according pump integrated closed loop control. (orig.)

The Activity of Escherichia coli Dihydroorotate Dehydrogenase Is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis, and Limited Proteolysis

DEFF Research Database (Denmark)

Björnberg, Olof; Grüner, Anne Charlotte; Roepstorff, Peter

1999-01-01

of dihydroorotate dehydrogenases, but sedimentation in sucrose gradients suggests a dimeric structure also of the E. coli enzyme. Product inhibition showed that the E. coli enzyme, in contrast to the L. lactis enzyme, has separate binding sites for dihydroorotate and the electron acceptor. Trypsin readily cleaved...... the E. coli enzyme into two fragments of 182 and 154 residues, respectively. Cleavage reduced the activity more than 100-fold but left other molecular properties, including the heat stability, intact. The trypsin cleavage site, at R182, is positioned in a conserved region that, in the L. lactis enzyme......, forms a loop where a cysteine residue is very critical for activity. In the corresponding position, the enzyme from E. coli has a serine residue. Mutagenesis of this residue (S175) to alanine or cysteine reduced the activities 10000- and 500-fold, respectively. The S175C mutant was also defective...

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

Science.gov (United States)

Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Science.gov (United States)

Hui, James Z; Tsourkas, Andrew

2014-09-17

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

A Role for the Fifth G-Track in G-Quadruplex Forming Oncogene Promoter Sequences during Oxidative Stress: Do These "Spare Tires" Have an Evolved Function?

Science.gov (United States)

Fleming, Aaron M; Zhou, Jia; Wallace, Susan S; Burrows, Cynthia J

2015-08-26

Uncontrolled inflammation or oxidative stress generates electron-deficient species that oxidize the genome increasing its instability in cancer. The G-quadruplex (G4) sequences regulating the c-MYC , KRAS , VEGF , BCL-2 , HIF-1α , and RET oncogenes, as examples, are targets for oxidation at loop and 5'-core guanines (G) as showcased in this study by CO 3 •- oxidation of the VEGF G4. Products observed include 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). Our previous studies found that OG and Gh, when present in the four G-tracks of the solved structure for VEGF and c-MY C, were not substrates for the base excision repair (BER) DNA glycosylases in biologically relevant KCl solutions. We now hypothesize that a fifth G-track found a few nucleotides distant from the G4 tracks involved in folding can act as a "spare tire," facilitating extrusion of a damaged G-run into a large loop that then becomes a substrate for BER. Thermodynamic, spectroscopic, and DMS footprinting studies verified the fifth domain replacing a damaged G-track with OG or Gh at a loop or core position in the VEGF G4. These new "spare tire"-containing strands with Gh in loops are now found to be substrates for initiation of BER with the NEIL1, NEIL2, and NEIL3 DNA glycosylases. The results support a hypothesis in which regulatory G4s carry a "spare-tire" fifth G-track for aiding in the repair process when these sequences are damaged by radical oxygen species, a feature observed in a large number of these sequences. Furthermore, formation and repair of oxidized bases in promoter regions may constitute an additional example of epigenetic modification, in this case of guanine bases, to regulate gene expression in which the G4 sequences act as sensors of oxidative stress.

G4S fuajee ruumiinstallatsioon = G4S lobby spatial installation / Ville Lausmäe

Index Scriptorium Estoniae

Lausmäe, Ville, 1981-

2013-01-01

Turvafirma G4S büroohoone (Paldiski mnt 80, Tallinn) fuajee sisekujundusest. Autorid: Ville Lausmäe, Kadi Karmann (sisearhitektuuribüroo VLS). Kultuuriministeeriumi kunstinõuniku Maria-Kristiina Soomre arvamus. Lühidalt sisearhitektuuribüroost VLS

Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

NARCIS (Netherlands)

Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

2018-01-01

The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure*

Science.gov (United States)

Bracher, Susanne; Guérin, Kamila; Polyhach, Yevhen; Jeschke, Gunnar; Dittmer, Sophie; Frey, Sabine; Böhm, Maret; Jung, Heinrich

2016-01-01

The available structural information on LeuT and structurally related transporters suggests that external loop 4 (eL4) and the outer end of transmembrane domain (TM) 10′ participate in the reversible occlusion of the outer pathway to the solute binding sites. Here, the functional significance of eL4 and the outer region of TM10′ are explored using the sodium/proline symporter PutP as a model. Glu-311 at the tip of eL4, and various amino acids around the outer end of TM10′ are identified as particularly crucial for function. Substitutions at these sites inhibit the transport cycle, and affect in part ligand binding. In addition, changes at selected sites induce a global structural alteration in the direction of an outward-open conformation. It is suggested that interactions between the tip of eL4 and the peptide backbone at the end of TM10′ participate in coordinating conformational alterations underlying the alternating access mechanism of transport. Together with the structural information on LeuT-like transporters, the results further specify the idea that common design and functional principles are maintained across different transport families. PMID:26728461

Applications of an anti-symmetry loop algebra and its expanding forms

International Nuclear Information System (INIS)

Zhang Yufeng; Yan Qingyou

2004-01-01

Constructing an anti-symmetry subalgebra A-tilde 2 of loop algebra A-tilde 2 gives the well-known Jaulent-Miodek (JM) hierarchy, the JM equation and its new Lax pair. Further, the Darboux transformation of the JM equation is deduced by anstaz method. By making use of a high-order loop algebra and Tu scheme, an expanding integrable model of the JM hierarchy is obtained. A direct expansion A-macron 2 * of loop algebra A-tilde 2 by considering the definition of Lie algebra is presented, which is used to establish two isospectral problems. It follows that corresponding two new integrable systems are engendered, which possess bi-Hamiltonian structures, respectively. Furthermore, a scalar transformation is applied to turn the loop algebra A-bar 2 * into its equivalent subalgebra A-tilde 1 of loop algebra A-tilde 1 . With the help of A-tilde 1 , another new high-order loop algebra G-bar is constructed, which is used to obtain an expanding integrable model of one of two integrable systems presented

IgG4 and IgE co-positive group found in idiopathic orbital inflammatory disease

Directory of Open Access Journals (Sweden)

Peng-Xiang Zhao

2018-01-01

Full Text Available AIM: To reveal the cytokines involved in idiopathic orbital inflammatory disease (IOID and the relationship between Th17 cells, IgE and IOID pathogenesis. METHODS: Whole blood samples were processed immediately after collection and serological IgG4, IgG, and IgE antibodies were tested using ELISA. IOID and orbital cavernous hemangioma (CH tissue samples underwent Bio-Plex multiplex cytokine detection. Hematoxylin-Eosin (HE staining of all paraffin samples suggested the histological features of IOIDs, and expressions of IgG4 and IL-17A in affected tissues were detected by immunohistochemistry. RESULTS: Among 40 IOID plasma samples, 52.5% (21/40 were positive for IgG4 and 25% (10/40 were positive for IgE. Overlapped IgG4 or IgE positive samples accounted for 22.5% (9/40. Therefore, IOID samples were separated into three groups. The IgE+/IgG4+ group had a relevantly lower level of pro-inflammatory cytokine expression. IL-4 (Th2 cell related, IL-10 and TGF-β1 (Treg cell immunity related were elevated in all three groups. Some of the Th17 cell related cytokines (i.e. IL-17A/F, IL-25, IL-23, and IL-33 displayed higher expression levels in the IgE-/IgG4- group compared to the other two groups. CONCLUSION: We discovered an IgG4-IgE co-positive group as well as Th17 cell immune involvement in IgG4-IgE co-negative subgtroup in IOID for the first time. The pathogenesis of IOID could differ from different subgroups according to the IgG4 and IgE detection. Therefore, we recommend that, Treatment stratagy should be made according to the clinical assessment of IgG4-IgE and Th17 profile detection.

Feminismo, identidade e gênero em Judith Butler: apontamentos a partir de “problemas de gênero”

Directory of Open Access Journals (Sweden)

Flávio Henrique Firmino

2017-06-01

Full Text Available Pretende-se nesse artigo acompanhar a proposta inicial de Judith Butler em Problemas de Gênero, de que o gênero não é uma essência nem uma construção social, mas uma produção do poder. Tomando o feminismo como mote para discutir inicialmente a identidade, vemos sua questão se expandir para o gênero, em geral, e chegar à própria noção de sujeito. A partir da crítica genealógica de Michel Foucault e de sua noção de poder, Butler pretende realizar uma crítica das categorias de identidade e, especificamente, da identidade enquanto fundamento da ação política do feminismo.

Three-loop mixed QCD-electroweak corrections to Higgs boson gluon fusion

Science.gov (United States)

Bonetti, Marco; Melnikov, Kirill; Tancredi, Lorenzo

2018-02-01

We compute the contribution of three-loop mixed QCD-electroweak corrections (αS2α2) to the g g →H scattering amplitude. We employ the method of differential equations to compute the relevant integrals and express them in terms of Goncharov polylogarithms.

Function and X-ray crystal structure of Escherichia coli YfdE.

Directory of Open Access Journals (Sweden)

Elwood A Mullins

Full Text Available Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC. OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT, YfdU (OXC, and YfdE, a class III CoA-transferase that is ~30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively that appear to encode substrate specificity.

A multiple-pass ring oscillator based dual-loop phase-locked loop

International Nuclear Information System (INIS)

Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning

2009-01-01

A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-μm RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

A multiple-pass ring oscillator based dual-loop phase-locked loop

Energy Technology Data Exchange (ETDEWEB)

Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning, E-mail: dfchen@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

2009-10-15

A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-{mu}m RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

Timely Diagnosis of Acute Kidney Injury Using Kinetic eGFR and the Creatinine Excretion to Production Ratio, E/eG - Creatinine Can Be Useful!

Science.gov (United States)

Endre, Zoltán H; Pianta, Timothy J; Pickering, John W

2016-01-01

Post transplant repeated measurements of urine volume and serum creatinine (sCr) are used to assess kidney function. Under non-steady state conditions, repeated measurement of sCr allows calculation of the kinetic estimated GFR (KeGFR). Additional measurement of urinary creatinine allows the calculation of the creatinine excretion to (estimated) production ratio (E/eG). We hypothesized that post-transplant KeGFR and E/eG would predict delayed graft function (DGF), as early as 4 h and outperform a validated clinical model at 12 h. This was a retrospective analysis of prospectively acquired data in a study of 56 recipients of deceased-donor kidney transplant. We assessed predictive performance with the area under the receiver operator characteristic curve (AUC) and the added value to a clinical model with integrated discrimination improvement analysis. At 4 h, the AUC for E/eG was 0.87 (95% CI 0.77-0.96) and for KeGFR 0.69 (95% CI 0.56-0.83). Both E/eG and KeGFR improved the risk prediction of a clinical model for DGF by 32 and 18%, and for non-DGF by 17 and 10%, respectively. While E/eG had better predictive performance of DGF than KeGFR, KeGFR might also facilitate perioperative management including drug dosing after kidney transplantation. Together these measurements may facilitate the possibility of conducting trials of early intervention to ameliorate the adverse effects of ischaemia-reperfusion injury on long-term DGF. © 2016 S. Karger AG, Basel.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

Science.gov (United States)

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Ligand-bound Structures and Site-directed Mutagenesis Identify the Acceptor and Secondary Binding Sites of Streptomyces coelicolor Maltosyltransferase GlgE*

Science.gov (United States)

Syson, Karl; Stevenson, Clare E. M.; Miah, Farzana; Barclay, J. Elaine; Tang, Minhong; Gorelik, Andrii; Rashid, Abdul M.; Lawson, David M.; Bornemann, Stephen

2016-01-01

GlgE is a maltosyltransferase involved in α-glucan biosynthesis in bacteria that has been genetically validated as a target for tuberculosis therapies. Crystals of the Mycobacterium tuberculosis enzyme diffract at low resolution so most structural studies have been with the very similar Streptomyces coelicolor GlgE isoform 1. Although the donor binding site for α-maltose 1-phosphate had been previously structurally defined, the acceptor site had not. Using mutagenesis, kinetics, and protein crystallography of the S. coelicolor enzyme, we have now identified the +1 to +6 subsites of the acceptor/product, which overlap with the known cyclodextrin binding site. The sugar residues in the acceptor subsites +1 to +5 are oriented such that they disfavor the binding of malto-oligosaccharides that bear branches at their 6-positions, consistent with the known acceptor chain specificity of GlgE. A secondary binding site remote from the catalytic center was identified that is distinct from one reported for the M. tuberculosis enzyme. This new site is capable of binding a branched α-glucan and is most likely involved in guiding acceptors toward the donor site because its disruption kinetically compromises the ability of GlgE to extend polymeric substrates. However, disruption of this site, which is conserved in the Streptomyces venezuelae GlgE enzyme, did not affect the growth of S. venezuelae or the structure of the polymeric product. The acceptor subsites +1 to +4 in the S. coelicolor enzyme are well conserved in the M. tuberculosis enzyme so their identification could help inform the design of inhibitors with therapeutic potential. PMID:27531751

Simulation of misfit dislocation loops at the Ag/Cu(111) interface

International Nuclear Information System (INIS)

Rasmussen, Torben

2000-01-01

Molecular dynamics simulations combined with the nudged elastic band method for finding transition states and corresponding activation energies are used to study mechanisms of nucleation, growth, and motion of misfit dislocation loops at the Ag/Cu(111) interface. A variety of mechanisms involving concerted motion of several atoms are identified. Nucleation has the highest activation energy, ∼1eV. Growth and motion of the loops have activation energies in the range 0.3--0.7eV

Experimental loop for SH2 (LECS)

International Nuclear Information System (INIS)

Strehar, N.R.; Bruzzoni, Pablo; Moras, J.J.; Cogozzo, E.O.

1981-01-01

An experimental loop is described for circulation of SH 2 that operates at 2 x 10 6 Pascal and 33 deg C. It was designed and constructed with the purpose of experimentally studying the hydraulic instability phenomenon that can be detected in cold isotopic exchange columns in the Girdler-Sulfide (GS) process of heavy water production. The main features of the different components of the loop are described, as well as the materials, the measurement and control instruments and the auxiliary equipment used, and finally the measuring methods to qualify and quantify the formation of froth. Furthermore, the loop's transportable metallic container is described, which allows to transport and connect it to CNEA's experimental heavy water plant or to any other heavy water plants using the GS method. Some tests made with inert gases that intended to verify the equipment's performance and to select the most adequate sieve trays for its operation are discussed. (M.E.L.) [es

Organohalogen pollutants in surface particulates from workshop floors of four major e-waste recycling sites in China and implications for emission lists.

Science.gov (United States)

Zeng, Yan-Hong; Tang, Bin; Luo, Xiao-Jun; Zheng, Xiao-Bo; Peng, Ping-An; Mai, Bi-Xian

2016-11-01

To examine the environmental pollution associated with e-waste recycling activities, the concentrations of organohologenated pollutants (OHPs), i.e., short- and medium-chain chlorinated paraffins (SCCPs and MCCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and several other halogenated flame retardants (OHFRs), were investigated in surface particulates from the workshop floors of four major e-waste recycling sites (Taizhou, Guiyu, Dali and Qingyuan) in China. The mean levels of SCCPs, MCCPs, PCBs, PBDEs and OHFRs in surface particulates ranged from 30,000-61,000, 170,000-890,000, 2700-27,000, 52,000-240,000, and 62,000-140,000ng/g dry weight (dw), respectively. OHFRs, including decabromodiphenyl ethane, dechlorane plus, 1,2-bis(2,4,6-tribromophenoxy)ethane, tetrabromobisphenol A, hexabromocyclododecanes, polybrominated biphenyls, hexabromobenzene, pentabromotoluene, and pentabromoethylbenzene, were frequently (>50% detection frequency) detected in surface particulates with mean concentration ranges of 39,000-63,000, 310-2700, 98-16,000, 21,000-56,000, 55-5700, 1700-27,000, 42-1600, 3.2-220, and 5.8-12ng/g dw, respectively. The composition of OHPs varied depend on the e-waste items processing in different regions. Guiyu and Dali were typical sites contaminated by halogenated flame retardants (HFRs) and CPs, respectively, while Qingyuan, and Taizhou were representative PCB-polluted regions. The evidence produced by this preliminary study indicated that electronic devices and plastics may account for the high content of HFRs and the metal products are likely the major source of CPs in these e-waste sites. Copyright © 2016. Published by Elsevier B.V.

eWOM credibility on social networking sites: A framework

OpenAIRE

Moran, Gillian; Muzellec, Laurent

2017-01-01

Social networking sites (SNS) offer brands the ability to spread positive electronic Word of Mouth (eWOM) for the purposes of building awareness and acquiring new customers. However, the credibility of eWOM is threatened of late as marketers increasingly try to manipulate eWOM practices on SNS. A greater understanding of eWOM credibility is necessary to better enable marketers to leverage true consumer engagement by generating credible peer-to-peer communications. Yet, to date, there is no on...

G2E3 is a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization

International Nuclear Information System (INIS)

Brooks, William S.; Banerjee, Sami; Crawford, David F.

2007-01-01

G2E3 was originally described as a G2/M-specific gene with DNA damage responsive expression. The presence of a conserved HECT domain within the carboxy-terminus of the protein indicated that it likely functions as a ubiquitin ligase or E3. Although HECT domains are known to function in this capacity for many proteins, we demonstrate that a portion of the HECT domain from G2E3 plays an important role in the dynamic subcellular localization of the protein. We have shown that G2E3 is a nucleo-cytoplasmic shuttling protein with nuclear export mediated by a novel nuclear export domain that functions independently of CRM1. In full-length G2E3, a separate region of the HECT domain suppresses the function of the NES. Additionally, G2E3 contains a nucleolar localization signal (NoLS) in its amino terminus. Localization of G2E3 to the nucleolus is a dynamic process, and the protein delocalizes from the nucleolus rapidly after DNA damage. Cell cycle phase-specific expression and highly regulated subcellular localization of G2E3 suggest a possible role in cell cycle regulation and the cellular response to DNA damage

Site-specific photoconjugation of antibodies using chemically synthesized IgG-binding domains.

Science.gov (United States)

Perols, Anna; Karlström, Amelie Eriksson

2014-03-19

Site-specific labeling of antibodies can be performed using the immunoglobulin-binding Z domain, derived from staphylococcal protein A (SpA), which has a well-characterized binding site in the Fc region of antibodies. By introducing a photoactivable probe in the Z domain, a covalent bond can be formed between the Z domain and the antibody by irradiation with UV light. The aim of this study was to improve the conjugation yield for labeling of different subclasses of IgG having different sequence composition, using a photoactivated Z domain variant. Four different variants of the Z domain (Z5BPA, Z5BBA, Z32BPA, and Z32BBA) were synthesized to investigate the influence of the position of the photoactivable probe and the presence of a flexible linker between the probe and the protein. For two of the variants, the photoreactive benzophenone group was introduced as part of an amino acid side chain by incorporation of the unnatural amino acid benzoylphenylalanine (BPA) during peptide synthesis. For the other two variants, the photoreactive benzophenone group was attached via a flexible linker by coupling of benzoylbenzoic acid (BBA) to the ε-amino group of a selectively deprotected lysine residue. Photoconjugation experiments using human IgG1, mouse IgG1, and mouse IgG2A demonstrated efficient conjugation for all antibodies. It was shown that differences in linker length had a large impact on the conjugation efficiency for labeling of mouse IgG1, whereas the positioning of the photoactivable probe in the sequence of the protein had a larger effect for mouse IgG2A. Conjugation to human IgG1 was only to a minor extent affected by position or linker length. For each subclass of antibody, the best variant tested using a standard conjugation protocol resulted in conjugation efficiencies of 41-66%, which corresponds to on average approximately one Z domain attached to each antibody. As a combination of the two best performing variants, Z5BBA and Z32BPA, a Z domain variant with

Structure of Staphylococcal Enterotoxin E in Complex with TCR Defines the Role of TCR Loop Positioning in Superantigen Recognition.

Directory of Open Access Journals (Sweden)

Karin E J Rödström

Full Text Available T cells are crucial players in cell-mediated immunity. The specificity of their receptor, the T cell receptor (TCR, is central for the immune system to distinguish foreign from host antigens. Superantigens are bacterial toxins capable of inducing a toxic immune response by cross-linking the TCR and the major histocompatibility complex (MHC class II and circumventing the antigen specificity. Here, we present the structure of staphylococcal enterotoxin E (SEE in complex with a human T cell receptor, as well as the unligated T cell receptor structure. There are clear structural changes in the TCR loops upon superantigen binding. In particular, the HV4 loop moves to circumvent steric clashes upon complex formation. In addition, a predicted ternary model of SEE in complex with both TCR and MHC class II displays intermolecular contacts between the TCR α-chain and the MHC, suggesting that the TCR α-chain is of importance for complex formation.

Structural studies on an internal loop from a hairpin ribozyme

Energy Technology Data Exchange (ETDEWEB)

Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)

1994-12-01

Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

Two-loop conformal generators for leading-twist operators in QCD

International Nuclear Information System (INIS)

Braun, V.M.; Strohmaier, M.; Manashov, A.N.; Hamburg Univ.; Moch, S.

2016-01-01

QCD evolution equations in minimal subtraction schemes have a hidden symmetry: One can construct three operators that commute with the evolution kernel and form an SL(2) algebra, i.e. they satisfy (exactly) the SL(2) commutation relations. In this paper we find explicit expressions for these operators to two-loop accuracy going over to QCD in non-integer d=4-2ε space-time dimensions at the intermediate stage. In this way conformal symmetry of QCD is restored on quantum level at the specially chosen (critical) value of the coupling, and at the same time the theory is regularized allowing one to use the standard renormalization procedure for the relevant Feynman diagrams. Quantum corrections to conformal generators in d=4-2ε effectively correspond to the conformal symmetry breaking in the physical theory in four dimensions and the SL(2) commutation relations lead to nontrivial constraints on the renormalization group equations for composite operators. This approach is valid to all orders in perturbation theory and the result includes automatically all terms that can be identified as due to a nonvanishing QCD β-function (in the physical theory in four dimensions). Our result can be used to derive three-loop evolution equations for flavor-nonsinglet quark-antiquark operators including mixing with the operators containing total derivatives. These equations govern, e.g., the scale dependence of generalized hadron parton distributions and light-cone meson distribution amplitudes.

Study on LOOP and SBO Frequency for Multi-Unit PSA

Energy Technology Data Exchange (ETDEWEB)

Jin, Kyung Ho; Heo, Gyun Young [Kyunghee University, Yongin (Korea, Republic of)

2016-05-15

In conventional single unit PSA, it was assumed that all accidents or events are independent and the risk of only one unit has been evaluated. In other words, the possibility that simultaneous events occur on multiple units was excluded because it was assumed that the probability of concurrent events were extremely low. After Fukushima accidents, however, it was found that external hazards such as tsunami may impact on multiple units; that means, for the sake of proper mitigation the risk of accidents in shared SSCs should be reevaluated. New risk metrics to improve conventional CDF (Core Damage frequency) based on reactor-year is needed to perform MUPSA (Multi-Unit Probabilistic Safety Assessment). IAEA suggested SCDF (Site CDF) as a risk metrics for MUPSA. The frequency based on reactor-year was converted to the frequency based on site-year. In addition, shared SSCs were modeled in single unit PSA as if those units have independent shared SSCs. Therefore, the risk of shared SSCs should be reevaluated. In this paper, the frequency of LOOP (Loss of Offsite Power), which is typically a multi-unit event, was evaluated and the frequency of SBO (Station Blackout) depending on LOOP frequency and emergency power systems such as EDG (Emergency Diesel Generator) and AAC (Alternate AC), that can mitigate SBO events, was modeled. This paper describes how to calculate LOOP and SBO frequency from the simple example for two-unit site with shared AAC. The events impacting on multiple units, which were excluded in conventional PSA, should be considered for MUPSA.

MINI-FILAMENT ERUPTION AS THE INITIATION OF A JET ALONG CORONAL LOOPS

International Nuclear Information System (INIS)

Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan

2016-01-01

Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST H α images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

MINI-FILAMENT ERUPTION AS THE INITIATION OF A JET ALONG CORONAL LOOPS

Energy Technology Data Exchange (ETDEWEB)

Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan, E-mail: hjcsolar@ynao.ac.cn [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China)

2016-10-20

Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST H α images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

On-site detection of Xylella fastidiosa in host plants and in “spy insects” using the real-time loop-mediated isothermal amplification method

Directory of Open Access Journals (Sweden)

Thaer YASEEN

2015-12-01

Full Text Available A recent severe outbreak of Xylella fastidiosa associated with ‘olive quick decline syndrome’ (OQDS was reported in Apulia (Southern Italy. In this study an on-site real-time loop-mediated isothermal amplification (real-time LAMP was developed for detecting X. fastidiosa in host plants and insects. A marked simplification of the DNA extraction procedure was obtained by heating the samples in a portable Smart-Dart device and using an optimized enhancer reaction buffer. The connection to a tablet or Smartphone allowed to visualize the results of the reaction in real time. Compared to PCR and ELISA, with which it showed comparable results in terms of sensitivity and reliability in the X. fastidiosa detection, this simplified real-time LAMP procedure proved to be “user friendly”, displaying the advantages to be an on-site detection method of easy handling, rapid execution and low cost.

A planar conducting micro-loop structure for transportation of magnetic beads: An approach towards rapid sensing and quantification of biological entities

KAUST Repository

Gooneratne, Chinthaka Pasan

2012-03-01

Magnetic beads are utilized effectively in a wide variety of medical applications due to their small size, biocompatibility and large surface to volume ratio. Microfluidic lab-on-a-chip (LOC) devices, which utilize magnetic beads, are promising tools for accurate and rapid cell sorting and counting. Effective manipulation of beads is a critical factor for the performance of LOC devices. In this paper we propose a planar conducting micro-loop structure to trap, manipulate and transport magnetic beads. Current through the micro-loops produces magnetic field gradients that are proportional to the force required to manipulate the beads. Numerical analyses were performed to study the magnetic forces and their spatial distributions. Experimental results showed that magnetic beads could not only be transported towards a target region, e.g., for sensing purposes, but also the trapping rate could be increased by switching current between the different loops in the micro-loop structure. This method could lead to rapid and accurate quantification of biological entities tagged with magnetic beads. Copyright © 2012 American Scientific Publishers. All rights reserved.

Regulation of Trib2 by an E2F1-C/EBPα feedback loop in AML cell proliferation

DEFF Research Database (Denmark)

Rishi, Loveena; Hannon, Maura; Salomè, Mara

2014-01-01

α (C/EBPα)-p42, occurs in acute myeloid leukemia (AML), resulting in the perturbation of cell cycle and apoptosis, emphasizing its importance in the molecular pathogenesis of AML. Here we show that E2F family members directly regulate Trib2 in leukemic cells and identify a feedback regulatory loop......The loss of regulation of cell proliferation is a key event in leukemic transformation, and the oncogene tribbles (Trib)2 is emerging as a pivotal target of transcription factors in acute leukemias. Deregulation of the transcription factor E2F1, normally repressed by CCAAT enhancer-binding protein...... for E2F1, C/EBPα, and Trib2 in AML cell proliferation and survival. Further analyses revealed that E2F1-mediated Trib2 expression was repressed by C/EBPα-p42, and in normal granulocyte/macrophage progenitor cells, we detect C/EBPα bound to the Trib2 promoter. Pharmacological inhibition of the cell cycle...

Conformational plasticity at the IgE-binding site of the B-cell receptor CD23.

Science.gov (United States)

Dhaliwal, Balvinder; Pang, Marie O Y; Yuan, Daopeng; Yahya, Norhakim; Fabiane, Stella M; McDonnell, James M; Gould, Hannah J; Beavil, Andrew J; Sutton, Brian J

2013-12-01

IgE antibodies play a central role in allergic disease. They recognize allergens via their Fab regions, whilst their effector functions are controlled through interactions of the Fc region with two principal cell surface receptors, FcɛRI and CD23. Crosslinking of FcɛRI-bound IgE on mast cells and basophils by allergen initiates an immediate inflammatory response, while the interaction of IgE with CD23 on B-cells regulates IgE production. We have determined the structures of the C-type lectin "head" domain of CD23 from seven crystal forms. The thirty-five independent structures reveal extensive conformational plasticity in two loops that are critical for IgE binding. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

Energy Technology Data Exchange (ETDEWEB)

CHERTKOV, MICHAEL [Los Alamos National Laboratory; CHERNYAK, VLADIMIR [Los Alamos National Laboratory

2007-01-10

Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problem invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe

Helium Loop for the HCPB Test Blanket Module

International Nuclear Information System (INIS)

Neuberger, H.; Boccaccini, L.V.; Ghidersa, B. E.; Jin, X.; Meyder, R.

2006-01-01

In the frame of the activities of the EU Breeder Blanket Programme and of the Test Blanket Working Group, the Helium loop for the Helium Cooled Pebble Bed Test Blanket Module (HCPB-TBM) in ITER has been investigated with regard to the layout definition, selection of components, control, dimensioning and integration. This paper presents the status of development. The loop design for the HCPB-TBM in ITER will mainly base on the experience gained from Helium Loop Karlsruhe (HELOKA) which is currently developed at the FZK for experiments under ITER relevant conditions. The ITER loop will be equipped with similar components like HELOKA and will mainly consist of a circulator with variable speed drive, a recuperator, an electric heater, a cooler, a dust filter and auxilary components e.g. pipework and valves. A Coolant Purification System (CPS) and a Pressure Control System (PCS) are foreseen to meet the requirements on coolant conditioning. To prepare a TBM for a new experimental campaign, a succession of operational states like '' cold maintenance '', '' baking '' and '' cold standby '' is required. Before a pulse operation, a '' hot stand-by '' state should be achieved providing the TBM with inlet coolant at nominal conditions. This operation modus is continued in the dwell time waiting for the successive pulse. A '' tritium out-gassing '' will be also required after several TBM-campaigns to remove the inventory rest of T in the beds for measurement purpose. The dynamic circuit behaviour during pulses, transition between different operational states as well as the behaviour in accident situations are investigated with RELAP. The main components of the loop will be accommodated inside the Tokamak Cooling Water System(TCWS)- vault from where the pipes require connection to the TBM which is attached to port 16 of the vacuum vessel. Therefore pipes across the ITER- building of about 110 m in length (each) are required. Additional equipment is also located in the port cell

OSCILLATION OF NEWLY FORMED LOOPS AFTER MAGNETIC RECONNECTION IN THE SOLAR CHROMOSPHERE

Energy Technology Data Exchange (ETDEWEB)

Yang, Shuhong [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Xiang, Yongyuan, E-mail: shuhongyang@nao.cas.cn [Fuxian Solar Observatory, Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China)

2016-03-10

With the high spatial and temporal resolution Hα images from the New Vacuum Solar Telescope, we focus on two groups of loops with an X-shaped configuration in the dynamic chromosphere. We find that the anti-directed loops approach each other and reconnect continually. The connectivity of the loops is changed and new loops are formed and stack together. The stacked loops are sharply bent, implying that they are greatly impacted by the magnetic tension force. When another reconnection process takes place, one new loop is formed and stacks with the previously formed ones. Meanwhile, the stacked loops retract suddenly and move toward the balance position, performing an overshoot movement, which led to an oscillation with an average period of about 45 s. The oscillation of newly formed loops after magnetic reconnection in the chromosphere is observed for the first time. We suggest that the stability of the stacked loops is destroyed due to the attachment of the last new loop and then suddenly retract under the effect of magnetic tension. Because of the retraction, another lower loop is pushed outward and performs an oscillation with a period of about 25 s. The different oscillation periods may be due to their difference in three parameters, i.e., loop length, plasma density, and magnetic field strength.

Innovative Waste Management in the Mercury Loop of the EURISOL Multi-MW Converter Target

CERN Document Server

PSI: Jörg Neuhausen, Dorothea Schumann, Rugard Dressler, Susanne Horn, Sabrina Lüthi, Stephan Heinitz, Suresh ChirikiCERN: Thierry Stora, Martin Eller

The choice of mercury as target material imposes various questions concerning the safe operation of such a system that are related to the physical and chemical properties of the target material itself and the nuclear reaction products produced within the target during its life time of several decades. Therefore, a subtask was created within the EURISOL-DS project that is concerned with studying an innovative waste management for the generated radioactivity by chemical means. Such a study strongly depends on the radioactive inventory and its distribution throughout the target and loop system. Radioactive inventory calculations were performed within task 5 [6]. The distribution of nuclear reaction products and their chemical state that can be expected within the target and loop system is one of the topics covered in this report. Based on the results obtained by theoretical studies as well as laboratory scale experiments, the feasibility of waste reduction using chemical methods, both conventional (e.g. leaching...

Clinicopathologic significance of HLA-G and HLA-E molecules in Tunisian patients with ovarian carcinoma.

Science.gov (United States)

Babay, Wafa; Ben Yahia, Hamza; Boujelbene, Nadia; Zidi, Nour; Laaribi, Ahmed Baligh; Kacem, Dhikra; Ben Ghorbel, Radhia; Boudabous, Abdellatif; Ouzari, Hadda-Imene; Rizzo, Roberta; Rebmann, Vera; Mrad, Karima; Zidi, Inès

2018-06-01

The human leukocyte antigen (HLA)-G and HLA-E, non classical HLA class I molecules, have been highly implicated in immune tolerance. HLA-G and HLA-E molecules were proposed as putative markers of several advanced cancers. As a step towards a better understanding of ovarian carcinoma, we evaluated the expression of both HLA-G and HLA-E molecules and explored their prognostic implication. HLA-G and HLA-E expression were studied by immunohistochemistry on ovarian carcinoma tissues. This expression was semi-quantitatively scored into four expression groups and correlated to clinicopathological parameters and patients' survival. HLA-G and HLA-E have been found to be highly expressed in ovarian carcinoma tissues (Respectively, 72.4% and 96.8%). They are frequently co-expressed. Univariate and multivariate analysis revealed that a positive HLA-G expression status in tumor tissue is a promising candidate parameter to predict disease recurrence in addition to the disease status in Tunisian patients with ovarian carcinoma. Moreover, the elevated HLA-E expression was associated with serous ovarian carcinoma subtype as well as with advanced stages of ovarian carcinoma. HLA-G and HLA-E are highly represented in ovarian carcinoma suggesting a potential association with progressive disease mechanism. HLA-G and HLA-E molecules might be new candidates' markers for ovarian carcinoma progression. Copyright © 2018 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.